Clinical Microbiology 12Th Edition

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Volume 1

Manual of Clinical Microbiology 12th Edition

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Manual of Clinical Microbiology

12th Edition

EDITORS-IN-CHIEF Karen C. Carroll Michael A. Pfaller Division of Medical Microbiology, Departments of Pathology and Epidemiology Department of Pathology, The Johns Hopkins (Emeritus), University of Iowa, University School of Medicine, Iowa City, and JMI Laboratories, Baltimore, Maryland North Liberty, Iowa

VOLUME EDITORS Marie Louise Landry Robin Patel Laboratory Medicine and Internal Medicine, Infectious Diseases Research Laboratory, Yale University, New Haven, Connecticut Mayo Clinic, Rochester, Minnesota

Alexander J. McAdam Sandra S. Richter Department of Laboratory Medicine, Boston Department of Laboratory Medicine, Children’s Hospital, Boston, Massachusetts Cleveland Clinic, Cleveland, Ohio David W. Warnock Atlanta, Georgia

Washington, DC

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Manual of Clinical Microbiology

12th Edition

Washington, DC

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MCM12_FM.indd 3 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM Copyright © 2019 American Society for Microbiology, Washington, DC ASM Press is a registered trademark of the American Society for Microbiology. All rights reserved. No part of this publication may be reproduced or transmitted in whole or in part or reutilized in any form or by any means, electronic or mechanical, including photocopying and recording, or by any information storage and retrieval system, without permission in writing from the publisher.

Disclaimer: To the best of the publisher’s knowledge, this publication provides information concerning the subject matter covered that is accurate as of the date of publication. The publisher is not providing legal, medical, or other professional services. Any reference herein to any specific commercial products, procedures, or services by trade name, trademark, manufacturer, or otherwise does not constitute or imply endorsement, recommendation, or favored status by the American Society for Microbiology (ASM). The views and opinions of the author(s) expressed in this publication do not necessarily state or reflect those of ASM, and they shall not be used to advertise or endorse any product.

Library of Congress Cataloging-in-Publication Data

Names: Carroll, Karen C., editor. | Pfaller, Michael A., editor. | Landry, Marie Louise, editor. | McAdam, Alexander J., editor. | Patel, Robin, M.D., editor. | Richter, Sandra S., editor. | Warnock, D. W., editor. Title: Manual of clinical microbiology / editors in chief, Karen C. Carroll, Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, Michael A. Pfaller, Departments of Pathology and Epidemiology (emeritus), University of Iowa, Iowa City, and JMI Laboratories, North Liberty, Iowa ; editors, Marie Louise Landry, Laboratory Medicine and Internal Medicine, Yale University, New Haven, Connecticut, Alexander J. McAdam, Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, Robin Patel, Infectious Diseases Research Laboratory, Mayo Clinic, Rochester, Minnesota, Sandra S. Richter, Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, David W. Warnock, Atlanta, Georgia. Description: 12th edition. | Washington, DC : ASM Press, [2019] | Includes bibliographical references and index. Identifiers: LCCN 2018057849 | ISBN 9781555819835 Subjects: LCSH: Medical microbiology—Handbooks, manuals, etc. | Diagnostic microbiology—Handbooks, manuals, etc. Classification: LCC QR46 .M425 2019 | DDC 616.9/041—dc23 LC record available at https://lccn.loc.gov/2018057849

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9 Prevention of Health Care-Associated Infections / 139 Volume 1 DANIEL J. DIEKEMA AND MICHAEL A. PFALLER 10 Investigation of Disease Outbreaks / 155 Editorial Board xi IONA MUNJAL, WENDY A. SZYMCZAK, AND Contributors xiii BELINDA OSTROWSKY 11 Molecular Epidemiology / 167 Preface xxv EIJA TREES, TERRY FEI FAN NG, Author and Editor Conflicts of Interest xxvi DUNCAN MacCANNELL, PAUL A. ROTA, AND PETER GERNER-SMIDT 12 Procedures for the Storage of Microorganisms / 197 ROSEMARY C. SHE AND SUSAN M. BUTLER-WU section I 13 Prevention of Laboratory-Acquired Diagnostic Strategies and Infections / 206 PHILIPPE LAGACÉ-WIENS AND General Topics / 1 MICHAEL PENTELLA VOLUME EDITOR: SANDRA S. RICHTER 14 Disinfection and Sterilization / 224 SECTION EDITOR: JAMES KARLOWSKY MATTHEW J. ARDUINO AND GERALD McDONNELL 1 Introduction to the 12th Edition of the Manual of Clinical Microbiology / 3 15 Biothreat Agents / 243 KAREN C. CARROLL AND MICHAEL A. PFALLER JAMES W. SNYDER, STEVEN D. MAHLEN, SUSAN E. SHARP, AND MICHAEL LOEFFELHOLZ 2 Laboratory Accreditation and Compliance / 5 16 The Human Microbiome / 254 MICHAEL LOEFFELHOLZ, LINOJ SAMUEL, AND SUSAN SHARP JAMES VERSALOVIC, SARAH K. HIGHLANDER, BHANU P. GANESH, AND JOSEPH F. PETROSINO 3 Microscopy / 16 17 Microbial Genomics and Pathogen Discovery / 269 STEVEN D. DALLAS JENNIFER K. SPINLER AND JAMES VERSALOVIC 4 Laboratory Detection of Bacteremia and Fungemia / 28 MICHAEL L. WILSON, MELVIN P. WEINSTEIN, AND L. BARTH RELLER section 5 Systems for Identification of Bacteria and Fungi / 45 II KAREN C. CARROLL AND ROBIN PATEL Bacteriology / 284 6 Automation and Design of the Clinical Microbiology Laboratory / 72 VOLUME EDITORS: ROBIN PATEL AND ALEXANDER J. McADAM CHRISTOPHER D. DOERN AND MARTIN HOLFELDER SECTION EDITORS: CAREY-ANN BURNHAM, J. STEPHEN DUMLER, MELISSA B. MILLER, 7 Molecular Microbiology / 86 ELISABETH NAGY, AND JOHANN PITOUT FREDERICK S. NOLTE 8 Immunoassays for the Diagnosis of Infectious General Diseases / 124 18 Taxonomy of Bacteria and Archaea / 287 ELITZA S. THEEL PAUL A. LAWSON AND KERIN L. TYRRELL v

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19 Specimen Collection, Transport, and Processing: 33 Mycobacterium: Laboratory Characteristics Bacteriology / 302 of Slowly Growing Mycobacteria Other than ERIN McELVANIA AND KAMALJIT SINGH Mycobacterium tuberculosis / 595 20 Reagents, Stains, and Media: ADAM J. CAULFIELD, ELVIRA RICHTER, Bacteriology / 331 BARBARA A. BROWN-ELLIOTT, RICHARD J. WALLACE, JR., AND NANCY L. WENGENACK RONALD ATLAS AND JAMES SNYDER 34 Mycobacterium: Clinical and Laboratory Characteristics of Rapidly Growing Gram-Positive Cocci Mycobacteria / 612 21 General Approaches to Identification of BARBARA A. BROWN-ELLIOTT AND Aerobic Gram-Positive Cocci / 362 RICHARD J. WALLACE, JR. JENS JØRGEN CHRISTENSEN, XIAOHUI CHEN NIELSEN, AND KATHRYN L. RUOFF Gram-Negative Bacteria Staphylococcus Micrococcus 22 , , and Other 35 Approaches to the Identification of Aerobic Catalase-Positive Cocci / 367 Gram-Negative Bacteria / 630 KARSTEN BECKER, ROBERT L. SKOV, AND NIELS NØRSKOV-LAURITSEN AND CHRISTOF von EIFF WINNIE RIDDERBERG Streptococcus 23 / 399 36 Neisseria / 640 BARBARA SPELLERBERG, CLAUDIA BRANDT, JOHANNES ELIAS, MATTHIAS FROSCH, AND AND PARHAM SENDI ULRICH VOGEL Enterococcus 24 / 418 37 Aggregatibacter, Capnocytophaga, Eikenella, LÚCIA MARTINS TEIXEIRA, MARIA DA GLÓRIA Kingella, Pasteurella, and Other Fastidious or SIQUEIRA CARVALHO, RICHARD R. FACKLAM, Rarely Encountered Gram-Negative Rods / 656 AND PATRICIA LYNN SHEWMAKER REINHARD ZBINDEN 25 Aerococcus, Abiotrophia, and Other Aerobic Catalase-Negative, Gram-Positive 38 Haemophilus / 670 Cocci / 436 MARK D. GONZALEZ AND NATHAN A. LEDEBOER JENS JØRGEN CHRISTENSEN, XIAOHUI CHEN NIELSEN, AND KATHRYN L. RUOFF 39 Escherichia, Shigella, and Salmonella / 688 BLAKE W. BUCHAN, MATTHEW L. FARON, ROMNEY M. HUMPHRIES, JOHN DEKKER, AND Gram-Positive Rods NATHAN A. LEDEBOER 26 General Approaches to the Identification of 40 Klebsiella and Selected Enterobacterales / 724 Aerobic Gram-Positive Rods / 451 STEPHEN J. FORSYTHE, JOHANN PITOUT, KATHRYN A. BERNARD ANGELLA CHARNOT-KATSIKAS, KEVIN ALBY, 27 Bacillus and Other Aerobic Endospore-Forming AND KAREN M. FRANK Bacteria / 455 41 Yersinia / 751 CHRISTINE Y. TURENNE AND LUKE C. KINGRY, CHERYL L. TARR, AND DAVID C. ALEXANDER JEANNINE M. PETERSEN 28 Listeria and Erysipelothrix / 477 42 Aeromonas / 765 NELE WELLINGHAUSEN BRIGITTE LAMY AND AMY J. HORNEMAN 29 Coryneform Gram-Positive Rods / 488 43 Vibrio and Related Organisms / 775 KATHRYN A. BERNARD CHERYL L. TARR, WILLIAM A. GLOVER II, 30 Nocardia, Rhodococcus, Gordonia, YAN BOUCHER, AND JOHN J. FARMER III Actinomadura, Streptomyces, and Other 44 Pseudomonas / 787 Aerobic Actinomycetes / 525 NIELS HØIBY, OANA CIOFU, AND PATRICIA S. CONVILLE, BARBARA A. THOMAS BJARNSHOLT BROWN-ELLIOTT, AND FRANK G. WITEBSKY 45 Burkholderia, Stenotrophomonas, Ralstonia, 31 Mycobacterium: General Characteristics, Cupriavidus, Pandoraea, Brevundimonas, Laboratory Detection, and Staining Comamonas, Delftia, and Acidovorax / 807 Procedures / 558 JOHN J. LiPUMA, BART J. CURRIE, SHARON J. ISABELLA MARTIN, GABY E. PFYFFER, AND PEACOCK, AND PETER A. R. VANDAMME NICOLE PARRISH 46 Acinetobacter, Chryseobacterium, 32 Mycobacterium tuberculosis Complex / 576 Moraxella, and Other Nonfermentative DAVID M. WARSHAUER, MAX SALFINGER, Gram-Negative Rods / 829 EDWARD DESMOND, AND SHOU-YEAN PIET COOLS, ALEXANDR NEMEC, PETER KÄMPFER, GRACE LIN AND MARIO VANEECHOUTTE

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47 Bordetella and Related Genera / 858 Mycoplasmas and Obligate PAUL E. KILGORE AND TOM COENYE Intracellular Bacteria 48 Francisella / 871 63 General Approaches to Identification of ELIZABETH A. DIETRICH AND Mycoplasma, Ureaplasma, and Obligate JEANNINE M. PETERSEN Intracellular Bacteria / 1109 49 Brucella / 883 CÉCILE BÉBÉAR AND J. STEPHEN DUMLER GEORGE F. ARAJ 64 Mycoplasma and Ureaplasma / 1117 50 Bartonella / 893 KEN B. WAITES AND CÉCILE BÉBÉAR J. STEPHEN DUMLER, KAREN C. CARROLL, 65 Chlamydia / 1137 AND ROBIN PATEL JULIUS SCHACHTER AND MAX CHERNESKY 51 Legionella / 905 66 Rickettsia and Orientia / 1149 PAUL H. EDELSTEIN LUCAS S. BLANTON, DAVID H. WALKER, AND DONALD H. BOUYER Anaerobic Bacteria 67 Ehrlichia, Anaplasma, and Related Intracellular 52 Approaches to the Identification of Anaerobic Bacteria / 1163 Bacteria / 921 BOBBI S. PRITT AND J. STEPHEN DUMLER ANDREJ WEINTRAUB 68 Coxiella / 1180 53 Peptostreptococcus, Finegoldia, GILBERT J. KERSH AND Anaerococcus, Peptoniphilus, Parvimonas, CHANTAL P. BLEEKER-ROVERS Murdochiella, Veillonella, and Other 69 Tropheryma whipplei / 1189 Anaerobic Cocci / 925 WALTER GEIßDÖRFER, ANNETTE MOTER, ALIDA C. M. VELOO AND CRYSTAL N. JOHNSON AND CHRISTIAN BOGDAN 54 Actinomyces, Lactobacillus, Cutibacterium, and Other Non-Spore-Forming Anaerobic Gram-Positive Rods / 938 SUSAN M. BUTLER-WU AND ROSEMARY C. SHE section III 55 Clostridium and Clostridioides / 968 ED KUIJPER AND FREDERIC BARBUT Antibacterial Agents 56 Bacteroides, Porphyromonas, Prevotella, and Susceptibility Test Fusobacterium, and Other Anaerobic Methods / 1199 Gram-Negative Rods / 995 GEORG CONRADS, ELISABETH NAGY, VOLUME EDITOR: SANDRA S. RICHTER AND EIJA KÖNÖNEN SECTION EDITOR: JEAN B. PATEL 70 Antibacterial Agents / 1201 Curved and Spiral-Shaped JAMES S. LEWIS II AND KAREN BUSH Gram-Negative Rods 71 Mechanisms of Resistance to Antibacterial 57 Algorithms for Identification of Agents / 1242 Curved and Spiral-Shaped Gram-Negative PATRICIA A. BRADFORD AND Rods / 1024 MARIANA CASTANHEIRA IRVING NACHAMKIN 72 Susceptibility Test Methods: General 58 Campylobacter and Arcobacter / 1028 Considerations / 1277 IRVING NACHAMKIN JOHN D. TURNIDGE AND JAMES H. JORGENSEN 59 Helicobacter / 1044 73 Antimicrobial Susceptibility Test Methods: MARC ROGER COUTURIER Dilution and Disk Diffusion Methods / 1284 LAURA M. KOETH AND LINDA A. MILLER 60 Leptospira / 1058 PAUL N. LEVETT AND RENEE L. GALLOWAY 74 Antimicrobial Susceptibility Testing Systems / 1300 61 Borrelia / 1066 JAMES A. KARLOWSKY AND SANDRA S. RICHTER MARIA E. AGUERO-ROSENFELD AND GEROLD STANEK 75 Special Phenotypic Methods for Detecting Antibacterial Resistance / 1316 Treponema Brachyspira 62 and : Human PATRICIA J. SIMNER AND ROMNEY HUMPHRIES Host-Associated Spirochetes / 1083 ARLENE C. SEÑA, ALLAN PILLAY, AND 76 Susceptibility Test Methods: Fastidious JUSTIN D. RADOLF Bacteria / 1348 ROMNEY M. HUMPHRIES AND JENNIFER DIEN BARD

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77 Susceptibility Test Methods: Anaerobic 88 Respiratory Syncytial Virus and Human Bacteria / 1377 Metapneumovirus / 1541 AUDREY N. SCHUETZ AND N. ESTHER BABADY AND YI-WEI TANG DARCIE E. CARPENTER 89 Measles and Rubella Viruses / 1560 78 Susceptibility Test Methods: Mycobacteria, CAROLE J. HICKMAN AND Nocardia, and Other Actinomycetes / 1398 JOSEPH P. ICENOGLE GAIL L. WOODS, SHOU-YEAN GRACE LIN, 90 Enteroviruses and Parechoviruses / 1576 BARBARA A. BROWN-ELLIOTT, AND KATHLEEN A. STELLRECHT, DARYL M. EDWARD P. DESMOND LAMSON, AND JOSÉ R. ROMERO 79 Molecular Detection of Antibacterial Drug 91 Rhinoviruses / 1592 Resistance / 1420 MARIE LOUISE LANDRY AND XIAOYAN LU APRIL N. ABBOTT AND FERRIC C. FANG 92 Coronaviruses / 1606 NAOMI J. GADSBY AND KATE E. TEMPLETON 93 Hepatitis A and E Viruses / 1625 Volume 2 JACQUES IZOPET AND NASSIM KAMAR 94 Hepatitis C Virus / 1640 MICHAEL S. FORMAN, BRYAN R. COBB, AND ALEXANDRA VALSAMAKIS 95 Gastroenteritis Viruses / 1656 section IV XIAOLI PANG AND MAREK SMIEJA 96 Rabies Lyssavirus / 1674 Virology / 1432 LILLIAN A. ORCIARI, PAMELA A. YAGER, VOLUME EDITOR: MARIE LOUISE LANDRY AND P. S. SATHESHKUMAR SECTION EDITORS: ANGELA M. CALIENDO, 97 Arboviruses / 1685 CHRISTINE C. GINOCCHIO, RANDALL T. HAYDEN, ELIZABETH A. HUNSPERGER AND YI-WEI TANG 98 Hantaviruses / 1706 General JOHN D. KLENA, CHENG-FENG CHIANG, AND WUN-JU SHIEH 80 Taxonomy and Classification of Viruses / 1435 99 Arenaviruses and Filoviruses / 1719 ELLIOT J. LEFKOWITZ JONATHAN S. TOWNER, PIERRE E. ROLLIN, YI-WEI TANG, AND THOMAS G. KSIAZEK 81 Specimen Collection, Transport, and Processing: Virology / 1446 JAMES J. DUNN AND BENJAMIN A. PINSKY DNA Viruses 82 Reagents, Stains, Media, and Cell Cultures: 100 Herpes Simplex Viruses and Herpes B Virology / 1462 Virus / 1740 GERALD A. CAPRARO AND ALEXANDER L. GRENINGER, RHODA ASHLEY CHRISTINE C. GINOCCHIO MORROW, AND KEITH R. JEROME 83 Algorithms for Detection and Identification 101 Varicella-Zoster Virus / 1757 of Viruses / 1472 ELISABETH PUCHHAMMER-STÖCKL AND MARIE LOUISE LANDRY, ANGELA M. STEPHAN W. ABERLE CALIENDO, CHRISTINE C. GINOCCHIO, 102 Human Cytomegalovirus / 1770 RANDALL HAYDEN, AND YI-WEI TANG RICHARD L. HODINKA 103 Epstein-Barr Virus / 1797 RNA Viruses BARBARA C. GÄRTNER AND 84 Human Immunodeficiency Viruses / 1477 FAUSTO BALDANTI S. MICHELE OWEN 104 Human Herpesviruses 6A, 6B, and 7 / 1814 85 Human T-Cell Lymphotropic Viruses / 1498 ALEXANDER L. GRENINGER, RUTH HALL WILLIAM M. SWITZER, WALID HENEINE, SEDLAK, AND KEITH R. JEROME AND S. MICHELE OWEN 105 Human Herpesvirus 8 / 1826 86 Influenza Viruses / 1510 SHEILA C. DOLLARD AND ROBERT L. ATMAR CLIFFORD J. GUNTHEL 87 Parainfluenza and Mumps Viruses / 1528 106 Adenoviruses / 1831 RYAN F. RELICH AND DIANE S. LELAND ALBERT HEIM AND RANDALL T. HAYDEN

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107 Human Papillomaviruses / 1847 117 Specimen Collection, Transport, and Processing: KATE CUSCHIERI AND ELIZABETH R. UNGER Mycology / 2016 108 Human Polyomaviruses / 1863 ELIZABETH L. BERKOW AND KARIN L. McGOWAN GREGORY A. STORCH AND RICHARD S. BULLER 118 Reagents, Stains, and Media: Mycology / 2025 109 Parvovirus B19 and Bocaviruses / 1880 MARK D. LINDSLEY KEVIN E. BROWN 119 General Approaches for Direct Detection and 110 Poxviruses / 1891 Identification of Fungi / 2035 VICTORIA A. OLSON, P. S. SATHESHKUMAR, H. RUTH ASHBEE AND INGER K. DAMON 111 Hepatitis B and D Viruses / 1905 Fungi YI-WEI TANG, REBECCA T. HORVAT, AND 120 Candida, Cryptococcus, and Other Yeasts of MARIE-LOUISE LANDRY Medical Importance / 2056 ANDREW M. BORMAN AND Subviral Agents ELIZABETH M. JOHNSON 112 Prion Diseases / 1923 121 Pneumocystis / 2087 DANIEL D. RHOADS AND JIRI G. SAFAR MELANIE T. CUSHION AND M. ALI RAI 122 Aspergillus, Talaromyces, and Penicillium / 2103 SHARON C.-A. CHEN, WIELAND MEYER, TANIA C. SORRELL, AND CATRIONA L. HALLIDAY section 123 Fusarium and Other Opportunistic Hyaline V Fungi / 2132 Antiviral Agents and SEAN X. ZHANG, KERRY O’DONNELL, AND Susceptibility Test DEANNA A. SUTTON 124 Agents of Systemic and Methods / 1935 Subcutaneous Mucormycosis and Entomophthoromycosis / 2163 VOLUME EDITOR: MARIE LOUISE LANDRY DEA GARCIA-HERMOSO, ALEXANDRE SECTION EDITORS: ANGELA M. CALIENDO, ALANIO, OLIVIER LORTHOLARY, AND CHRISTINE C. GINOCCHIO, RANDALL T. HAYDEN, FRANÇOISE DROMER AND YI-WEI TANG 125 Histoplasma, Blastomyces, Coccidioides, 113 Antiviral Agents / 1937 Paracoccidioides, and Other Dimorphic Fungi CARLOS A. Q. SANTOS AND NELL S. LURAIN Causing Systemic Mycoses / 2187 114 Mechanisms of Resistance to Antiviral GEORGE R. THOMPSON III AND Agents / 1962 BEATRIZ L. GÓMEZ ROBERT W. SHAFER, GUY BOIVIN, AND 126 Trichophyton, Microsporum, Epidermophyton, SUNWEN CHOU and Agents of Superficial Mycoses / 2208 115 Susceptibility Test Methods: Viruses / 1985 ANDREW M. BORMAN AND DIANA D. HUANG, BENJAMIN A. PINSKY, RICHARD C. SUMMERBELL AND MATTHEW J. BANKOWSKI 127 Curvularia, Exophiala, Scedosporium, Sporothrix, and Other Melanized Fungi / 2234 JOSEP GUARRO, HUGO MADRID, AND section SYBREN de HOOG VI 128 Fungi Causing Eumycotic Mycetoma / 2261 Mycology / 2005 SARAH ABDALLAH AHMED, G. SYBREN de HOOG, AND WENDY W. J. van de SANDE VOLUME EDITOR: DAVID W. WARNOCK 129 Mycotoxins / 2278 SECTION EDITORS: MARY E. BRANDT AND JOANNA TANNOUS AND NANCY P. KELLER ELIZABETH M. JOHNSON 130 Lacazia, Lagenidium, Pythium, and General Rhinosporidium / 2291 116 Taxonomy, Classification, and Nomenclature RAQUEL VILELA AND LEONEL MENDOZA of Fungi / 2007 131 Microsporidia / 2305 MARY E. BRANDT AND DAVID W. WARNOCK RAINER WEBER, PETER DEPLAZES, AND ALEXANDER MATHIS

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142 Pathogenic and Opportunistic Free-Living section Amebae / 2486 VII JENNIFER R. COPE, IBNE KARIM M. ALI, Antifungal Agents AND GOVINDA S. VISVESVARA and Susceptibility Test 143 Intestinal and Urogenital Amebae, Flagellates, and Ciliates / 2497 Methods / 2317 SUSAN NOVAK-WEEKLEY AND AMY L. LEBER VOLUME EDITOR: DAVID W. WARNOCK 144 Cystoisospora, Cyclospora, and SECTION EDITORS: MARY E. BRANDT AND Sarcocystis / 2526 ELIZABETH M. JOHNSON DAVID S. LINDSAY AND LOUIS M. WEISS 132 Antifungal Agents / 2319 145 Cryptosporidium / 2536 SHAWN R. LOCKHART AND LIHUA XIAO AND VITALIANO CAMA ELIZABETH L. BERKOW 146 Nematodes / 2551 133 Mechanisms of Resistance to Antifungal HARSHA SHEOREY, BEVERLEY-ANN BIGGS, Agents / 2334 AND NORBERT RYAN DAVID S. PERLIN 147 Filarial Nematodes / 2570 134 Susceptibility Test Methods: Yeasts and CARMELLE T. NORICE-TRA AND Filamentous Fungi / 2351 THOMAS B. NUTMAN ELIZABETH M. JOHNSON AND 148 Cestodes / 2582 MAIKEN CAVLING ARENDRUP HECTOR H. GARCIA, JUAN A. JIMENEZ, AND HERMES ESCALANTE 149 Trematodes / 2590 MALCOLM K. JONES, JENNIFER KEISER, AND section VIII DONALD P. McMANUS 150 Less Common Helminths / 2606 Parasitology / 2377 GARY W. PROCOP AND RONALD C. NEAFIE VOLUME EDITOR: DAVID W. WARNOCK 151 Arthropods of Medical Importance / 2620 SECTION EDITORS: BOBBI S. PRITT AND SAM R. TELFORD III AND BLAINE A. MATHISON GARY W. PROCOP General 135 Taxonomy and Classification of Human Eukaryotic Parasites / 2379 section IX SINA M. ADL AND BLAINE A. MATHISON Antiparasitic Agents 136 Specimen Collection, Transport, and Processing: Parasitology / 2389 and Susceptibility Test ROBYN Y. SHIMIZU AND LYNNE S. GARCIA Methods / 2643 137 Reagents, Stains, and Media: VOLUME EDITOR: DAVID W. WARNOCK Parasitology / 2406 SECTION EDITORS: GARY W. PROCOP ANDREA J. LINSCOTT AND SUSAN E. SHARP 138 General Approaches for Detection and 152 Antiparasitic Agents / 2645 Identification of Parasites / 2414 KARIN LEDER, SARAH L. McGUINNESS, AND PETER F. WELLER LYNNE S. GARCIA, GRAEME P. PALTRIDGE, AND ROBYN Y. SHIMIZU 153 Mechanisms of Resistance to Antiparasitic Agents / 2669 W. EVAN SECOR, JACQUES LE BRAS, AND Parasites JÉRÔME CLAIN 139 Plasmodium and Babesia / 2438 154 Susceptibility Test Methods: Parasites / 2682 BOBBI S. PRITT JÉRÔME CLAIN, JACQUES LE BRAS, AND 140 Leishmania and Trypanosoma / 2458 W. EVAN SECOR DAVID A. BRUCKNER AND JAIME A. LABARCA Author Index xxix 141 Toxoplasma / 2473 JAMES B. McAULEY AND KAMALJIT SINGH Subject Index xxxi

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Mary E. Brandt Sections VI and VII Melissa B. Miller Section II Office of Laboratory Science and Safety, Centers for Department of Pathology and Laboratory Medicine, Disease Control and Prevention, Atlanta, Georgia University of North Carolina, Chapel Hill, North Carolina Carey-Ann D. Burnham Section II Department of Pathology & Immunology, Elisabeth Nagy Section II Division of Laboratory and Genomic Medicine, Institute of Clinical Microbiology, University of Szeged, Washington University in St. Louis School of Medicine, Szeged, Hungary St. Louis, Missouri Jean Patel Section III Angela Caliendo Sections IV and V The Division of Healthcare Quality Promotion, Centers Alpert Medical School of Brown University, for Disease Control and Prevention, Atlanta, Georgia Providence, Rhode Island Johann Pitout Section II J. Stephen Dumler Section II Department of Pathology and Laboratory Medicine, Joint Departments of Pathology, Uniformed Services University of Calgary, and Division of Microbiology, University of the Health Sciences, Walter Reed Calgary Laboratory Services, Calgary, Alberta, Canada National Military Medical Center, Joint Pathology Center, Bethesda, Maryland Bobbi S. Pritt Section VIII Laboratory Medicine and Pathology, Mayo Clinic, Christine C. Ginocchio Sections IV and V Rochester, Minnesota Medical Affairs, bioMérieux/BioFire Diagnostics, Durham, North Carolina Gary W. Procop Sections VIII and IX Department of Laboratory Medicine, Pathology and Randall T. Hayden Sections IV and V Laboratory Medicine Institute, Cleveland Clinic, Department of Pathology, St. Jude Children’s Research Cleveland, Ohio Hospital, Memphis, Tennessee Yi-Wei Tang Sections IV and V Elizabeth M. Johnson Sections VI and VII Department of Laboratory Medicine, Memorial Sloan Mycology Reference Laboratory, Public Health England Kettering Cancer Center, and Department of Pathology National Infection Service, Bristol, United Kingdom and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York James Karlowsky Section I Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada

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MCM12_FM.indd 12 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM Contributors

APRIL N. ABBOTT GEORGE F. ARAJ Department of Laboratory Medicine, Deaconess Health Department of Pathology and Laboratory Medicine, American System, Evansville, Indiana University of Beirut Medical Center, Beirut, Lebanon

STEPHAN W. ABERLE MATTHEW J. ARDUINO Center for Virology, Medical University of Vienna, Division of Healthcare Quality Promotion, National Center Vienna, Austria for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia SINA M. ADL University of Saskatchewan, Soil Sciences, College of Maiken Cavling Arendrup Agriculture, Saskatoon, Saskatchewan, Canada Department of Microbiology & Infection Control, Statens Serum Institut; Department of Clinical Microbiology, MARIA E. AGUERO-ROSENFELD Rigshospitalet; and Department of Clinical Medicine, New York University Langone Health, Pathology, New York, University of Copenhagen, Copenhagen, Denmark New York H. RUTH ASHBEE SARAH ABDALLAH AHMED School of Molecular and Cellular Biology, Faculty of Biological Westerdijk Fungal Biodiversity Institute, Utrecht, Sciences, University of Leeds, Leeds, United Kingdom The Netherlands RONALD M. ATLAS ALEXANDRE ALANIO Department of Biology, University of Louisville, Louisville, Unité Mycologie Moléculaire, CNRS UMR2000, Kentucky (Retired) Centre National de Référence des Mycoses Invasives et Antifongiques, Institut Pasteur, 75724 Paris cedex 15, France ROBERT L. ATMAR Departments of Medicine and Molecular Virology & KEVIN ALBY Microbiology, Baylor College of Medicine, Houston, Texas Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania N. ESTHER BABADY Department of Laboratory Medicine, Memorial Sloan- DAVID C. ALEXANDER Kettering Cancer Center, New York, New York Cadham Provincial Laboratory and Department of Medical Microbiology & Infectious Diseases, University of Manitoba, FAUSTO BALDANTI Winnipeg, Manitoba, Canada Department of Clinical, Surgical, Diagnostics and Pediatric Sciences, University of Pavia, and Molecular Virology Unit, IBNE M. KARIM ALI Fondazione IRCCS Policlinico San Matteo, Pavia, Italy National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, MATTHEW J. BANKOWSKI Atlanta, Georgia Baptist Medical Center Jacksonville, Infectious Diagnostics Laboratory, Jacksonville, Florida

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MCM12_FM.indd 13 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM xiv n CONTRIBUTORS

FRÉDÉRIC BARBUT DONALD H. BOUYER National Reference Laboratory for Clostridium difficile, Department of Pathology, University of Texas Medical Hôpital Saint-Antoine, and EA4065, Université Paris Branch, Galveston, Texas Descartes, Paris, France PATRICIA A. BRADFORD JENNIFER DIEN BARD Antimicrobial Development Specialists, LLC, Nyack, New York Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine, University of CLAUDIA BRANDT Southern California, Los Angeles, California Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany CÉCILE BÉBÉAR USC EA 3671, University of Bordeaux, Department of MARY E. BRANDT Bacteriology, French National Reference Center for bacterial Office of Laboratory Science and Safety, Centers for Disease STI, Bordeaux University Hospital, Bordeaux, France Control and Prevention, Atlanta, Georgia

KARSTEN BECKER KEVIN E. BROWN University Hospital Münster, Institute of Medical Virus Reference Department, Public Health England, London, Microbiology, Münster, Germany United Kingdom

ELIZABETH L. BERKOW BARBARA A. BROWN-ELLIOTT Centers for Disease Control and Prevention, Mycotic Diseases Department of Microbiology, The University of Texas Branch, Atlanta, Georgia Health Science Center at Tyler, Department of Microbiology, Tyler, Texas KATHRYN A. BERNARD National Microbiology Laboratory-CSCHAH, Public Health DAVID A. BRUCKNER Agency of Canada, and Department of Medical Microbiology, Department of Pathology & Laboratory Medicine, David University of Manitoba, Winnipeg, Manitoba, Canada Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California BEVERLEY-ANN BIGGS Victorian Infectious Diseases Service, Royal Melbourne BLAKE W. BUCHAN Hospital, Parkville, Victoria, and Department of Medicine Medical College of Wisconsin and Wisconsin Diagnostic at the Peter Doherty Institute for Infection and Immunity, Laboratories, Milwaukee, Wisconsin University of Melbourne, Melbourne, Australia RICHARD S. BULLER THOMAS BJARNSHOLT Department of Pediatrics, Washington University School of Department of Clinical Microbiology, Rigshospitalet, and Medicine, St. Louis, Missouri Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, SUSAN M. BUTLER-WU University of Copenhagen, Copenhagen, Denmark Department of Pathology and Laboratory Medicine, Keck School of Medicine of USC, Los Angeles, California LUCAS S. BLANTON Department of Internal Medicine – Infectious Diseases, ANGELA M. CALIENDO University of Texas Medical Branch, Galveston, Texas Alpert Medical School of Brown University, Providence, Rhode Island CHANTAL BLEEKER-ROVERS Radboud University Medical Center, Department of Internal VITALIANO CAMA Medicine, and Radboud Expertise Center for Q Fever, Division of Parasitic Diseases and Malaria, Centers for Disease Nijmegen, The Netherlands Control and Prevention, Atlanta, Georgia

CHRISTIAN BOGDAN GERALD A. CAPRARO Mikrobiologisches Institut - Klinische Mikrobiologie, Carolinas HealthCare System, Clinical Microbiology, Immunologie und Hygiene, Friedrich-Alexander-Universität Charlotte, North Carolina (FAU) Erlangen-Nürnberg und Universitätsklinikum Erlangen, Erlangen, Germany DARCIE E. CARPENTER IHMA, Inc., Schaumburg, Illinois GUY BOIVIN Department of Microbiology and Infectious Diseases, Laval Karen C. Carroll University, Quebec City, QC, Canada Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, ANDREW M. BORMAN Baltimore, Maryland United Kingdom National Mycology Reference Laboratory, Public Health England, Bristol, United Kingdom Maria da Glória Siqueira Carvalho Streptococcus Laboratory, Respiratory Diseases Branch, YAN BOUCHER Division of Bacterial Diseases, Centers for Disease Control University of Alberta, Edmonton, Alberta, Canada and Prevention, Atlanta, Georgia

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MCM12_FM.indd 14 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM CONTRIBUTORS n xv

Mariana Castanheira Piet Cools JMI Laboratories, North Liberty, Iowa Laboratory Bacteriology Research, Department of Microbiology, Immunology and Clinical Chemistry, Faculty Adam J. Caulfield of Medicine and Health Sciences, Ghent University, Spectrum Health Regional Laboratory, Grand Rapids, Ghent, Belgium Michigan Jennifer R. Cope Angella Charnot-Katsikas National Center for Emerging and Zoonotic Infectious Department of Pathology, University of Chicago, Diseases, Centers for Disease Control and Prevention, Chicago, Illinois Atlanta, Georgia

Sharon C.-A. Chen Marc Roger Couturier Westmead Hospital, Infectious Diseases, Westmead, University of Utah/ARUP Laboratories, Pathology/Infectious NSW 2145, Australia Disease Microbiology, Salt Lake City, Utah

Max Chernesky Bart J. Currie Pediatrics, Pathology and Molecular Medicine, Menzies School of Health Research and Northern Territory McMaster University/St Josephs Healthcare, Hamilton, Medical Program, Royal Darwin Hospital, Darwin, Northern Ontario, Canada Territory, Australia

Cheng-Feng Chiang Kate Cuschieri Viral Special Pathogens Branch, Division of Scottish HPV Reference Laboratory, Department of High Consequence Pathogens and Pathology, Laboratory Medicine, Royal Infirmary of Edinburgh, National Center for Emerging and Zoonotic Infectious Edinburgh, Scotland Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia Melanie T. Cushion Department of Internal Medicine, Division of Infectious Sunwen Chou Diseases, University of Cincinnati College of Medicine, and Department of Medicine, Oregon Health and Sciences the Cincinnati VA Medical Center, Cincinnati, Ohio University, Portland, Oregon Steven D. Dallas Jens Jørgen Christensen UT Health San Antonio, Department of Pathology and Institute of Clinical Medicine, University of Copenhagen, Laboratory Medicine, San Antonio, Texas and Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark Inger K. Damon Centers for Disease Control and Prevention, Division of High Oana Ciofu Consequence Pathogens and Pathology, Atlanta, Georgia Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, G. Sybren de Hoog University of Copenhagen, Copenhagen, Denmark Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands Jérôme Clain UMR 216 IRD MERIT, Faculty of Pharmacy, Paris Descartes John Dekker University, 75006 Paris, France National Institutes of Health, Bethesda, Maryland

Bryan R. Cobb Peter Deplazes Roche Molecular Systems, Pleasanton, California Institute of Parasitology, University of Zurich, Zurich, Switzerland Tom Coenye Laboratory of Pharmaceutical Microbiology, Ghent University, Edward P. Desmond Ghent, Belgium Mycobacteriology Section, Microbial Diseases Laboratory, California Department of Public Health, Richmond, Georg Conrads California Division of Oral Microbiology and Immunology, RWTH Aachen University Hospital, Aachen, Germany Daniel J. Diekema Division of Infectious Diseases, Department of Internal Patricia S. Conville Medicine, and Division of Medical Microbiology, Department Division of Microbiology Devices, Office of In-Vitro of Pathology, University of Iowa College of Medicine, Iowa Diagnostics and Radiological Health, Center for Devices City, Iowa and Radiological Health, Food and Drug Administration, Silver Spring, Maryland Elizabeth A. Dietrich Bacterial Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado

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MCM12_FM.indd 15 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM xvi n CONTRIBUTORS

Christopher D. Doern Matthias Frosch Department of Pathology, Virginia Commonwealth Institute of Hygiene and Microbiology, University of University Medical Center, Richmond, Virginia Wuerzburg, Wuerzburg, Germany

Sheila C. Dollard Naomi J. Gadsby Division of Viral Diseases, Centers for Disease Control and Royal Infirmary of Edinburgh, Specialist Virology Centre, Prevention, Atlanta, Georgia Dept. Laboratory Medicine, Edinburgh, Lothian EH16 4SA, United Kingdom Françoise Dromer Institut Pasteur, Unité de Mycologie Moléculaire, Renee L. Galloway Centre National de Référence des Mycoses Invasives et Centers for Disease Control and Prevention, Atlanta, Georgia Antifongiques, CNRS UMR2000, Paris, France Bhanu P. Ganesh J. Stephen Dumler Department of Neurology, The University of Texas Health Joint Departments of Pathology, Uniformed Services Science Center at Houston, Houston, Texas University of the Health Sciences, Walter Reed National Military Medical Center, Joint Pathology Center, Hector H. Garcia Bethesda, Maryland Universidad Peruana Cayetano Heredia, Center for Global Health, Lima, Peru James J. Dunn Department of Pathology, Texas Children’s Hospital, and Lynne S. Garcia Department of Pathology and Immunology, Baylor College of LSG & Associates, Santa Monica, California Medicine, Houston, Texas Dea Garcia-Hermoso Paul H. Edelstein Unité Mycologie Moléculaire, CNRS UMR2000, University of Pennsylvania Perelman School of Medicine, Centre National de Référence des Mycoses Invasives et Pathology and Laboratory Medicine, Philadelphia, Antifongiques, Institut Pasteur, 75724 Paris cedex 15, France Pennsylvania Barbara C. Gärtner Johannes Elias Institute for Microbiology and Hygiene, Saarland University, Instiute of Microbiology, DRK Kliniken Berlin, Berlin, Faculty of Medicine and Medical Center, Homburg/Saar, Germany Germany

Hermes Escalante Walter Geißdörfer Universidad Nacional de Trujillo, Trujillo, Peru Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität Richard R. Facklam (FAU) Erlangen-Nürnberg and Universitätsklinikum Streptococcus Laboratory, Respiratory Diseases Branch, Erlangen, Erlangen, Germany Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia Peter Gerner-Smidt National Center for Emerging and Zoonotic Infectious Diseases, Ferric C. Fang Centers for Disease Control and Prevention, Atlanta, Georgia Departments of Laboratory Medicine and Microbiology, University of Washington School of Medicine, Christine C. Ginocchio Seattle, Washington Medical Affairs, bioMérieux/BioFire Diagnostics, Durham, North Carolina John J. Farmer III United States Public Health Service (Retired), William A. Glover II Stone Mountain, Georgia Washington State Public Health Laboratories, Shoreline, Washington Matthew L. Faron Medical College of Wisconsin, Milwaukee, Wisconsin Beatriz L. Gómez Giraldo School of Medicine and Health Sciences, Translational Michael S. Forman Microbiology and Emerging Diseases Group (MICROS), Division of Medical Microbiology, Department of Universidad del Rosario, Bogotá, Colombia Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland Mark D. Gonzalez Department of Pathology, Children’s Healthcare of Atlanta, Stephen J. Forsythe Atlanta, Georgia foodmicrobe.com, Nottingham, United Kingdom Alexander L. Greninger Karen M. Frank Department of Laboratory Medicine, University of Department of Laboratory Medicine, National Institutes of Washington, and Vaccine and Infectious Disease Division, Fred Health, Bethesda, Maryland Hutchinson Cancer Research Center, Seattle, Washington

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Josep Guarro Elizabeth A. Hunsperger Universitat Rovira i Virgili, Mycology Unit, Medical School Diagnostics and Laboratory Systems Program, Centers for and IISPV, Reus, Spain Disease Control and Prevention, Centers for Global Health, Division of Global Health Protection, Nairobi, Kenya Clifford J. Gunthel Infectious Disease Program, Grady Health System, Joseph P. Icenogle Emory University School of Medicine, Atlanta, Georgia Viral Vaccine Preventable Diseases Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Catriona L. Halliday Atlanta, Georgia Westmead Hospital, Infectious Diseases, Westmead, NSW 2145, Australia Jacques Izopet Department of Virology, National Reference Center Randall T. Hayden for Hepatitis E virus, CHU Toulouse, and Center for Department of Pathology, St. Jude Children’s Research Pathophysiology of Toulouse-Purpan, INSERM UMR1043 / Hospital, Memphis, Tennessee CNRS UMR 5282, CPTP, Toulouse University Paul Sabatier, Toulouse, France Albert Heim Hannover Medical School, Virology, Hannover, Germany Keith R. Jerome Department of Laboratory Medicine, University of Walid Heneine Washington, Vaccine and Infectious Disease Division, Fred Division of HIV/AIDS Prevention, National Center for Hutchinson Cancer Research Center, Seattle, Washington HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia Juan A. Jimenez Universidad Nacional Mayor de San Marcos, Laboratorio de Carole J. Hickman Parasitología en Fauna Silvestre y Zoonosis, Lima, Peru Viral Vaccine Preventable Diseases Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Crystal N. Johnson Atlanta, Georgia APC Microbiome Institute and Teagasc Food Research Centre, Moorepark Biosciences Department, Fermoy, Co. Cork, Ireland Sarah K. Highlander Pathogen and Microbiome Division, Translational Genomics Elizabeth M. Johnson Research Institute, Flagstaff, Arizona Mycology Reference Laboratory, Public Health England National Infection Service, Bristol, United Kingdom Richard L. Hodinka Department of Biomedical Sciences, University of South Malcolm K. Jones Carolina School of Medicine Greenville and Greenville School of Veterinary Sciences, The University of Queensland, Health System, Greenville, South Carolina Brisbane, Qld 4072, Australia

Niels Høiby James H. Jorgensen Department of Clinical Microbiology, Rigshospitalet, and University of Texas Health Science Center at San Antonio, Department of Immunology and Microbiology, Costerton San Antonio, Texas Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark Nassim Kamar Center for Pathophysiology of Toulouse-Purpan, INSERM Martin Holfelder UMR1043 / CNRS UMR 5282, CPTP, Toulouse University Department of Microbiology, Limbach Laboratory, Paul Sabatier, and Department of Nephrology and Organ Heidelberg, Germany Transplantation, CHU Toulouse, Toulouse, France

Amy J. Horneman Peter Kämpfer VA Maryland Health Care System, Pathology and Laboratory Institut für Angewandte Mikrobiologie, Universität Giessen, Service, Baltimore, Maryland Giessen, Germany

Rebecca T. Horvat James A. Karlowsky Department of Pathology and Laboratory Medicine, University Department of Medical Microbiology and Infectious Diseases, of Kansas School of Medicine, Kansas City, Kansas University of Manitoba, Winnipeg, Manitoba, Canada

Diana D. Huang Jennifer Keiser Department of Microbial Pathogens and Immunity, Rush Department of Medical Parasitology and Infection Biology, University Medical Center, Chicago, Illinois Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland Romney M. Humphries Accelerate Diagnostics, Tucson, and Department of Nancy P. Keller Pathology and Laboratory Medicine, University of Arizona, University of Wisconsin-Madison, Medical Microbiology and Tucson, Arizona Immunology and Bacteriology, Madison, Wisconsin

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MCM12_FM.indd 17 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM xviii n CONTRIBUTORS

Gilbert J. Kersh Amy L. Leber Centers for Disease Control and Prevention, Rickettsial Nationwide Children’s Hospital, Clinical Microbiology Zoonoses Branch, Atlanta, Georgia and Immunoserology, Department of Laboratory Medicine, Columbus, Ohio Paul E. Kilgore Eugene Applebaum College of Pharmacy and Health Sciences Nathan A. Ledeboer and Department of Family Medicine and Public Health Department of Pathology, Medical College of Wisconsin, Sciences, School of Medicine, Wayne State University, Milwaukee, Wisconsin Detroit, Michigan Karin Leder Luke C. Kingry Infectious Disease Epidemiology Unit, School of Epidemiology Bacterial Diseases Branch, Division of Vector-Borne Diseases, and Preventive Medicine, Monash University, Victorian Centers for Disease Control and Prevention, Fort Collins, Infectious Disease Service, Royal Melbourne Hospital, Colorado Victoria, Australia

John D. Klena Elliot J. Lefkowitz Viral Special Pathogens Branch, Division of High Department of Microbiology, The University of Alabama at Consequence Pathogens and Pathology, National Center Birmingham, Birmingham, Alabama for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia Diane S. Leland Department of Pathology and Laboratory Medicine, Indiana Laura M. Koeth University School of Medicine, Indianapolis, Indiana Laboratory Specialists, Inc., Westlake, Ohio Paul N. Levett Eija Könönen BC Centre for Disease Control Public Health Laboratory, Institute of Dentistry, University of Turku, Turku, Finland Vancouver, British Columbia, Canada

Thomas G. Ksiazek James S. Lewis, II Galveston National Laboratory, Department of Pathology, Oregon Health and Science University, Departments of University of Texas Medical Branch, Galveston, Texas Pharmacy & Infectious Diseases, Portland, Oregon

Ed Kuijper Shou-Yean Grace Lin Department of Medical Microbiology, Leiden University Mycobacteriology Section, Microbial Diseases Laboratory, Medical Centre, 2333 ZA Leiden, The Netherlands California Department of Public Health, Richmond, California

Jaime Labarca David S. Lindsay Departamento de Enfermedades Infecciosas, Escuela de Virginia Tech, Biomedical Sciences and Pathobiology, Medicina, Pontificia Universidad Católica de Chile, Diagonal Blacksburg, Virginia Paraguay 362, Santiago 8330077, Chile Mark D. Lindsley Philippe Lagacé-Wiens Mycotic Diseases Branch, Centers for Disease Control and Diagnostic Services, Shared Health, and Department of Medical Prevention, Atlanta, Georgia Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada Andrea J. Linscott Ochsner Medical Center, Department of Pathology and Daryl M. Lamson Laboratory Medicine, New Orleans, Louisiana Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York John J. LiPuma Department of Pediatrics and Communicable Diseases, Brigitte Lamy University of Michigan Medical School, Ann Arbor, Michigan CHU Nice, Université Côte d’Azur and INSERM U1065, Bactériologie, Nice, France Shawn R. Lockhart Mycotic Diseases Branch, National Center for Emerging and Marie Louise Landry Zoonotic Infectious Diseases, Centers for Disease Control and Laboratory Medicine and Internal Medicine, Yale University, Prevention, Atlanta, Georgia New Haven, Connecticut Michael Loeffelholz Paul A. Lawson Department of Pathology and Clinical Microbiology Department of Microbiology and Plant Biology, University of Laboratory, University of Texas Medical Branch, Oklahoma, Norman, Oklahoma Galveston, Texas

Jacques Le Bras Olivier LOrtholary UMR 216 IRD MERIT, Faculty of Pharmacy, Paris Descartes Unité Mycologie Moléculaire, CNRS UMR2000, Centre University, 75006 Paris, France National de Référence des Mycoses Invasives et Antifongiques, Institut Pasteur, 75724 Paris cedex 15, France

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MCM12_FM.indd 18 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM CONTRIBUTORS n xix

Xiaoyan Lu Linda A. Federici Miller Division of Viral Diseases, Centers for Disease Control and CMID Pharma Consulting, LLC, Dresher, Pennsylvania Prevention, Atlanta, Georgia Rhoda Ashley Morrow Nell S. Lurain University of Washington and Fred Hutchinson Cancer Department of Microbial Pathogens and Immunity, Research Center, Seattle, Washington Rush University Medical Center, Chicago, Illinois Annette Moter Duncan MacCannell Charité-Universitätsmedizin Berlin, Biofilmzentrum des National Center for Emerging and Zoonotic Infectious Deutschen Herzzentrums Berlin, Berlin, Germany Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia Iona Munjal Department of Pediatrics, Montefiore Medical Center and Hugo Madrid Albert Einstein College of Medicine, and Pfizer Vaccine Universidad Mayor, Centro de Genómica y Bioinformática, Clinical Research & Development, Bronx, New York Santiago, Chile Irving Nachamkin Steven D. Mahlen Department of Pathology and Laboratory Medicine, Affiliated Laboratory, Inc., Clinical Microbiology, Perelman School of Medicine, University of Pennsylvania, Bangor, Maine Philadelphia, Pennsylvania

Isabella Martin Elisabeth Nagy Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, Institute of Clinical Microbiology, University of Szeged, New Hampshire Szeged, Hungary

Alexander Mathis Ronald C. Neafie Institute of Parasitology, University of Zurich, Retired, Former Armed Forces Institute of Pathology, Zurich, Switzerland Washington, DC

Blaine Mathison Alexandr Nemec ARUP Laboratories, Infectious Disease Division, Laboratory of Bacterial Genetics, Centre for Epidemiology Salt Lake City, Utah and Microbiology, National Institute of Public Health, Prague, Czech Republic James B. McAuley Rush University Medical Center, Chicago, Illinois Terry Fei Fan Ng National Center for Immunization and Respiratory Diseases, Gerald McDonnell Centers for Disease Control and Prevention, Atlanta, Georgia DePuy Synthes Companies, Johnson & Johnson, Raritan, New Jersey Xiaohui Chen Nielsen Department of Clinical Microbiology, Slagelse Hospital, Erin McElvania Slagelse, Denmark Pathology, Evanston Hospital/NorthShore University HealthSystem, Evanston, Illinois Frederick S. Nolte Department of Pathology and Laboratory Medicine, Medical Karin L. McGowan University of South Carolina, Charleston, South Carolina University of Pennsylvania, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Carmelle T. Norice-Tra Philadelphia, Pennsylvania (Emeritus) Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Sarah L. McGuinness Bethesda, Maryland Infectious Disease Epidemiology Unit, School of Epidemiology and Preventive Medicine, Monash University, Department of Niels Nørskov-Lauritsen Infectious Diseases, The Alfred Hospital, Victoria, Australia Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark Donald P. McManus QIMR Berghofer Medical Research Institute, Herston, Susan Novak-Weekley Queensland 4006, Australia Qvella, Carlsbad, California

Leonel Mendoza Thomas B. Nutman Michigan State University, Microbiology and Molecular Laboratory of Parasitic Diseases, National Institute of Allergy Genetics, East Lansing, Michigan and Infectious Diseases, National Institutes of Health, Bethesda, Maryland Wieland Meyer Westmead Millennium Institute for Medical Research, Infectious Diseases, Westmead, NSW 2145, Australia

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MCM12_FM.indd 19 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM xx n CONTRIBUTORS

Kerry O’Donnell Michael A. Pfaller Mycotoxin Prevention and Applied Microbiology Research Departments of Pathology and Epidemiology (Emeritus), Unit, National Center for Agricultural Utilization Research, University of Iowa, Iowa City, and JMI Laboratories, ARS-USDA, Peoria, Illinois North Liberty, Iowa

Victoria A. Olson Allan Pillay Poxvirus and Rabies Branch, Division of High Consequence Molecular Surveillance of T. pallidum Unit, Laboratory Pathogens and Pathologies, Centers for Disease Control and Reference and Research Branch, Division of STD Prevention, Prevention, Atlanta, Georgia Centers for Disease Control and Prevention, Atlanta, Georgia

Lillian A. Orciari Benjamin A. Pinsky Poxvirus and Rabies Branch, Division of High Consequence Departments of Pathology and Medicine, Stanford University Pathogens and Pathologies, Centers for Disease Control and School of Medicine, Stanford, California Prevention, Atlanta, Georgia Johann Pitout Belinda Ostrowsky Department of Pathology and Laboratory Medicine, Department of Medicine, Division of Infectious Disease, University of Calgary, and Division of Microbiology, Montefiore Medical Center and Albert Einstein College of Calgary Laboratory Services, Calgary, Alberta, Canada Medicine, Bronx, New York Bobbi S. Pritt S. Michele Owen Laboratory Medicine and Pathology, Mayo Clinic, National Center for HIV/AIDS, Viral Hepatitis, STD, and Rochester, Minnesota TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia Gary W. Procop Department of Laboratory Medicine, Pathology and Laboratory Graeme P. Paltridge Medicine Institute, Cleveland Clinic, Cleveland, Ohio Canterbury Health Laboratories, Microbiology Laboratory, Christchurch 8011, New Zealand Elisabeth Puchhammer-Stöckl Center for Virology, Medical University of Vienna, Xiaoli Pang Vienna, Austria Provincial Laboratory for Public Health and Department of Laboratory Medicine and Pathology, University of Alberta, Justin D. Radolf Edmonton, Alberta, Canada Departments of Medicine, Pediatrics, Immunology, Molecular Biology and Biophysics, and Genetics and Genome Sciences, Nicole Parrish UConn Health, Farmington, Connecticut Pathology, Johns Hopkins University, Baltimore, Maryland M. Ali Rai Robin Patel Cincinnati Veterans Affairs Medical Center, Cincinnati, Ohio Infectious Diseases Research Laboratory, Mayo Clinic, Rochester, Minnesota Ryan F. Relich Department of Pathology and Laboratory Medicine, Indiana Sharon J. Peacock University School of Medicine, Indianapolis, Indiana Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom L. Barth Reller Departments of Pathology and Medicine, Duke University Michael Pentella School of Medicine, Durham, North Carolina University of Iowa, College of Public Health, Department of Epidemiology, Iowa City, Iowa Daniel D. Rhoads Case Western Reserve University, Cleveland, Ohio David S. Perlin Public Health Research Institute, New Jersey Medical Elvira Richter School, Rutgers Biomedical and Health Sciences, Newark, MVZ Labor Dr. Limbach, TB Laboratory, Heidelberg, New Jersey Germany

Jeannine M. Petersen Sandra S. Richter Bacterial Diseases Branch, Division of Vector-Borne Diseases, Clinical Pathology, Cleveland Clinic, Cleveland, Ohio Centers for Disease Control and Prevention, Fort Collins, Colorado Winnie Ridderberg Qiagen Bioinformatics, Aarhus, Denmark Joseph F. Petrosino Department of Molecular Virology & Microbiology, Baylor Pierre E. Rollin College of Medicine, Houston, Texas Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia

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MCM12_FM.indd 20 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM CONTRIBUTORS n xxi

José R. Romero Parham Sendi Section of Pediatric Infectious Diseases, University of Institute for Infectious Diseases, University of Bern, Bern, and Arkansas for Medical Sciences and Arkansas Children’s Department of Infectious Diseases and Hospital Epidemiology, Hospital, Little Rock, Arkansas University Hospital Basel, University Basel, Basel, Switzerland

Paul A. Rota Robert W. Shafer National Center for Immunization and Respiratory Departments of Medicine and Pathology, Stanford University, Diseases, Centers for Disease Control and Prevention, Stanford, California Atlanta, Georgia Susan E. Sharp Kathryn L. Ruoff Kaiser Permanente, Department of Pathology, Portland, O’Toole Lab, Department of Microbiology and Immunology, Oregon Geisel School of Medicine at Dartmouth, Hanover, New Hampshire Rosemary C. She Department of Pathology, Keck School of Medicine of the Norbert Ryan University of Southern California, Los Angeles, California Bacteriology Laboratory, Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Harsha Sheorey Infection and Immunity, 792 Elizabeth St., Melbourne 3000, Department of Microbiology, St Vincent’s Hospital Australia Melbourne, Fitzroy, Victoria 3065, Australia

Jiri G. Safar Patricia Lynn Shewmaker Case Western Reserve University, Cleveland, Ohio Streptococcus Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control Max Salfinger and Prevention, Atlanta, Georgia Advanced Diagnostic Laboratories, National Jewish Health, Department of Medicine & Mycobacteriology Laboratory, Wun-Ju Shieh Denver, Colorado Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, National Center Linoj Samuel for Emerging and Zoonotic Infectious Diseases, Centers for Clinical Microbiology, Henry Ford Health System, Detroit, Disease Control and Prevention, Atlanta, Georgia Michigan Robyn Y. Shimizu Carlos A. Q. Santos UCLA HealthSystem, Pathology and Laboratory Medicine, Division of Infectious Diseases, Rush University Medical Los Angeles, California Center, Chicago, Illinois Patricia J. Simner P. S. Satheshkumar John Hopkins University School of Medicine, Pathology, Poxvirus and Rabies Branch, Division of High Consequence Baltimore, Maryland Pathogens and Pathologies, Centers for Disease Control and Prevention, Atlanta, Georgia Kamaljit Singh NorthShore University HealthSystem, Department of Julius Schachter Pathology, Evanston, Illinois Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California Robert L. Skov MVZ Synlab Leverkusen GmbH, Leverkusen, Germany, and Audrey N. Schuetz Statens Serum Institut, Copenhagen, Denmark Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota Marek Smieja Department of Pathology and Molecular Medicine, McMaster W. Evan Secor University, Hamilton, Ontario, Canada Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia James W. Snyder University of Louisville, Department of Pathology and Ruth Hall Sedlak Laboratory Medicine, ULH, Louisville, Kentucky Veterinary Medicine Research and Development, Zoetis, Kalamazoo, Michigan Tania C. Sorrell Westmead Hospital, Infectious Diseases, Westmead, Arlene C. Seña NSW 2145, Australia Department of Medicine, Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, Barbara Spellerberg and Durham County Department of Public Health, Durham, Institute of Medical Microbiology and Hygiene, University North Carolina of Ulm, Ulm, Germany

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MCM12_FM.indd 21 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM xxii n CONTRIBUTORS

Jennifer K. Spinler Elitza S. Theel Department of Pathology & Immunology, Baylor College of Department of Laboratory Medicine and Pathology, Medicine, and Department of Pathology, Texas Children’s Division of Clinical Microbiology Hospital, Houston, Texas Mayo Clinic, Rochester, Minnesota

Gerold Stanek George R. Thompson, III Medical University of Vienna, Center for Pathophysiology, Department of Internal Medicine, Division of Infectious Diseases, Infectiology and Immunology, Institute for Hygiene and and Department of Medical Microbiology and Immunology, Applied Immunology, Vienna, Austria University of California - Davis, Davis, California

Kathleen A. Stellrecht Jonathan S. Towner Department of Pathology and Laboratory Medicine, Albany Viral Special Pathogens Branch, Centers for Disease Control Medical College and Albany Medical Center Hospital, and Prevention, Atlanta, Georgia Albany, New York Eija Trees Gregory A. Storch National Center for Emerging and Zoonotic Infectious Diseases, Department of Pediatrics, Washington University School of Centers for Disease Control and Prevention, Atlanta, Georgia Medicine, St. Louis, Missouri Christine Y. Turenne Richard C. Summerbell Clinical Microbiology, Shared Health (Diagnostic Services), and Sporometrics Inc. and Dalla Lana School of Public Health, Department of Medical Microbiology & Infectious Diseases, University of Toronto, Toronto, Ontario, Canada University of Manitoba, Winnipeg, Manitoba, Canada

Deanna A. Sutton John D. Turnidge Department of Pathology, University of Texas Health Science Adelaide Medical School, University of Adelaide, Center at San Antonio, San Antonio, Texas Adelaide, Australia

William M. Switzer Kerin Tyrrell Division of HIV/AIDS Prevention, National Center for Los Angeles, California HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia Elizabeth R. Unger Chronic Viral Diseases Branch, National Center for Emerging Wendy A. Szymczak and Zoonotic Diseases, Centers for Disease Control and Department of Pathology, Montefiore Medical Center and Prevention, Atlanta, Georgia Albert Einstein College of Medicine, Bronx, New York Alexandra Valsamakis Yi-Wei Tang Roche Molecular Systems, Pleasanton, California, and Department of Laboratory Medicine, Memorial Sloan Division of Medical Microbiology, Department of Pathology, Kettering Cancer Center, and Department of Pathology The Johns Hopkins Medical Institutions, Baltimore, Maryland and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York Wendy W. J. van de Sande Erasmus MC, Department of Medical Microbiology and Joanna Tannous Infectious Diseases, Rotterdam, The Netherlands University of Wisconsin-Madison, Medical Microbiology and Immunology, Madison, Wisconsin Peter A. R. Vandamme Laboratorium voor Microbiologie, Faculteit Wetenschappen, Cheryl L. Tarr Universiteit Gent, Ghent, Belgium Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Mario Vaneechoutte Control and Prevention, Atlanta, Georgia Laboratory Bacteriology Research, Department of Microbiology, Immunology and Clinical Chemistry, Faculty of Medicine and Lúcia Martins Teixeira Health Sciences, Ghent University, Ghent, Belgium Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil Alida C. M. Veloo Department of Medical Microbiology and Infection Sam R. Telford III Prevention, University of Groningen, University Medical Cummings School of Veterinary Medicine, Tufts University, Center Groningen, Groningen, The Netherlands North Grafton, Massachusetts James Versalovic Kate E. Templeton Departments of Pathology & Immunology and Molecular Royal Infirmary of Edinburgh, Specialist Virology Centre, Virology & Microbiology, Baylor College of Medicine, Dept. Laboratory Medicine, Edinburgh, Lothian EH16 4SA, and Department of Pathology, Texas Children’s Hospital, United Kingdom Houston, Texas

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Raquel Vilela Louis M. Weiss Universidade Federal do Minas Gerais, Faculdade de Farmacia, Albert Einstein College of Medicine, Pathology, Bronx, Campus Pampulha, Belo Horizonte, Minas Gerais CEP: New York 31.270.901, Brazil Peter F. Weller Govinda S. Visvesvara Harvard Medical School and Division of Infectious Diseases Centers for Disease Control and Prevention, Atlanta, Georgia and Allergy and Inflammation Division, Beth Israel Deaconess (Retired) Medical Center, Boston, Massachusetts

Ulrich Vogel Nele Wellinghausen Institute of Hygiene and Microbiology, University of Wuerzburg, Medical Laboratory Ravensburg, Infection Serology, Wuerzburg, Germany Ravensburg, Germany

Christof von Eiff Nancy L. Wengenack University Hospital Münster, Institute of Medical Microbiology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Münster, Germany, and Pfizer Pharma GmbH, Berlin, Germany Minnesota

Ken B. Waites Michael L. Wilson Department of Pathology, Diagnostic Mycoplasma Laboratory, Department of Pathology and Laboratory Services, Denver University of Alabama at Birmingham, Birmingham, Alabama Health Medical Center, Denver, and Department of Pathology, University of Colorado School of Medicine, David H. Walker Aurora, Colorado Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Frank G. Witebsky Galveston, Texas Microbiology Service, Department of Laboratory Medicine, Warren G. Magnuson Clinical Center, National Institutes of Richard J. Wallace, Jr. Health, Bethesda, Maryland (Retired) The University of Texas Health Science Center at Tyler, Department of Microbiology, Tyler, Texas Gail L. Woods University of Arkansas for Medical Sciences and David W. Warnock Arkansas Children’s Hospital, Pathology, Little Rock, Atlanta, Georgia Arkansas

David M. Warshauer Lihua Xiao Communicable Disease Division, Wisconsin State Laboratory College of Veterinary Medicine, South China Agricultural of Hygiene, Madison, Wisconsin University, Guangzhou, China

Rainer Weber Pamela A. Yager Division of Infectious Diseases and Hospital Epidemiology, Poxvirus and Rabies Branch, Division of High Consequence University Hospital Zurich, University of Zurich, Zurich, Pathogens and Pathologies, Centers for Disease Control and Switzerland Prevention, Atlanta, Georgia

Melvin P. Weinstein Reinhard Zbinden Departments of Medicine and Pathology & Laboratory Institute of Medical Microbiology, University of Zurich, Medicine, Rutgers Robert Wood Johnson Medical School, Zurich, Switzerland New Brunswick, New Jersey Sean X. Zhang Andrej Weintraub Division of Medical Microbiology, Department of Pathology, Karolinska Institutet, Department of Laboratory Medicine, The Johns Hopkins Hospital, The Johns Hopkins School of Division of Clinical Microbiology, Stockholm, Sweden Medicine, Baltimore, Maryland

Acknowledgment of Previous Contributors The Manual of Clinical Microbiology is by its nature a continuously revised work which refines and extends the contributions of previous editions. Since its first edition in 1970, many eminent scientists have contributed to this important reference work. The American Society for Microbiology and ASM Press gratefully acknowledge the contributions of all of these generous authors over the life of this Manual.

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MCM12_FM.indd 24 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM Preface

The Manual of Clinical Microbiology (MCM) is the most second- and third-generation next-generation sequenc- authoritative reference text in the field of clinical mi- ing, and other molecular methods) that are profoundly crobiology. This edition of the Manual benefited from influencing our approaches to organism detection and the talents of a team of 22 editors and over 300 authors identification. TheManual continues to include classic who were supported by a very capable production team microbiological techniques such as microscopy and cul- at ASM Press. This, the 12th edition, is presented after ture as a foundation in addition to the newer methods the usual 4-year publication cycle following the 11th edi- cited above. Some organisms have become prominent tion. All of the editorial team are proud members of the causes of disease recently, e.g., Ebola virus, Zika virus, American Society for Microbiology and strong support- enterovirus D-68, Gram-negative bacteria that produce ers of its book publishing arm, ASM Press. We have fol- carbapenemases, and multi-drug-resistant fungi such as lowed in the footsteps of previous authors and editors Candida auris and Lomentospora prolificans. Every effort of the Manual and remain steadfastly committed to the was made to include up-to-date information on these utmost quality and timeliness that the MCM readership recently emergent organisms in the Manual. Likewise, has come to expect. It is now clear that the strategy of advances in molecular taxonomy have resulted in ma- employing two co-editors in chief of MCM is a good jor changes in genus and species designations among one. The length and scope of the Manual now require bacteria, fungi, and protozoan parasites, all of which this division of labor to ensure thoroughness and timeli- are reflected in this edition. In addition, the continuing ness of the editing process. We hope that readers of the studies of the human microbiome have informed our un- Manual will recognize the commitment to excellence by derstanding of normal microbial communities and have everyone associated with its production. posed the possibility of polymicrobial rather than single- We represent the sixth and seventh editors in chief in agent infections. the 50-year history of the Manual. We are grateful for the In conclusion, we are profoundly grateful for the privi- example set by our predecessors and for the sage advice lege of guiding the Manual through the publication of offered by recent editors in chief Patrick Murray, James this 12th edition. We hope that the efforts of the MCM Versalovic, and James Jorgensen. We offer our deep ap- editors and authors will continue to prove useful to the preciation to Ellie Tupper, Senior Production Editor at clinical microbiology community. ASM Press, who provided calm competence in driving the editorial production process. Karen C. Carroll This is a very dynamic era in clinical microbiology, Michael A. Pfaller with new technical tools (MALDI-TOF MS, Sanger and

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MCM12_FM.indd 26 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM Author and Editor Conflicts of Interest

April N. Abbott (coauthor on chapter 79) has participated in Maiken Cavling-Arendrup (coauthor on chapter 134) has re- research studies supported by BioFire, Cepheid, ELITech, and ceived research grants/contract work (paid to Statens Serum Luminex. Institut) from Amplyx, Basilea, Cidara, F2G, Gilead, Pfizer, and T2Candida, and speaker honoraria from Astellas, Basilea, Patricia A. Bradford (coauthor on chapter 71) is a consultant Gilead, MSD, Novartis, Pfizer, and T2Candida. Dr. Cavling- for Adenium, Allecra, Antabio, Avego, Aviragen, Bay City, Arendrup is Chair(wo)man for EUCAST-AFST and has served Colgate-Palmolive, Contrafect, Cosmo, Emergent, Entasis, on past advisory boards for MSD, Pcovery, and Pfizer. Everest, Genentech, IHMA, Pontifax, Roche, Syndegen, Tet- raphase, Theravance, TPG, Wellcome, Zavante, and Zolex. Bryan R. Cobb (coauthor on chapter 94) is an employee of Roche Diagnostics. Gerald A. Capraro (coauthor on chapter 82) has received speaking honoraria from Quidel Diagnostics and is an Advisory Daniel J. Diekema (coauthor on chapter 9) has received re- Board member for Roche and for DiaSorin Molecular. search funding from bioMérieux, Inc.

Karen C. Carroll (coauthor on chapters 1, 5, and 50; Editor Christopher D. Doern (coauthor on chapter 6) is on a scien- in Chief) has received research funds from Curetis, Inc., Gen- tific advisory board for ThermoFisher. Mark, Inc., and GenePOC, Inc. These funds are paid to Johns Hopkins University School of Medicine. Dr. Carroll also re- Ferric C. Fang (coauthor on chapter 79) has participated in ceives travel reimbursement from ASM and IDSA. research studies supported by BioFire, Cepheid, ELITech, and Luminex. Mariana Castanheira (coauthor on chapter 71) holds finan- cial interests or benefits in JMI Laboratories and was con- Christine C. Ginocchio (coauthor on chapter 82) is an em- tracted to perform services in 2016 for Achaogen, Actelion, ployee of bioMérieux/BioFire Diagnostics. Allecra Therapeutics, Allergan, AmpliPhi Biosciences, API, Astellas Pharma, AstraZeneca, Basilea Pharmaceutica, Bayer Walid Heneine (coauthor on chapter 85) has patents for AG, BD, Biomodels, Cardeas Pharma Corp., CEM-102 HTLV-3 and HTLV-4 described in the chapter. Pharma, Cempra, Cidara Therapeutics, Inc., CorMedix, CSA Biotech, Cutanea Life Sciences, Inc., Debiopharm Group, Romney M. Humphries (coauthor on chapters 39, 75, and 76) Dipexium Pharmaceuticals, Inc., Duke University, Entasis is the Chief Scientific Officer at Accelerate Diagnostics and a Therapeutics, Inc., Fortress Biotech, Fox Chase Chemical Di- member of the CLSI Subcommittee on Antimicrobial Suscep- versity Center, Inc., Geom Therapeutics, Inc., GSK Laboratory tibility Testing. Specialists, Inc., Medpace, Melinta Therapeutics, Inc., Merck & Co., Inc., Micromyx, MicuRx Pharmaceuticals, Inc., Motif Amy L. Leber (coauthor on chapter 143) is on the Advisory Bio, N8 Medical, Inc., Nabriva Therapeutics, Inc., Nexcida Board at BioFire Diagnostics. Therapeutics, Inc., Novartis, Paratek Pharmaceuticals, Inc., Pfizer, Polyphor, Rempex, Scynexis, Shionogi, Spero Thera- James S. Lewis, II (chapter 70), is a consultant to Accelerate peutics, Symbal Therapeutics, Synlogic, TenNor Therapeutics, Diagnostics, Achaogen, Medicines Company, Merck, Paratek, TGV Therapeutics, The Medicines Company, Theravance and Tetraphase. Biopharma, ThermoFisher Scientific, VenatoRx Pharmaceuti- cals, Inc., Wockhardt, and Zavante Therapeutics, Inc.

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MCM12_FM.indd 27 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM xxviii n Author and Editor Conflicts of Interest

Iona Munjal (coauthor on chapter 10) is the Associate Di- Justin D. Radolf (coauthor on chapter 62) receives royalties rector of Pfizer Vaccine Clinical Research & Development. for syphilis serodiagnostic recombinant proteins from Biokit, Dr. Munjal holds an appointment as an Assistant Professor in SA, through a licensing agreement with UT Southwestern the Department of Pediatrics at Montefiore Medical Center/ Medical Center, and from Span Diagnostics through a licens- Albert Einstein College of Medicine. ing agreement with the University of Connecticut.

Susan Novak-Weekley (coauthor on chapter 143) is an em- Winnie Ridderberg (coauthor on chapter 35) is employed ployee of Qvella and consultant to GenMark, Asolva, and Co- by Qiagen. pan Diagnostics. Julius Schachter (coauthor on chapter 65) receives research Robin Patel (coauthor on chapters 5 and 50; Volume Editor) funding from Abbott, Becton Dickinson, and Roche. reports grants from Accelerate Diagnostics, Allergan, BioFire, CD Diagnostics, Curetis, Hutchison Biofilm Medical Solutions, Arlene C. Seña (coauthor on chapter 62) receives grant fund- The Medicines Company, and Merck. Dr. Patel is or has been ing from Gilead Sciences and royalties from UpToDate, Inc. a consultant to Beckman Coulter, CORMATRIX, Curetis, Di- axonit, Genentech, GenMark Diagnostics, Heraeus Medical Robert W. Shafer (coauthor on chapter 114) has received GmbH, LBT Innovations Ltd., Morgan Stanley, PathoQuest, research support from Bristol Myers Squibb, Gilead Sciences, Qvella, Selux Dx, St. Jude, and Specific Technologies; monies Janssen Pharmaceuticals, and Merck Pharmaceuticalss within are paid to Mayo Clinic. In addition, Dr. Patel has a patent the past three years. on Bordetella pertussis/parapertussis PCR issued; a patent on a device/method for sonication, with royalties paid by Samsung Patricia J. Simner (coauthor on chapter 75) is an Advisor for the to Mayo Clinic; and a patent on an anti-biofilm substance CLSI Subcommittee on Antimicrobial Susceptibility Testing. issued. Dr. Patel has served on an Actelion data monitoring board. Dr. Patel receives travel reimbursement from ASM and Richard C. Summerbell (coauthor on chapter 126) is Research IDSA, an editor’s stipend from ASM and IDSA, and honoraria Director at Sporometrics Inc. from the NBME, UpToDate, Inc., and the Infectious Diseases Board Review Course. William M. Switzer (coauthor on chapter 85) has patents for HTLV-3 and HTLV-4 described in the chapter. David S. Perlin (chapter 133) serves on scientific advisory boards and has received grant support from Amplyx, Astellas, Alexandra Valsamakis (coauthor on chapter 94) has been a Cidara, Scynexis, Matinas, and Merck. Dr. Perlin holds a U.S. consultant for and has had studies funded by Roche Diagnostics. patent for the detection of echinocandin resistance.

Michael A. Pfaller (coauthor on chapters 1 and 9; Editor in Chief) has been an employee of T2 diagnostics and is currently a consultant for JMI Laboratories in North Liberty, Iowa.

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MCM12_FM.indd 28 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM Author Index

Volume 1 comprises pages 1–1431; volume 2 comprises pages 1432–2690.

Abbott, April N., 1420 Carroll, Karen C., 3, 45, 893 Forsythe, Stephen J., 724 Aberle, Stephan W., 1757 Carvalho, Maria da Glória Siqueira, 418 Frank, Karen M., 724 Adl, Sina M., 2379 Castanheira, Mariana, 1242 Frosch, Matthias, 640 Aguero-Rosenfeld, Maria E., 1066 Caulfield, Adam J., 595 Ahmed, Sarah Abdallah, 2261 Cavling-Arendrup, Maiken, 2351 Alanio, Alexandre, 2163 Charnot-Katsikas, Angella, 724 Gadsby, Naomi J., 1606 Alby, Kevin, 724 Chen, Sharon C.-A., 2103 Galloway, Renee L., 1058 Alexander, David C., 455 Chernesky, Max, 1137 Ganesh, Bhanu P., 254 Ali, Ibne M. Karim, 2486 Chiang, Cheng-Feng, 1706 Garcia, Hector H., 2582 Araj, George F., 883 Chou, Sunwen, 1962 Garcia, Lynne S., 2389, 2414 Arduino, Matthew J., 224 Christensen, Jens Jørgen, 362, 436 Garcia-Hermoso, Dea, 2163 Ashbee, H. Ruth, 2035 Ciofu, Oana, 787 Gärtner, Barbara C., 1797 Atlas, Ronald M., 331 Clain, Jérôme, 2669, 2682 Geißdörfer, Walter, 1189 Atmar, Robert L., 1510 Cobb, Bryan R., 1640 Gerner-Smidt, Peter, 167 Coenye, Tom, 858 Ginocchio, Christine C., 1462, 1472 Conrads, Georg, 995 Glover, William A., II,775 Babady, N. Esther, 1541 Conville, Patricia S., 525 Gómez Giraldo, Beatriz L., 2187 Baldanti, Fausto, 1797 Cools, Piet, 829 Gonzalez, Mark D., 670 Bankowski, Matthew J., 1985 Cope, Jennifer R., 2486 Greninger, Alexander L., 1740, 1814 Barbut, Frédéric, 968 Couturier, Marc Roger, 1044 Guarro, Josep, 2234 Bard, Jennifer Dien, 1348 Currie, Bart J., 807 Gunthel, Clifford J., 1826 Bébéar, Cécile, 1109, 1117 Cuschieri, Kate, 1847 Becker, Karsten, 367 Cushion, Melanie T., 2087 Berkow, Elizabeth L., 2016, 2319 Halliday, Catriona L., 2103 Bernard, Kathryn A., 451, 488 Hayden, Randall T., 1472, 1831 Biggs, Beverley-Ann, 2551 Dallas, Steven D., 16 Heim, Albert, 1831 Bjarnsholt, Thomas, 787 Damon, Inger K., 1891 Heneine, Walid, 1498 Blanton, Lucas S., 1149 de Hoog, G. Sybren, 2234, 2261 Hickman, Carole J., 1560 Bleeker-Rovers, Chantal, 1180 Dekker, John, 688 Highlander, Sarah K., 254 Bogdan, Christian, 1189 Deplazes, Peter, 2305 Hodinka, Richard L., 1770 Boivin, Guy, 1962 Desmond, Edward P., 576, 1398 Høiby, Niels, 787 Borman, Andrew M., 2056, 2208 Diekema, Daniel J., 139 Holfelder, Martin, 72 Boucher, Yan, 775 Dietrich, Elizabeth A., 871 Horneman, Amy J., 765 Bouyer, Donald H., 1149 Doern, Christopher D., 72 Horvat, Rebecca T., 1905 Bradford, Patricia A., 1242 Dollard, Sheila C., 1826 Huang, Diana D., 1985 Brandt, Claudia, 399 Dromer, Françoise, 2163 Humphries, Romney M., 688, 1316, Brandt, Mary E., 2007 Dumler, J. Stephen, 893, 1109, 1163 1348 Brown, Kevin E., 1880 Dunn, James J., 1446 Hunsperger, Elizabeth A., 1685 Brown-Elliott, Barbara A., 525, 595, 612, 1398 Bruckner, David A., 2458 Edelstein, Paul H., 905 Icenogle, Joseph P., 1560 Buchan, Blake W., 688 Elias, Johannes, 640 Izopet, Jacques, 1625 Buller, Richard S., 1863 Escalante, Hermes, 2582 Butler-Wu, Susan M., 197, 938 Jerome, Keith R., 1740, 1814 Facklam, Richard R., 418 Jimenez, Juan A., 2582 Caliendo, Angela M., 1472 Fang, Ferric C., 1420 Johnson, Crystal N., 925 Cama, Vitaliano, 2536 Farmer, John J., III,775 Johnson, Elizabeth M., 2056, 2351 Capraro, Gerald A., 1462 Faron, Matthew L., 688 Jones, Malcolm K., 2590 Carpenter, Darcie E., 1377 Forman, Michael S., 1640 Jorgensen, James H., 1277

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MCM12_FM.indd 29 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM xxx ■ Author Index Kamar, Nassim, 1625 Nørskov-Lauritsen, Niels, 630 Snyder, James W., 243, 331 Kämpfer, Peter, 829 Novak-Weekley, Susan, 2497 Sorrell, Tania C., 2103 Karlowsky, James A., 1300 Nutman, Thomas B., 2570 Spellerberg, Barbara, 399 Keiser, Jennifer, 2590 Spinler, Jennifer K., 269 Keller, Nancy P., 2278 Stanek, Gerold, 1066 Kersh, Gilbert J., 1180 O’Donnell, Kerry, 2132 Stellrecht, Kathleen A., 1576 Kilgore, Paul E., 858 Olson, Victoria A., 1891 Storch, Gregory A., 1863 Kingry, Luke C., 751 Orciari, Lillian A., 1674 Summerbell, Richard C., 2208 Klena, John D., 1706 Ortholary, Olivier, 2163 Sutton, Deanna A., 2132 Koeth, Laura M., 1284 Ostrowsky, Belinda, 155 Switzer, William M., 1498 Könönen, Eija, 995 Owen, S. Michele, 1477, 1498 Szymczak, Wendy A., 155 Ksiazek, Thomas G., 1719 Kuijper, Ed, 968 Paltridge, Graeme P., 2414 Tang, Yi-Wei, 1472, 1541, 1719, 1905 Pang, Xiaoli, 1656 Tannous, Joanna, 2278 Labarca, Jaime, 2458 Parrish, Nicole, 558 Tarr, Cheryl L., 751, 775 Lagacé-Wiens, Philippe, 206 Patel, Robin, 45, 893 Teixeira, Lúcia Martins, 418 Lamson, Daryl M., 1576 Peacock, Sharon J., 807 Telford, Sam R., III,2620 Lamy, Brigitte, 765 Pentella, Michael, 206 Templeton, Kate E., 1606 Landry, Marie Louise, 1472, 1592, 1905 Perlin, David S., 2334 Theel, Elitza S., 124 Lawson, Paul A., 287 Petersen, Jeannine M., 751, 871 Thompson, George R., III,2187 Le Bras, Jacques, 2669, 2682 Petrosino, Joseph F., 254 Towner, Jonathan S., 1719 Leber, Amy L., 2497 Pfaller, Michael A., 3, 139 Trees, Eija, 167 Ledeboer, Nathan A., 670, 688 Pillay, Allan, 1083 Turenne, Christine Y., 455 Leder, Karin, 2645 Pinsky, Benjamin A., 1446, 1985 Turnidge, John D., 1277 Lefkowitz, Elliot J., 1435 Pitout, Johann, 724 Tyrrell, Kerin, 287 Leland, Diane S., 1528 Pritt, Bobbi S., 1163, 2438 Levett, Paul N., 1058 Procop, Gary W., 2606 Lewis, James S., II,1201 Puchhammer-Stöckl, Elisabeth, 1757 Unger, Elizabeth R., 1847 Lin, Shou-Yean Grace, 576, 1398 Lindsay, David S., 2526 Lindsley, Mark D., 2025 Radolf, Justin D., 1083 Valsamakis, Alexandra, 1640 Linscott, Andrea J., 2406 Rai, M. Ali, 2087 van de Sande, Wendy W. J., 2261 LiPuma, John J., 807 Relich, Ryan F., 1528 Vandamme, Peter A. R., 807 Lockhart, Shawn R., 2319 Reller, L. Barth, 28 Vaneechoutte, Mario, 829 Loeffelholz, Michael, 5, 243 Rhoads, Daniel D., 1923 Veloo, Alida C. M., 925 Lu, Xiaoyan, 1592 Richter, Elvira, 595 Versalovic, James, 254, 269 Lurain, Nell S., 1937 Richter, Sandra S., 1300 Vilela, Raquel, 2291 Ridderberg, Winnie, 630 Visvesvara, Govinda S., 2486 Rollin, Pierre E., 1719 Vogel, Ulrich, 640 MacCannell, Duncan, 167 Romero, José R., 1576 von Eiff, Christof, 367 Madrid, Hugo, 2234 Rota, Paul A., 167 Mahlen, Steven D., 243 Ruoff, Kathryn L., 362, 436 Martin, Isabella, 558 Ryan, Norbert, 2551 Waites, Ken B., 1117 Mathis, Alexander, 2305 Walker, David H., 1149 Mathison, Blaine, 2379, 2620 Wallace, Richard J., Jr.,595, 612 McAuley, James B., 2473 Safar, Jiri G., 1923 Warnock, David W., 2007 McDonnell, Gerald, 224 Salfinger, Max, 576 Warshauer, David M., 576 McElvania, Erin, 302 Samuel, Linoj, 5 Weber, Rainer, 2305 McGowan, Karin L., 2016 Santos, Carlos A. Q., 1937 Weinstein, Melvin P., 28 McGuinness, Sarah L., 2645 Satheshkumar, P. S., 1674, 1891 Weintraub, Andrej, 921 McManus, Donald P., 2590 Schachter, Julius, 1137 Weiss, Louis M., 2526 Mendoza, Leonel, 2291 Schuetz, Audrey N., 1377 Weller, Peter F., 2645 Meyer, Wieland, 2103 Secor, W. Evan, 2669, 2682 Wellinghausen, Nele, 477 Miller, Linda A., 1284 Sedlak, Ruth Hall, 1814 Wengenack, Nancy L., 595 Morrow, Rhoda Ashley, 1740 Seña, Arlene C., 1083 Wilson, Michael L., 28 Moter, Annette, 1189 Sendi, Parham, 399 Witebsky, Frank G., 525 Munjal, Iona, 155 Shafer, Robert W., 1962 Woods, Gail L., 1398 Sharp, Susan E., 5, 243, 2406 She, Rosemary C., 197, 938 Nachamkin, Irving, 1024, 1028 Sheorey, Harsha, 2551 Xiao, Lihua, 2536 Nagy, Elisabeth, 995 Shewmaker, Patricia Lynn, 418 Neafie, Ronald C., 2606 Shieh, Wun-Ju, 1706 Nemec, Alexandr, 829 Shimizu, Robyn Y., 2389, 2414 Yager, Pamela A., 1674 Ng, Terry Fei Fan, 167 Simner, Patricia, 1316 Nielsen, Xiaohui Chen, 362, 436 Singh, Kamaljit, 302, 2473 Nolte, Frederick S., 86 Skov, Robert L., 367 Zbinden, Reinhard, 656 Norice-Tra, Carmelle T., 2570 Smieja, Marek, 1656 Zhang, Sean X., 2132

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MCM12_FM.indd 27 On: Thu, 18 Apr 2019 08:17:55 12/19/18 3:30 AM xxviii n Author and Editor Conflicts of Interest

Michael A. Pfaller (coauthor on chapters 1 and 9; Editor in Chief) has been an employee of T2 diagnostics and is currently a consultant for JMI Laboratories in North Liberty, Iowa.

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MCM12_FM.indd 28 On: Thu, 18 Apr 2019 08:17:55 12/19/18 3:30 AM Subject Index

Volume 1 comprises pages 1–1431; volume 2 comprises pages 1432–2690.

16S rRNA Acari, summary of, 2621 Acinetobacter baumannii, clinical significance, Clostridium identification, 976 Acarines, arthropods as vectors, 2626–2628 829 gene sequencing in genus Enterococcus, Accelerate Pheno System, 1307–1308 Acquired resistance 418, 419 Accreditation, 5–7 by DNA transfer, 1244 categorization of test complexity and Pseudomonas, 796–797 regulatory requirements, 5–6 Acremonium spp. A7 agar, 341 CLIA Certificates, 6 clinical significance, 2151 A8 agar, 341 Acetamide agar, 341 hyphomycetes, 2147 AABB (American Association of Blood Acetamide hydrolysis test (Nessler reagent), morphology by direct examination, 2039 Banks), 6 331 Acridine orange stain, 337 Abacavir Acetate ascospore agar, mycology, 2029 Acrophialophora drug interactions, 1940 Acetate differential agar, 341–342 clinical significance, 2152 HIV therapy, 1938 Achaetomium genus, 2245 hyphomycetes, 2149 mechanism of resistance, 1965 Achromobacter genus Actinomucor genus pharmacology, 1940 antimicrobial susceptibilities, 865 branched sporangiophores, 2173 Abbe, Ernst, 16 clinical significance, 861 identification, 2171–2172 Abiotrophia genus collection, transport, and storage of Actinobacillus spp. antimicrobial susceptibilities, 444–445 specimens, 862 antimicrobial susceptibility, 665 cellular morphology, 437 description of, 859 biochemical reactions of, 662 clinical significance, 438 epidemiology and transmission, 860–861 clinical significance, 658 description of, 437 identification, 863–864 direct examination, 659 epidemiology and transmission, 438 isolation procedures, 863 isolation procedures, 661 evaluation, interpretation, and reporting neighbor-joining dendrograms of, 636 serologic tests, 665 of results, 445 taxonomy, 858 taxonomy, 656 identification, 440 Acid-fast stains, 337 Actinobacteria, class, 289 molecular methods for identification, parasitology, 2409–2410 predominant phyla in humans, 256 443–444 stool specimens, 2418 taxonomy and description, 938–939 phenotypic differentiation, 440–441 Acid-fast trichrome stain, 2411, 2413 Actinobacteria, phylum susceptibility testing, 1360 Acidovorax, 808 Actinobacteria class, 938–939 taxonomy, 436 antimicrobial susceptibility, 820 biochemical characteristics of, 953 testing conditions, 1351 characteristics of, 818 clinical significance, 941–946 See also Catalase-negative, Gram-positive clinical significance, 811 Coriobacteriia class, 939–940 cocci description of, 808 taxonomy and description, 938–940 Abscess specimens identification, 818–819 Actinobaculum spp. collection and transport, 2017 Acid production, term, 631 biochemical characteristics, 951 pretreatment, 2020 Acinetobacter spp. clinical significance, 944 processing and culture guidelines, antimicrobial susceptibilities, 836, 848 Actinomadura genus, 1413 2018–2019 characteristics of, 830 classification, 526 Abyssicoccus genus, 368 clinical significance, 829, 831 clinical significance, 534 epidemiology and transmission, 377 colonies, 835 colonial morphology, 530 Acanthamoeba genus epidemiology and transmission, 829 description, 527 classification, 2383 evaluation, interpretation and reporting of epidemiology and transmission, 533 description of, 2486–2487 results, 848 microscopic morphology, 532 detection in humans, 2381 genotyping and epidemiology, 836 morphologic characteristics, 528 encephalitis, 2490 identification of, 831–832, 834–836 recovered from human specimens, 535 epidemiology, 2488 MALDI-TOF mass spectrometry, 833, 835 See also Actinomycetes keratitis, 2490 species diversity, 834–836 Actinomyces odontolyticus, 1194 taxonomy, 2486 taxonomy, 829 Actinomyces spp. See also Free-living amebae tetracycline specific resistance determi- antimicrobial susceptibilities, 955 Acanthocephala, classification, 2384 nant in, 1256 biochemical characteristics, 951

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Actinomyces spp. (continued) identification, 1839 Aeromonas genus clinical significance, 941, 943–944 isolation procedures, 1838–1839 antimicrobial susceptibilities, 770, 772 detection of, 323 microscopy, 1836 biochemical identification of, 770 resistance patterns of, 1387 model of adenovirus particle, 1832 clinical significance, 767–768 Actinomycetaceae family nucleic acid detection, 1837–1838 description of, 765 description, 493 properties of human serotypes, 1832 direct examination, 768 identification, 513–514 serologic tests, 1840–1841 epidemiology and transmission, 765–767 Actinomycetes, 525 taxonomy, 1831 evaluation, interpretation and reporting of aerial hyphae, 544 term, 1831 results, 770 antimicrobial susceptibilities, 548–549 treatment and prevention, 1840–1841 extraintestinal infections, 767–768 classification of genera, 526 typing systems, 1839–1840 gastroenteritis, 767 clinical significance, 533–541 ultrastructure of adenovirus particles, identification, 768–769 collection, transport and storage of speci- 1833 identification at genus level, 768–769 mens, 541–542 See also Enteric adenoviruses identification at species level, 769 colonial morphology, 544 Adiaspiromycosis, 2192, 2193, 2196, 2200, isolation procedures, 768 colony morphology of various, 530 2202 members of, 766 description of genera, 527–533 Advenella properties of genus, 776 direct examination, 542–543 antimicrobial susceptibilities, 865 serologic tests, 769 epidemiology and transmission, 533 clinical significance, 861 specimen collection, transport and storage, evaluation, interpretation and reporting of collection, transport, and storage of 768 results, 549–550 specimens, 862 susceptibility testing, 1361 genus assignment, 544 description of, 859–860 taxonomy, 765 identification, 543–547 epidemiology and transmission, 860–861 testing conditions, 1351 isolation procedures, 543 identification, 864 tests for separation of members, 771 microscopic morphology, 543–544 isolation procedures, 863 typing systems, 769 microscopic morphology of various, 532 taxonomy, 858 Aflatoxins microscopy, 542–543 Advisory Committee on Immunization classification and biosynthesis of, molecular identification, 544–547 Practices (ACIP), 470, 641 2278–2279, 2281 morphologic characteristics of genera, Aerobic actinomycetes, 1413 common food substrates, 2282 528–529 Aerobic bacteria, MALDI-TOF MS identifi- genetic structure, 2280 nucleic acid detection, 543 cation of, 57–59 pathological effects and toxicological refer- proteomics, 547 Aerobic Gram-negative bacteria, 630–631 ence values, 2283 serologic tests, 548 16S rRNA gene-based identification, 635 structure of, 2279 species assignment, 544 16S rRNA gene repositories, 635 See also Mycotoxins taxonomy, 525, 527 algorithm for initial identification of, 632 African histoplasmosis, 2192 typing systems, 547–548 bacterial identification using rRNA gene African trypanosomiasis Actinotignum spp. sequences, 634–636 mechanisms of resistance, 2674–2675 biochemical characteristics, 951 definition of, 630–631 proposed mechanisms of resistance for drugs clinical significance, 944 development of new discriminative PCRs, against, 2670 Actinotignum schaalii, resistance patterns of, 637–638 selected antiparasitic agents and suscepti- 1387–1388 facultative anaerobic Gram-negative bility testing method, 2683 Acute retroviral syndrome, 1479–1480 bacteria, 633 susceptibility test methods, 2686 Acyclovir Gram-negative nonfermenters, 633 Agar dilution against herpes B virus, 1750 identification and phylogenetic inference of advantages and disadvantages, 1291 against herpesviruses, 1952 bacterial species, 634–635 incubation, 1291 antiviral therapy for herpes simplex virus identification and typing, 636–637 incubation conditions, 1379 (HSV), 1742 limitations, 635 inoculation procedure, 1291, 1379 drug interactions, 1953 matrix-assisted laser desorption ioniza- inoculum preparation, 1378 Epstein-Barr virus (EBV), 1798 tion–time of flight mass spectrometry, interpretation and reporting of results, herpes viruses, 1962–1964 633–634 1291, 1380 mechanism of resistance, 1963 neighbor-joining dendrograms of medium, 1378 pharmacology, 1953 Achromobacter strains, 636 method, 1290–1291 spectrum of activity, 1953 phenotypic test methods and identification, preparation, supplementation and storage varicella-zoster virus, 1765 631, 633 of media, 1290–1291 Adaptive resistance, Pseudomonas, 797–798 taxonomic resolution at species level, quality control, 1379–1380 Adefovir, mechanism of resistance, 1969, 1970 635–636 susceptibility testing, 1378–1380 Adefovir dipivoxil whole-genome sequences, 636–637 See also Dilution testing drug interactions, 1951 Aerobic Gram-positive cocci Agar proportion method HBV therapy, 1950 general approaches to identification, drug susceptibility test (DST), 1405–1406 pharmacology, 1950–1951 362–365 inoculum and incubation, 1405 Adenoviruses See also Gram-positive cocci media, 1405 antigen detection, 1836–1837 Aerococcus genus quality control, 1406 clinical significance, 1834–1835 cellular morphology, 437 reading and interpreting results, 1405–1406 collection, transport and storage of speci- clinical significance, 438 Agar slide culture plate, mycology, 2029 mens, 1835–1836 epidemiology and transmission, 438 Agents against Gram-positive bacteria commercial PCR assays for detecting infec- identification, 441 daptomycin resistance, 1260–1261 tion, 1837 molecular methods for identification, fusidic acid resistance, 1264 description of agent, 1832 443–444 glycopeptide resistance, 1261–1262 detection and identification methods, 1473 phenotypic differentiation, 441 linezolid resistance, 1263 direct detection, 1836–1838 susceptibility testing, 1360–1361 lipoglycopeptide resistance, 1262–1263 diseases, hosts and specimens, 1834 taxonomy, 436–437 macrolide and ketolide resistance, epidemiology and transmission, 1832–1834 testing conditions, 1351 1263–1264 evaluation, interpretation and reporting of See also Catalase-negative, Gram-positive mupirocin resistance, 1264 results, 1841–1842 cocci quinupristin-dalfopristin resistance, 1264

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Aggregatibacter spp. commercial diagnostic tests, 1692 Amithiozone, 1401 antimicrobial susceptibility, 665 genome, 1688 Amniotic fluid biochemical reactions of, 662 Alternaria genus, 2244, 2245, 2247, 2248 collection and processing of virus speci- clinical significance, 658 Alveolar echinococcoci, commercially avail- mens, 1453 direct examination, 659 able kits for diagnosis, 2392 parasite detection, 2401 epidemiology and transmission, 657 Alveolar hydatid disease, Echinococcus multi- specimen preparation and procedures, 2396 isolation procedures, 661 locularis, 2588 Amoebozoa supergroup taxonomy, 656 Amantadine, against influenza virus, 1954, eukaryotes, 2380–2382 Agilent MassCode (Agilent Technologies), 1955 parasitic protists, 2383 180 Amebae Amoxicillin, 1201, 1202, 1229 Agricultural Select Agent Program, 245 collection, transport and storage of speci- Amphotericin B Agromyces genus, description, 492 mens, 2498 acquired resistance, 2325–2326 AIDS (acquired immunodeficiency syn- description of agents, 2497 clinical breakpoints for Candida spp., 2352 drome), 1477 direct examination, 2498 clinical use, 2326 disease progression to, 1480–1481 Entamoeba histolytica, 2498–2504 drug interactions, 2326 prognosis, 110 epidemiology, transmission and prevention, mechanism of resistance, 2670 AIDS patients 2497 pharmacokinetics, 2326 cytomegalovirus (CMV) infection, 1770, evaluation, interpretation and reporting of spectrum of activity, 2320, 2325 1772, 1787 results, 2498 susceptibility testing, 2359 Epstein-Barr virus (EBV)-related lympho- microscopy, 2498 therapeutic drug monitoring, 2326 mas, 1800 nonpathogenic, 2504–2507 toxicity and adverse effects, 2326 human adenovirus (HAdV), 1833–1834 sensitivity and specificity of diagnostic tests Ampicillin, 1202, 1229 Kaposi’s sarcoma in, 1826–1827 for, 2502 Bacteroides spp., 1384 l-Alanine-7-amido-4-methylcoumarin taxonomy, 2497 Cutibacterium spp., 1388 (Gram-Sure), 331 See also Entamoeba histolytica Ampicillin-sulbactam, activity against Albaconazole, 2328 Amebiasis, commercially available kits for Clostridium spp., 987 Albendazole, 2645, 2647 diagnosis, 2392 Amplification Alcaligenes Amenamevir, against herpesviruses, 1954 nucleic acid sequence-based (NASBA), antimicrobial susceptibilities, 865 American Association for Laboratory 96, 97 clinical significance, 861 Accreditation (A2LA), 6 See also Target amplification techniques collection, transport, and storage of American Association for the Study of Liver Amplification techniques, signal, 87–89 specimens, 862 Disease, 1993 branched-DNA (bDNA) assays, 87–88 description of, 859 American Biological Safety Association, 226 cleavage-invader technology, 88–89, 90 epidemiology and transmission, 860–861 American Board of Bioanalysis, 116 hybrid capture assays, 88, 89 identification, 864 American Board of Clinical Chemistry, 116 Amplified fragment length polymorphisms isolation procedures, 863 American Committee on Immunization (AFLP), 295 taxonomy, 858 Practices (ACIP), 213, 1512 Amycolata genus, microscopic morphology, Alcian blue stain American Osteopathic Association (AOA), 6 532 fungi detection, 2036 American Society for Clinical Pathology Amycolatopsis genus mycology, 2027 (ASCP), 74, 116 classification, 526 Aliicoccus genus, 368 American Society for Histocompatibility and clinical significance, 534 epidemiology and transmission, 377 Immunogenetics (ASHI), 6 colonial morphology, 530 Alishewanella fetalis American Society for Testing and Materials description, 527 characteristics of, 840 (ASTM), 226 morphologic characteristics, 528 identification, 839 American Society of Microbiology (ASM), 9, recovered from human specimens, 535 Alistipes genus, 995, 996 302, 419, 755 See also Actinomycetes characteristics of, 997 American Thoracic Society, 597, 1410, 1411 Anaerobes, infections, 921 clinical importance, 1000 American Trudeau Society medium, 342 Anaerobic bacteria common in human infection, 999 American Type Culture Collection (ATCC), Actinomyces spp., 1387 identification, 1005 199, 1420 Actinotignum schaalii, 1387–1388 phenotypic characteristics of, 1008 Amies transport media, 342 agar dilution method, 1378–1380 Alkaline peptone salt broth, 342 Aminocyclitols, 1211–1212 antibiograms, 1392 Alkaline peptone water, 342 Aminoglycoside-modifying enzymes (AMEs) antimicrobial agents for testing and report- Alkaline phosphatase, 331 aminoglycoside inactivation by, 1246, 1247 ing, 1391 Allele-specific hybridization, postamplifica- in pathogenic bacteria, 1244 antimicrobial testing guidelines, 1390–1392 tion analysis, 103 Aminoglycosides, 1211–1212, 1400–1401 approaches to identification of, 921–923 Alloiococcus family adverse effects, 1212 Bacteroides spp., 1383–1385 clinical significance, 379 mechanism of action, 1211 Bifidobacterium spp., 1388 description of, 374 pharmacology, 1211–1212 Bilophila wadsworthia, 1385 epidemiology and transmission, 377 Pseudomonas resistance to, 796–797 broth microdilution method, 1379, identification, 386 as resistance target, 1426 1380–1381 taxonomy of, 367 resistance to, 1246–1247 broth microdilution panels, 1382 See also Catalase-positive cocci spectrum of activity, 1212 Campylobacter gracilis, 1385 Alloprevotella genus, phenotypic characteris- 4-Aminoquinolines Clostridium difficile, 1386 tics of, 1010 adverse effects, 2653–2654 Clostridium perfringens, 1386–1387 Allylamines mechanism of action, 2652–2653 commercial test methods, 1381–1383 mechanism of action, 2319 pharmacokinetics, 2653 Cutibacterium spp., 1388–1389 terbinafine, 2319–2320 spectrum of activity, 2653 disk diffusion, 1382–1383 Alphapapillomavirus sp., 1847, 1850 8-Aminoquinolines Eubacterium spp., 1389 nucleotide sequence of L1 gene, 1848 adverse effects, 2656 Fusobacterium spp., 1385 Alphapolyomavirus genus, 1863, 1864 mechanism of action, 2656 gradient diffusion method, 1381–1382 Alphaviruses pharmacokinetics, 2656 Gram-negative bacilli, 1383–1385 characteristics of, 1686 spectrum of activity, 2656 Gram-positive, non-spore-forming bacilli, clinical significance, 1693 p-Aminosalicylic acid (PAS), 1402 1387–1389

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Anaerobic bacteria (continued) Anaplasmataceae family chloramphenicol, 1224–1225 Gram-positive, spore-forming bacilli, antimicrobial susceptibilities, 1173 fosfomycin, 1227–1228 1386–1387 clinical significance, 1168–1169 glycopeptides and lipopeptides, 1218–1220 Gram-positive and Gram-negative cocci, collection, transport, and storage of speci- ketolides, 1214–1215 1389–1390 mens, 1169–1170 b-lactamase inhibitors, 1207–1209 identification methods, 1377 ehrlichiosis, 1169 lincosamides, 1215–1216 indications for susceptibility testing, 1391 evaluation, interpretation, and reporting of macrolides, 1212–1214 b-lactamase testing, 1382 results, 1173–1174 monobactams, 1202, 1206 Lactobacillus spp., 1389 human ehrlichiosis, 1167–1168 mupirocin, 1228 MALDI-TOF MS identification of, 59, human granulocytic anaplasmosis, nitrofurantoin, 1226–1227 922–923 1166–1167, 1168–1169 oxazolidinones, 1221–1222 Porphyromonas spp., 1385 neoehrlichiosis, 1168 penicillins, 1201–1203 Prevotella spp., 1385 neorickettsiosis, 1168, 1169 polymyxins, 1223–1224 reference test methods, 1378–1381 taxonomy, 1163 quinolones, 1209–1211 reportable organisms for MALDI–TOF MS, Ancylistaceae family, 2178–2179 rifamycins, 1225–1226 55, 56 Andes virus (ANDV), 1707, 1708, 1709 streptogramins, 1220–1221 resistance patterns in, 1383–1390 Anidulafungin sulfonamides and trimethoprim, 1222–1223 as resistance target, 1426 clinical breakpoints for Candida spp., 2352 tetracyclines and glycylcyclines, 1216–1218 RIC group (C. ramosum, C. innocuum, and clinical use, 2325 Antibacterial drug resistance. See Detection C. clostridioforme), 1387 echinocandin, 2324–2325 of antibacterial drug resistance surveys and studies of resistance, 1392–1393 spectrum of activity, 2320, 2324 Antibacterial susceptibility testing, common susceptibility testing and quality control, Animal and Plant Health Inspection Service error sources in, 1296 1378–1383 (APHIS), 245 Antibiograms, reporting susceptibility data, susceptibility testing for, 923 Anisakis and related species 1392 Anaerobic colistin nalidixic acid (CNA) clinical significance, 2606 Antibiotic resistance agar, 342 description of agents, 2606 acquired resistance by DNA transfer, 1244 Anaerobiospirillum genus, 998 direct examination and microscopy, 2608 emergence and spread of, 1242–1243 characteristics of, 997 epidemiology, transmission, and preven- genetic basis of, 1243–1244 clinical importance, 1003 tion, 2606 mechanisms of, 1244–1246 identification, 1006 microscopy, 2607 by mutation, 1243 phenotypic characteristics of, 1012 serologic tests, 2608 selection of bacterial pathogens, 1243 Anaerococcus spp. taxonomy, 2606 See also Resistance mechanisms antimicrobial susceptibilities, 933 treatment, 2608 Antibiotic-resistant pathogens, media for biochemical features, 930 Anncaliia spp. detection of, 338 changes in classification, 926 description, 2305–2306 Antibiotic tolerance, biofilm-grown clinical significance, 928 life cycle of microsporidia, 2307 Pseudomonas aeruginosa, 798 flow scheme for identification of, 931 Anogenital warts (AGWs), human papillo- Antibiotics, choice and use for Bartonella spe- taxonomy, 925 mavirus (HPV), 1851 cies, 900–901 Anal cancer, human papillomavirus (HPV) Anthelmintic agents Antifolates and, 1852 benzimidazoles, 2645–2648 adverse effects, 2657 Anamorphic molds diethylcarbamazine, 2651 mechanism of action, 2657 blastic conidiogenesis, 2012 ivermectin, 2649–2651 pharmacokinetics, 2657 classification and identification of, nitazoxanide, 2652 spectrum of activity, 2657 2011–2012 praziquantel, 2648–2649 Antifungal agents form-class Coelomycetes, 2011–2012 pyrantel pamoate, 2651 allylamines, 2319–2320 form-class Hyphomycetes, 2012 See also Antiparasitic agents azoles, 2320–2324 thallic conidiogenesis, 2012 Anthopsis genus, 2240 defining clinical and microbiological resis- See also Molds Anthrax tance, 2334–2335 Anaplasma spp. Bacillus anthracis, 457–458 echinocandins, 2324–2325 antimicrobial susceptibilities, 1173 biothreat agent, 246–247 flucytosine, 2326–2327 clinical significance, 1168–1169 cutaneous, 458, 460, 462 griseofulvin, 2327 collection, transport, and storage of speci- epidemiology and transmission, 456–457 mechanisms of 5FC resistance, 2343 mens, 1169–1170 gastrointestinal, 458, 462 mechanisms of azole resistance, 2336–2340 description of, 1163–1164 inhalational, 458, 462 mechanisms of echinocandin resistance, direct examination, 1170–1171 injectional, 458, 462 2340–2342 epidemiology and transmission, 1164, meningeal, 462 mechanisms of polyene resistance, 1166–1168 Robert Koch’s work on, 457 2342–2343 evaluation, interpretation and reporting of specimens from animals suspected to have, MIC ranges for broth microdilution meth- results, 1173–1174 462 ods for yeasts, 2356–2357 features of human and veterinary interest, specimens from patients suspected to have, microbial drivers of resistance, 2343–2344 1165 460, 461, 462 novel, in development, 2327–2328 immunochemistry for antigen detection, 1171 Anthrax BioThreat Alert, 464 polyenes, 2325–2326 isolation procedures, 1171–1172 Anthrax in Humans and Animals (WHO), 460 resistance to azoles, 2335–2336 laboratory confirmation, 1170–1173 Anthrax Vaccine Adsorbed (AVA), 470 spectrum and extent of activity, 2320 neighbor-joining phylogenetic tree, 1164 Anthrax Vaccine Precipitated (AVP), 470 targets, drug resistance mechanisms and nucleic acid detection of A. phagocytophi- Antianaerobe agents, resistance to, effectors, 2337 lum, 1171 1264–1265 Antifungal susceptibility testing serologic tests, 1172 Antibacterial agents agar-based alternative approaches, treatment and prevention, 1173 aminoglycosides and aminocyclitols, 2362–2363 See also Anaplasmataceae family 1211–1212 alternative approaches for yeasts, Anaplasma phagocytophilum approximate concentrations in serum, 2360–2363 diagnostic tests for, 1112 1228, 1229–1230 amphotericin B, 2359 epidemiology and clinical diseases associ- carbapenems, 1202, 1206–1207 azole agar screening plate, 2353 ated with, 1110 cephalosporins, 1203–1206 basic test principles, 2352–2353

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broth microdilution guidelines for, of yeasts, synthetic quinoline compounds, 2654–2655 pentavalent antimonial compounds, 2355–2357 treating mycobacterial infections, 2658–2659 caspofungin, 2359 1398–1399 suramin, 2660–2661 clinical resistance and clinical breakpoint See also Antiparasitic agents See also Antiparasitic agents setting, 2353–2354 Antimicrobial stewardship Antiretroviral (ARV) drugs CLSI and EuCAST breakpoints for hospital, 144–145 genetic mechanisms of resistance to, 1965 Candida spp., 2359–2360 rapid diagnostic testing, 146 HIV-1 replication cycle showing action of, colorimetric methods, 2361 Antimicrobial susceptibility testing systems, 1966 direct susceptibility testing, 2363 1300–1301, 1316 Antisepsis, 225 flow cytometry, 2361–2362 ability of automated systems to detect Antiviral agents methods for, 2361 resistance, 1304–1307 against hepatitis B virus (HBV), 1950–1951 MIC, 2352 Accelerate Pheno System, 1307–1308 against hepatitis C virus (HCV), minimum fungicidal/lethal concentration, advantages of automated systems, 1304 1946–1950 2352–2353 automated broth microdilution systems, against herpesviruses, 1951, 1953–1954 molecular methods, 2363 1302–1307 against HIV-1 and HIV-2, 1937, 1940–1946 mycology of media, 2029 BD Phoenix, 1303–1304 against influenza viruses, 1954–1955 proteomics and, 2363 computerized expert systems, 1309 for HCV therapy, 1947 rationale, 2351–2352 critical review, 1309 for herpesviruses, 1952 standardized broth dilution methods for disadvantages of automated systems, 1304 for HIV therapy, 1938–1940 molds, 2363–2369 future directions, 1309–1310 Antiviral resistance standardized broth dilution methods for investigational methodologies, 1308–1309 causes of drug failure, 1985–1986 yeasts, 2354–2358 MALDI-TOF mass spectrometry, 1308 host factors, 1985 standardized disk diffusion method for manual broth microdilution systems, 1302 patient sociobehavioral influence, 1985–1986 yeasts, 2362 manual gradient diffusion method, 1301 true, 1985 Vitek 2 yeast, 2361 MicroScan WalkAway, 1303 See also Susceptibility test methods: viruses yeast genera other than Candida, selecting, 1309 Antiviral susceptibility testing 2358–2359 semiautomated broth microdilution sys- clinical indications for, 1986 Antimicrobial agents tems, 1302 emerging technologies, 1997 activity against Gram-negative anaerobes, semiautomated instrumentation for disk future directions, 1997 1013 diffusion testing, 1301–1302 test interpretation, 1994, 1997 aminoglycosides, 1400–1401 Sensititre ARIS 2x, 1304 See also Susceptibility test methods: viruses 4-aminoquinolines, 2652–2654 VITEK Systems, 1302–1303 Apiotrichum yeasts, description, 2064 8-aminoquinolines, 2656 See also Phenotypic tests Apophysomyces genus p-aminosalicylic acid, 1402 Antimicrobial susceptibility tests (ASTs) identification, 2172 amithiozone, 1401 broth methods for dilution testing, unbranched sporangiophores, 2174 antifolates, 2657 1286–1291 Approved List of Bacterial Names, 291 artemisinin (qinghaosu) derivatives, choice of methods, 1284, 1286 APx001 (E1210, Amplyx), 2327 2656–2657 common error sources in, 1296 Arachnida, 2638 atovaquone-proguanil (Malarone), dilution methods, 1286 Arboviruses 2657–2658 disk diffusion testing, 1293–1295 antigen detection, 1696 bedaquiline, 1401 future of, 1297–1298 characteristics of, 1686–1687 capreomycin, 1401 international breakpoint differences, 1297 clinical significance, 1693–1694 cinchona alkaloids, 2654 problem organisms, 1296–1297 collection, transport, and storage of speci- clofazimine, 1401 quality control for dilution methods, mens, 1694–1695 cycloserine, 1401 1291–1293 commercial diagnostic tests, 1690–1692 dapsone, 1401 quality control for disk diffusion method, description of agent, 4–5, 1685, 1688–1689 delamanid, 1401 1295–1296 detection and identification methods, 1473 drugs used for susceptibility testing, reporting results, 1286 direct detection, 1695–1697 1402–1403 resistance mechanisms, 1296–1297 enzyme-linked immunosorbent assay, ethambutol, 1400 specific method preferences, 1297 1698–1699 ethionamide, 1402 See also Dilution testing; Disk diffusion epidemiology and transmission, 1689, 1693 halofantrine, 2655 testing evaluation, interpretation, and reporting of isoniazid, 1399 Antiparasitic agents results, 1700–1701 lumefantrine, 2655 anthelmintic agents, 2645–2652 hemagglutination, 1698 macrolides, 1402 antimalarials, 2652–2658 identification, 1697–1698 mechanism of Plasmodium falciparum resis- antiprotozoal agents, 2652, 2658–2662 isolation procedures, 1697 tance to, 2670–2672 national and regional medicine regulatory microscopy, 1695–1696 mefloquine, 2654–2655 authorities, 2662 neutralization, 1699–1700 metronidazole, 1225 treatment of intestinal, blood and tissue, nucleic acid detection, 1696–1697 MIC range for Mycoplasma and Ureaplasma and urogenital protozoal infections, optimal laboratory testing algorithm, 1695 spp., 1129 2646 RT-LAMP, 1697 Mycobacterium avium complex (MAC), treatment of major helminthic infections, RT-PCR, 1696–1697 1410 2647 serological tests, 1698–1700 Mycobacterium tuberculosis complex (MTC), treatment regimens for malaria, 2653 taxonomy, 1685 1404 Antiprotozoal agents Arcanobacterium genus new antituberculous drugs, 1402 diloxanide furoate, 2658 description, 493 pyrazinamide, 1400 eflornithine, 2661 identification, 513–514 quinoline derivatives, 2652–2656 iodoquinol, 2658 Archaea, 289, 295 quinolones, 1402 melarsoprol, 2661 classification of, 288–289 rapidly growing mycobacteria, 1413 miltefosine, 2659 Archaeplastida supergroup, eukaryotes, rifabutin and rifapentine, 1400 nifurtimox and benznidazole, 2661–2662 2380–2382 rifampin, 1399–1400 nitazoxanide, 2652 Arcobacter spp. rifamycins, 1225–1226 paromomycin, 2660 algorithm for identification of, 1025 susceptibility testing methods, 2683 pentamidine, 2659–2660 antimicrobial susceptibilities, 1037

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Arcobacter spp. (continued) scorpions, 2636 evaluation, interpretation and reporting of bacteremia, 1026 spiders, 2636–2637 results, 2120 clinical significance, 1031 stinging and biting resulting in envenom- b-1,3-d-glucan detection, 2048, 2112–2113 description of, 1028 ation, 2635–2637 identification, 2114, 2116–2117 epidemiology and transmission, 1028, 1030 typically thought of as vectors, 2631–2632 in vitro antifungal susceptibility testing, gastrointestinal-tract infections, 1024, 1026 urticating caterpillars, 2635–2636 2119 identification, 1035–1036 Arthropods as scalars, 2628, 2630–2631 isolation procedures, 2114 isolation procedures, 1034–1035 cockroaches, 2630–2631 known uncommon pathogenic, 2104 phenotypic properties of, 1032 muscoid flies, 2630 MALDI-TOF methods, 2117 reservoirs for and diseases associated with, Arthropods as vectors maximum-likelihood tree of pathogenic, 1029–1030 Acarina, 2626–2628 2105 taxonomy, 1028 Diptera, 2620–2622 methods and MIC determination, typing systems, 1037 Hemiptera, 2622–2623 2119–2120 Arenaviridae family, 1719 Psocodea, 2624–2626 microscopy, 2111, 2114, 2115 animal inoculation, 1730 Siphonaptera, 2623–2624 molecular identification, 2116–2117 antigen detection, 1729 summary of infectious agents, 2621 morphology by direct examination, 2039 antiviral susceptibilities, 1733 Arthropods of medical importance nucleic acid detection, 2049–2050, cell culture, 1730 common arthropod classes, subclasses, and 2113–2114 clinical significance, 1724–1725 orders, 2639 serologic tests, 2118–2119 collection, transport, and storage of speci- identifying specimens, 2637–2640 sporulating species, 2116 mens, 1727–1728 summary of features, 2638 taxonomy, 2103–2104 current arenaviruses and associated human ARuP Laboratories, human herpesvirus 6 typing systems, 2117–2118 diseases, 1721–1722 (HHV-6) testing, 1818 Aspergillus candidus, characteristics of, 2110 description of agents, 1719–1720 Asaia spp. Aspergillus flavipes, characteristics of, 2107 direct examination, 1728–1730 characteristics of, 846 Aspergillus flavus electron microscopy, 1728–1729 identification, 846–847 characteristics of, 2107 epidemiology and transmission, 1720 Ascaris lumbricoides (roundworm), 2555–2558 identification, 2114, 2115 evaluation and interpretation of results, adult worms of, 2556 Aspergillus fumigatus 1733–1734 clinical significance, 2558 Calcofluor white stain, 2044 identification, 1730, 1732 description of agent, 2556–2557 characteristics of, 2107 isolation procedures, 1730 direct examination, 2558 Gomori methenamine silver (GMS), 2036, Lassa virus, 1719, 1725 eggs, 2553, 2556 2044 LCM (lymphocytic choriomeningitis) epidemiology and prevention, 2557 Gram stain, 2042, 2043 virus, 1719, 1725, 1728 larvae, 2556–2557 H&E stain, 2044 Lujo virus, 1719, 1725 life cycle of, 2557 identification, 2114, 2115 New World arenaviruses, 1721–1722 life cycle completion time, 2558 nucleic acid detection, 2072 nucleic acid detection, 1729 macroscopic examination, 2558 Aspergillus nidulans Old World arenaviruses, 1721 microscopy, 2558 characteristics of, 2108 safety and security of agents, 1727 relative sizes of eggs, 2552 identification, 2114, 2115 serologic diagnosis, 1732–1733 summary of, 2559 morphology by direct examination, 2039 taxonomy, 1719–1720 taxonomy, 2555–2556 Aspergillus niger, characteristics of, 2108 Arenaviruses transmission and life cycle, 2557–2558 Aspergillus restrictus, characteristics of, 2110 detection and identification methods, 1473 treatment, 2558 Aspergillus terreus, characteristics of, 2109 See also Arenaviridae family See also Nematodes Aspergillus tubingensis, characteristics of, 2108 Arginine arylamidase, 331 Ascomycetes Aspergillus versicolor, characteristics of, 2109 Arginine dihydrolase, 331 clinical significance, 2151 Assessing Worldwide Antimicrobial Arginine hydrolysis, streptococci, 411 description, 2145, 2147 Resistance Evaluate (AWARE) sur- Artemisinin (qinghaosu) derivatives Ascomycetous yeasts veillance program, 1349 adverse effects, 2657 description, 2059 Association of Official Analytical Chemists mechanism of action, 2656 taxonomy and nomenclature, 2056–2058 (AOAC), 226 pharmacokinetics, 2656 Ascomycota, phylum of kingdom Fungi, Astroviruses spectrum of activity, 2656 2010–2011 clinical features, 1659 Artemisinins, mechanism of resistance, 2670 Ascospore stain, mycology, 2027 description of, 1658 Artesunate, human herpesvirus 6 (HHV-6), Ashdown’s medium, 342 electron micrographs, 1658 1817 Aspergillus spp. epidemiology and transmission, 1660 Arthrobacter genus, 401, 511 antibody detection, 2037 molecular assays for detection, 1664 Arthrocladium genus, 2241 antigen detection, 2041–2042, 2111–2113 taxonomy of, 1657 Arthroderma spp. antigen detection using lateral flow tech- See also Gastroenteritis viruses description of, 2227 nology, 2112 Atazanavir taxonomy, 2208 antimicrobial susceptibilities, 2119–2120 drug interactions, 1943 Arthrographis characteristics of medically important, HIV therapy, 1939 clinical significance, 2151–2152 2107–2110 mechanism of resistance, 1965 hyphomycetes, 2147, 2149 clinical categorization of infection and pharmacology, 1943 Arthropods, classification, 2385–2387 causative species, 2110 Atherosclerosis, 1086 Arthropods, direct injury due to clinical significance, 2106, 2111 Atopobium spp. accidental myiasis, 2633 collection, transport, and storage of speci- antimicrobial susceptibilities, 955 centipedes and millipedes, 2636 mens, 2111 clinical significance, 946 Demodex folliculorum and D. brevis, 2633 description, 2104 enzyme reactions, 952 endoparasitic, 2632–2635 direct examination, 2111–2114 Atovaquone, mechanism of resistance, 2670 Hymenoptera, 2635 drugs for treating invasive aspergillosis, Atovaquone-proguanil (Malarone) maggots, 2633–2635 2119 adverse effects, 2658 miscellaneous injury, 2637 epidemiology and transmission, 2104–2106 mechanism of action, 2657 myiasis, 2633, 2634 epidemiology of azole resistance, 2336 pharmacokinetics, 2657 scabies, 2632–2633 EuCAST breakpoints for, 2366 spectrum of activity, 2657–2658

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Audits, biosafety program, 209 Bacillary angiomatosis (BA), 893, 896 See also Laboratory detection of bacteremia Aum Shinrikyo, Tokyo subway attack, 243 Bacillary peliosis hepatis, 893 and fungemia Auramine-rhodamine stain, 337 Bacilli class, taxonomy and description, 940 Bacteria, 289, 295 Aureobasidium genus, 2242, 2249 Bacillus genus classification of, 288–289 Auritidibacter genus, 401, 511 aerobic endospore-forming bacteria, 457 identification by nucleic acid sequencing, Automation antimicrobial susceptibilities, 470–471 109–110 molecular assays, 107–108 B. anthracis, 457–458 preservation methods, 201, 202 See also Microbiology laboratory B. cereus group, 458–459 See also Anaerobic bacteria; Fastidious automation bioterrorism-related specimens, 460 bacteria; Human microbiome Autopsy samples characters for differentiating species, 468 Bacterial classification collection and processing tissue, 1457 clinical significance, 457–459 genotypic methods for, 295–296 processing recommendations, 317 collection, transport, and storage of speci- Bacterial pathogens Avibactam, 1208 mens, 459–462 laboratory safety issues, 316–317 Axiom Microbial Detection Analysis description of, 455–456 Bacteriological and Analytical Manual Software (MiDAS), 273 direct examination, 462–465 (FDA), 479 Azithromycin, 1212–1214, 1229 epidemiology and transmission, 456–457 Bacteriological media, 341–359 Pseudomonas resistance to, 797 evaluation, interpretation, and reporting of Bacteroides bile esculin agar, 342 Azoles results, 471–472 Bacteroides genus biofilms, 2340 identification, 466–469 antimicrobial activities of potential agents, chromosomal abnormalities, 2340 isolation procedures, 465–466 1013 clinical and microbiological resistance, photomicrographs of endospore-forming characteristics of, 997 2335 bacteria, 463, 464 clinical importance, 999–1000 drug efflux transporters, 2339 serologic tests, 470 epidemiology and transmission, 998 drug interactions, 2321 specimens from anthrax-suspected patients, isolation procedures, 1004 drug target modification, 2336–2337 460, 462 molecular detection, 1004 environmentally acquired resistance as susceptibility testing, 1361–1362 phenotypic characteristics of, 1007 major factor, 2337–2338 taxonomy, 455 resistance patterns of, 1383–1385 epidemiology of resistance, 2335–2336 testing conditions, 1351 Bacteroides fragilis, 1377 fluconazole, 2320, 2321 toxins and virulence factors for B. cereus antimicrobial susceptibility of, 1013–1014 increasing target abundance, 2338–2339 group, 459 phenotypic characteristics of, 1007 isavuconazole, 2320, 2321–2322 typing systems, 469–470 resistance patterns of, 1383–1385 itraconazole, 2320, 2322 Bacillus anthracis, 269 Bacteroidetes, 256, 289 ketoconazole, 2322–2323 antimicrobial susceptibilities, 471 Baird-Parker medium, 342 loss of heterozygosity, 2340 bioterrorism potential, 1359 Balamuthia genus mechanism of action, 2320, 2335 biothreat agent, 246–247 classification, 2383 pharmacokinetics, 2320–2321 clinical significance, 457–458 description of, 2487–2488 posaconazole, 2320, 2323 collection, transport, and storage of speci- detection in humans, 2381 regulation of resistance, 2339–2340 mens, 460 encephalitis, 2490 resistance and virulence, 2340 colonies of endospore-forming bacteria, epidemiology, 2488 resistance mechanisms, 2336–2340 467 taxonomy, 2486 resistance to, 2335–2336 epidemiology and transmission, 456 See also Free-living amebae structural modeling of resistance, 2338 identification, 466–469 Balneatrix alpica voriconazole, 2320, 2323–2324 isolation procedures, 465–466 characteristics of, 843 Azospirillum spp. laboratory-acquired infection, 214 identification, 844 characteristics of, 846 serologic tests, 470 Barbour-Stoenner-Kelly medium, 342 identification, 847 testing conditions, 1350 Bartonella genus Aztreonam, 1206 typing systems, 469 anthroponotic bartonelloses, 896 Bacillus cereus biovar anthracis antigen detection, 898 biothreat agent, 246–247 antimicrobial susceptibility testing, Babesia genus collection, transport and storage of speci- 900–901 classification, 2383 mens, 460 choice and use of antibiotics in vivo, clinical significance, 2452 colonies of endospore-forming bacteria, 467 900–901 collection, transport and storage of speci- identification, 466–469 clinical significance, 895–897 mens, 2452 isolation procedures, 465–466 collection, transport, and storage of speci- comparative morphology of, 2453 laboratory-acquired infection, 214 mens, 897 description of agent, 2450 typing systems, 469 direct examination, 897–898 detection in humans, 2381 Bacillus cereus group electron micrographs of B. henselae, 894 direct examination, 2452–2453 antimicrobial susceptibilities, 471 epidemiology and transmission, 893–895 epidemiology and transmission, 2450–2452 clinical significance, 458–459 evaluation, interpretation, and reporting of evaluation, interpretation, and reporting of epidemiology and transmission, 456 results, 901 results, 2454 taxonomy, 455 identification, 898–899 isolation procedures, 2453 Bacillus cereus medium (BCM), 342 isolation procedures, 898 life cycle of Ixodes scapularis and B. microti, Bacillus cereus selective agar base, 342 microscopy, 897–898 2451 Bacillus licheniformis, clinical significance, nucleic acid detection, 898 microscopy, 2452–2453 457 serologic tests, 899–900 morphology, 2452, 2453 Bacillus subtilis, clinical significance, 457 species and subspecies descriptions, 895 nucleic acid detection, 2453 Bacitracin susceptibility, Streptococcus pyo- taxonomy and description of, 893 serologic tests, 2453 genes, 408 typing systems, 899 taxonomy, 2438 Bacteremia zoonotic bartonellosis, 896–897 techniques for parasite recovery and identi- clostridial, 970–971 Basidiobolales family, genus Basidiobolus, 2179, fication, 2436 curved Gram-negative rods, 1024, 2180 treatment and prevention, 2452 1026–1027 Basidiobolus genus Babesiosis, epidemiology and transmission, diagnostic importance, 28 antifungal susceptibilities, 2179 2450–2452 interpretation of blood culture, 31–33 identification, 2179, 2180

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Basidiomycetes direct examination, 515–516 BK polyomavirus (BKPyV), 1863 clinical significance, 2151 epidemiology and transmission, 515 commercial nucleic acid amplification description, 2147 identification, 515–516 products, 1871 key phenotypic features of, 2137–2138 isolation, 515–516 disease associated with, 1865 Basidiomycetous yeasts Bifidobacterium spp. serologic tests, 1871–1872 description, 2059, 2064 antimicrobial susceptibilities, 955 See also Human polyomaviruses (HPyVs) taxonomy and nomenclature, 2058 resistance patterns of, 1388 Black Death, 751 Basidiomycota, phylum of kingdom Fungi, Bifidobacterium spp., clinical significance, 945 Black piedra, 2229 2009–2010 Bile esculin agar, 342 BLAST (Basic Local Alignment Search Baylisascaris procyonis Bile esculin agar with kanamycin, 342–343 Tool), 179, 263, 278 clinical significance, 2615 Bile esculin azide agar, 343 Blastic conidiogenesis, 2012 description of agent, 2615 Bile esculin test, streptococci, 411 Blastocystis genus direct examination, 2615 Bile solubility test, 332 classification, 2383–2384 epidemiology, transmission, and preven- streptococci, 410–411 clinical significance, 2506 tion, 2615 Bilophila genus description of, 2506 microscopy, 2615 characteristics of, 997 detection in humans, 2381 serologic tests, 2615–2616 clinical importance, 1002–1003 direct examination, 2506–2507 taxonomy, 2615 identification, 1005 epidemiology, transmission, and preven- treatment, 2616 isolation procedures, 1004 tion, 2506 BCM O0157:H7(1) plating medium, 342 Bilophila wadsworthia, resistance patterns of, 1385 evaluation, interpretation, and reporting of BCPD agar (bromocresol purple deoxycholate Biochemical tests, reagents for, 331–334 results, 2507 agar), 342 Biocides, resistance and tolerance to, 236 microscopy, 2506 BD Phoenix, automated broth microdilution, Biofilms nonpathogenic, 2505–2507 3, 1303–1304 azole resistance, 2340 taxonomy, 2505 BD Phoenix Automated Microbiology System, echinocandin resistance, 2342 treatment, 2507 phenotypic identification system, 49–50 Bioinformatics Blastocystis hominis BEAST (Bayesian Evolutionary Analysis and age of, 296 intestinal amebae of humans, 2500 Sampling Trees), 182 definitions used in, 178 key features, 2499 Beauveria sites for analysis of resistance, 1995–1996 Blastomyces spp. clinical significance, 2152 virtual phenotypes, 1994 antibody detection, 2037, 2041 hyphomycetes, 2149 Biological Weapons Convention of 1972, 243 antigen detection, 2042, 2045, 2195 Bedaquiline (BDQ), 1401 Biolog Microbial Identification Systems, phe- antimicrobial susceptibilities, 2200, 2201 Bed bugs (Cimex lectularius), 2623 notypic identification system, 50–51 biosafety, 2196 Benzidine test, 332 BIOMIC V3 imaging system, phenotypic blastoconidia of, 2189 Benzimidazoles identification system, 51 blastomycosis, 2191–2192, 2192–2193, adverse effects, 2648 Biopsy tissue, collection and processing, 1457 2195–2196, 2199 albendazole, 2645, 2647 Biosafety, 206 B. parvus adiaspore in mouse tissue, flubendazole, 2645 Biosafety in Microbiological and Biomedical 2190 mebendazole, 2645, 2647 Laboratories (CDC), 72, 980 clinical significance, 2192–2193 mechanism of action, 2646 Biosafety program clinical specimens, 2194 pharmacokinetics, 2646, 2648 audits, 209 culture for yeast phase, 2196 spectrum of activity, 2648 Chlamydia spp., 1142–1143 description of, 2189–2190 thiabendazole, 2645 committee, 209 epidemiology and transmission, 2191–2192 triclabendazole, 2645–2646 components, 207 evaluation, interpretation and reporting of See also Anthelmintic agents management, 209–210 results, 2201, 2202 Bergeyella zoohelcum manual, 210 (1,3)-b-d-glucan detection, 2048 characteristics of, 843 standard operating procedures, 210 identification, 2197 identification, 844 Biosecurity, 206 microscopy, 2194 Bergey’s Manual of Determinative Bacteriology, 288 Bioterrorism mycelial phase, 2189 Bergey’s Manual of Systematic Bacteriology, 288 botulinum toxin as agent, 975 nucleic acid detection, 2195–2196 Bergey’s Manual of Systematics of Archaea and mycotoxins and, 2284–2285 serologic tests, 2199 Bacteria, 288, 367 potential bacterial agents of, 1359–1360 taxonomy, 2188 Bernhard-Nocht-Institute for Tropical Bioterrorism Act, 245 typing systems, 2198 Medicine, 1728 Biothreat agents, 243–244 Blastomyces dermatitidis Berson, Solomon, 124 anthrax (Bacillus anthracis and B. cereus Gram stain, 2046 Bertiella spp., human infection, 2616 biovar anthracis), 246–247 morphology by direct examination, 2038 Beta-lactams, beta-lactamase. See also botulism (Clostridium botulinum), 247 Blood b-Lactam; b-Lactamase brucellosis (Brucella spp.), 251–252 agitation, 30 Beta-lactamase resistance Burkholderia mallei and B. pseudomallei, anticoagulants, 30 in Gram-negative bacteria, 1424 250–251 antigen detection for parasites, 2403 molecular assays for detection in Gram- hemorrhagic fever viruses (HFVs), 249 automated culture systems, 34 negative bacteria, 1425 Laboratory Response Network (LRN), buffy coat films, 2403, 2436 Beta-lactam-resistant pneumococci, as resis- 243–245 collection and processing of virus speci- tance target, 1426 plague (Yersinia pestis), 247–248 mens, 1453–1454 Betapapillomavirus sp., 1847, 1850 Q fever (Coxiella burnetii), 252 concentration procedures, 2436–2437 nucleotide sequence of L1 gene, 1848 smallpox, 248 criteria for CLABSI (central line-associated Betapolyomavirus, 1863, 1864 staphylococcal enterotoxins, 252–253 bloodstream infections), 32 Biatriospora mackinnonii, morphology by direct tularemia (Francisella tularensis), 248–249 critical factors for detecting bacteremia or examination, 2040 See also Tier 1 select agents fungemia, 29–31 Bictegravir, mechanism of resistance, 1965 Bipolaris genus, 2244 Delafield’s hematoxylin, 2437 Bifidobacteriaceae family Birdseed agar, mycology, 2029 dilution of, 30 clinical significance, 515 Bismuth sulfite agar, 343 dried blood spots, 1454 collection, transport, and storage of speci- Bismuth sulfite-glucose-glycine yeast examination of thin and thick films, 2435 mens, 515 (BiGGY) agar, mycology, 2029 Giemsa stain, 2434

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immunochromatographic tests for malaria, Bordetella parapertussis Botryosphaeriales order 2435 antimicrobial susceptibilities, 864 Lasiodiplodia genus, 2234 Knott concentration procedure, 2403, clinical significance, 861 Macrophomina genus, 2234 2436–2437 epidemiology and transmission, 860 Neoscytalidium genus, 2238 manual blood culture system, 33–34 evaluation, interpretation, and reporting of overview of genera in, 2235 medium and additives, 30–31 results, 865–866 phaeohyphomycosis, 2247–2248, 2249 membrane filtration technique, 2403, 2437 identification, 863 taxonomy and description, 2234, 2238 methods for detecting microorganisms in, isolation procedures, 862 Botulinum neurotoxin (BoNT), 970, 981 28 serologic tests, 864 Botulinum toxin, as bioterrorism agent, 975 molecular detection for parasites, 2403 typing systems, 864 Botulism number of cultures, 29–30 Bordetella pertussis biothreat agent, 247 parasites, 2390 antimicrobial susceptibilities, 864 infant, 975 processing and storage conditions, 1452 clinical significance, 861 inhalational, 975 processing recommendations, 317, 319 epidemiology and transmission, 860 organism and toxin, 974–975 QBC microhematocrit centrifugation evaluation, interpretation, and reporting of types, 974 method, 2436 results, 865–866 wound botulism, 975 screening methods, 2403 identification, 863 Boutonneuse fever, 1151, 1152 staining films, 2434–2435 isolation procedures, 862 Bovine albumin fraction V, 334–335 stains, 2403 serologic tests, 864 Bovine albumin Tween 80 medium, 343 techniques for parasite recovery and identi- typing systems, 864 Bovine spongiform encephalitis (BSE), 1923, fication, 2436 Bordetella pertussis selective medium, 343 1925 thick films, 2402–2403, 2433–2434 Bordetella pertussis selective medium with Brachybacterium genus thin films, 2402, 2434 charcoal agar base, 343 description, 492 triple-centrifugation method for trypano- Bordet-Gengou agar, 343 identification, 512 somes, 2437 Borrelia genus Brachyspira spp. volume of cultured, 29 antimicrobial susceptibility, 1077 antimicrobial susceptibilities, 1098 Wright’s stain, 2434 B. burgdorferi sensu lato (Lyme Borrelia collection, transport, and storage of speci- Blood agar, 343 group), 1068, 1073 mens, 1089 Blood-borne pathogens, laboratory-acquired bacteremia, 1026 description of, 1084–1085 infection, 217 clinical significance, 1069–1071 direct detection, 1091 Blood-free Campylobacter selectivity agar, 343 culture, 1072–1073 gastroenteritis, 1026 Blood-glucose-cystein agar, mycology, 2029 description of, 1067–1068 identification, 1091 Blood specimens epidemiology and transmission, 1068–1069 isolation procedures, 1091 collection and transport, 303, 2017 evaluation, interpretation, and reporting primers and thermocycling conditions for for parasite detection, 2433–2437 of Lyme borreliosis test results, PCR, 1091 preparation and procedures, 2393 1077–1078 taxonomy, 1083 pathogenic fungi recovery, 2019 evaluation, interpretation, and reporting of typing systems, 1091 preparation and procedures, 2393 results, 1077–1078 Brain pretreatment, 2020 genomes, 1067–1068 pathogenic fungi recovery, 2019 processing and culture guidelines, 2019–2020 laboratory diagnosis, 1071–1072 specimen for parasite detection, 2427, Bocaviruses methods, 1072 2428, 2429–2430 detection and identification methods, 1473 microscopy, 1072 Brain heart infusion (BHI), 343 See also Human bocaviruses nucleic acid detection, 1073 Brain heart infusion agar Body lice (Pediculus humanus humanus), 1153 relapsing fever Borrelia group, 1068, mycology, 2029 Body sites 1073 Breakpoints parasite analysis, 2428–2429 serology, 1073–1077 definitions, 1285 parasites, 2390 species, 1068 establishing susceptibility, 1279–1281 Bone marrow specimens species causing human disease, 1067 international differences, 1297 collection and processing of virus speci- taxonomy, 1066 Brevibacteriaceae family, 490, 512 mens, 1454 tissue infections, 1027 Brevibacterium genus collection and transport, 2017 Borrelia burgdorferi sensu lato (Lyme Borrelia description, 490 for parasite detection, 2427, 2428 Group), 1066, 1068 identification, 512 parasites, 2390 antigens, 1073 Brevundimonas pathogenic fungi recovery, 2019 causing human disease, 1067 antimicrobial susceptibility, 820 preparation and procedures, 2393 cerebrospinal fluid testing for intrathecal characteristics of, 818 pretreatment, 2020 production of antibodies, 1077 clinical significance, 811 processing and culture guidelines, 2020 clinical manifestations of, 1070 description of, 808 transport and culture, 325 clinical significance, 1070–1071 identification, 818–819 Bordetella spp., 1348 culture, 1072–1073 typing systems, 819 antimicrobial susceptibilities, 864–865 enzyme immunoassays, 1075 Bright-field microscopy, 20 characteristics of species, 863 epidemiology and transmission, 1069 Brilliance CRE agar, 343 clinical significance, 861 immunoblots, 1075–1076 Brilliance ESBL agar, 343 collection, transport, and storage of immunodominant antigens of, 1074 Brilliance MRSA agar, 343 specimens, 862 indirect immunofluorescent antibody assay, Brilliance Salmonella agar, 344 description of, 858–859 1075 Brilliance Staph 24 agar, 344 direct fluorescent antibody staining (DFA), laboratory diagnosis, 1071–1072 Brilliance uTI agar, 344 862 microscopy, 1072 Brilliance uTI Clarity Agar, 344 epidemiology and transmission, 860–861 modified two-tier testing, 1076–1077 Brilliance VRE Agar, 344 identification, 863 nucleic acid detection, 1073 Brilliant green agar, 344 isolation procedures, 863 performance of standard two-tier and modi- Brilliant green phenol red agar, 344 members of, 859 fied two-tier tests for, 1077 Brincidofovir nucleic acid detection, 862 recommended laboratory tests, 1070 against herpesviruses, 1954 possible targets for detection of, 860 serology, 1073–1077 human adenovirus (HAdV), 1840–1841 taxonomy, 858 two-tier testing, 1076 Broad Institute, 419

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Broad-spectrum agents, resistance to Brucella blood culture broth, 344 Burkholderia cepacia selective agar, 345 aminoglycoside, 1246–1247 Brucella broth, 344 Burkholderia gladioli chloramphenicol, 1259–1260 Brucella laked sheep blood agar with kanamy- characteristics of, 814 b-lactamase-mediated, 1250–1254 cin and vancomycin, 344 clinical significance, 809–810 b-lactam, 1247–1250 Brucella spp. identification, 813–815 nitrofurantoin, 1259 anti-Brucella therapy, 888–889 Burkholderia mallei polymyxin B, 1257–1259 antigenic components, 883–884 antimicrobial susceptibility, 820 polymyxin E (colistin), 1257–1259 antimicrobial susceptibilities, 888 bioterrorism potential, 1359 quinolone, 1254–1256 biothreat agent, 251–252 biothreat agent, 250–251 rifampin, 1260 clinical categories of human brucellosis, characteristics of, 816 tetracycline, 1256–1257 884–885 clinical significance, 810 trimethoprim-sulfamethoxazole, 1260 complications, 885 identification, 815–816 Bromcresol purple milk solids glucose me- culture, 885–886 laboratory-acquired infection, 215 dium, mycology, 2029–2030 description of, 883 reporting results, 821 Bronchiectasis, rapidly growing mycobacteria, direct examination, 885 testing conditions, 1350 616 epidemiology and transmission, 884 Burkholderia pseudomallei Bronchoscopy, specimens collected during, evaluation, interpretation, and reporting of antimicrobial susceptibility, 820 323–324 results, 889 bioterrorism potential, 1359 Broth dilution methods identification, 886 biothreat agent, 250–251 agar-based alternative approaches for immune response, 884 characteristics of, 816 filamentous fungi, 2367–2368 laboratory-acquired infection, 213 clinical significance, 810 dermatophytes, 2367 pathogenic mechanisms, 884 direct examination, 811–812 fungicidal activity for molds, 2368–2319 prevention, 889 identification, 815–816 guidelines for antifungal testing of molds, serologic tests, 887–888 isolation procedures, 812–813 2364–2365 specimen handling, storage, and transport, laboratory-acquired infection, 215 guidelines for susceptibility testing of 885 reporting results, 821 yeasts, 2355 taxonomy, 883 serologic tests, 819 interpretation and results for breakpoints testing conditions, 1350 testing conditions, 1350 for molds, 2366–2367 typing systems, 887 Burkholderia pseudomallei selective agar, 345 macrodilution for yeasts, 2358 virulence factors, 884 Burkholderia thailandensis, characteristics of, MIC ranges for yeasts, 2356–2357 Brucellaceae family, 883 816 microdilution for molds, 2365–2366 Brucellosis Burn wound infections, Pseudomonas, 789 microdilution for yeasts, 2357–2358 biothreat agent, 251–252 molecular tests for molds, 2368 categories of human, 884–885 quality control for mold testing, 2366 common tests for laboratory diagnosis of, Caffeic agar, mycology, 2030 quality control for yeast testing, 2358 887 Calcofluor white standardized, for molds, 2363–2369 Brugia malayi fungi detection, 2036 standardized, for yeasts, 2354–2358 description of, 2570 mycology, 2027 Broth macrodilution (tube) method diagrammatic representation of extremities, Calcofluor white stain, parasitology, 2413 advantages and disadvantages, 1290 2573 Caliciviruses dilution of antimicrobial agents, 1289 epidemiology and transmission, 2571 clinical features, 1659 incubation, 1290 microfilariae in humans, 2572 description of, 1657 inoculation procedures, 1289 parasite of humans, 2571 epidemiology and transmission, 1659–1660 interpretation and reporting of results, 1290 taxonomy, 2570 taxonomy of, 1656, 1657 preparation, supplementation, and storage Brugia timori See also Gastroenteritis viruses of tubes, 1289 description of, 2570 California Department of Public Health See also Dilution testing epidemiology and transmission, 2571 Infant Botulism Treatment and Broth microdilution parasite of humans, 2571 Prevention Program, 975, 980 automated systems, 1302–1307 taxonomy, 2570 Calosphaeriales order incubation conditions, 1381 Buffered charcoal yeast extract agar with overview of genera in, 2235 inoculation procedure, 1381 cysteine, 345 phaeohyphomycosis, 2248 inoculum preparation, 1380–1381 Buffered charcoal yeast extract differential Pleurostoma genus, 2238–2239 interpretation of results, 1381 agar, 345 taxonomy and description of, 2238–2239 manual systems, 1302 Buffers, reagents, 334–335 CAMP test, 332 media, 1380 Bundibugyo ebolavirus, 271 streptococci, 408 panels, 1382 Bunyaviridae family, 1685, 1686 Campylobacter agar, Blaser’s, 345 quality control, 1381 Bunyavirus Campylobacter agar, Skirrow’s, 345 semiautomated systems, 1302 clinical significance, 1693 Campylobacter blood agar, 345 susceptibility testing, 1379, 1380–1381 commercial diagnostic tests, 1692 Campylobacter charcoal differential agar, 345 See also Antimicrobial susceptibility testing genome, 1688 Campylobacter spp. systems Burkholderia genus algorithm for identification of, 1025 Broth microdilution method description of, 808 antigen detection, 1033 advantages and disadvantages, 1288–1289 epidemiology and transmission, 808–809 antimicrobial susceptibilities, 1037 dilution of antimicrobial agents, 1286–1287 species, 807 bacteremia, 1027 incubation, 1288 typing systems, 819 blood samples, 1033 inoculation procedures, 1287–1288 whole-genome SNP typing, 177 C. coli, 1030–1031, 1036 interpretation and reporting of results, 1288 Burkholderia cepacia agar, 345 C. fetus subsp. fetus, 1031 preparation, supplementation, and storage Burkholderia cepacia complex C. jejuni, 1030–1031, 1036 of panels, 1287 characteristics of, 814 C. lari, 1031 See also Dilution testing clinical significance, 809–810 clinical significance of, 1030–1031 Brucella agar, 344 development of new discriminative PCRs, collection, transport, and storage of speci- Brucella agar base Campylobacter medium, 344 637–638 mens, 1033 Brucella agar base with blood and selective identification, 813–815 C. upsaliensis, 1031 supplement, 344 Burkholderia cepacia outbreak, 163 description of, 1028

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direct examination, 1033–1034 isolation procedures, 2072 mechanism of action, 1206 enrichment cultures, 1035 MALDI-TOF-based methods, 2075 pharmacology, 1206–1207 epidemiology and transmission, 1028, 1030 morphological features of, 2060 resistance mechanisms among Gram- evaluation, interpretation, and reporting of morphology by direct examination, 2038 negative bacilli, 1334 results, 1037–1038 non-C. albicans species, 2057–2058 spectrum of activity, 1207 fecal samples, 1033 nucleic acid detection, 2049–2050, Carboxycinicillins, 1203 filtration, 1035 2071–2072 Cardiac samples, virus detection methods, gastrointestinal tract infections, 1024, 1026 pyrosequencing, 2075 1447 identification, 1035–1036 restriction enzyme analysis (REA), 2075 Cardiobacterium spp. isolation procedures, 1034–1035 serologic tests, 2077 antimicrobial susceptibility, 665 microscopy, 1033 taxonomy and nomenclature, 2056–2058 biochemical reactions of, 664 nucleic acid detection techniques, typing systems, 2076–2077 clinical significance, 658 1033–1034 See also Yeasts direct examination, 660 performance characteristics of NAATs for Candida albicans, Gram stain, 2042, 2043 epidemiology and transmission, 657 detecting, 1034 Candida albicans species complex, taxonomy identification of, 663 phenotypic properties of, 1032 and nomenclature, 2056–2057 isolation procedures, 661 reflex cultures, 1035 Candida auris, 4 taxonomy, 657 reservoirs for and diseases associated with, Candida glabrata, Gram stain, 2042, 2043 Cardiomyopathy, human herpesviruses 1029 Candidatus, 292 (HHV), 1816 serologic tests, 1037 “Candidatus Neoehrlichia” Cardiovascular disease, human herpesviruses taxonomy, 1028 clinical significance, 1168–1169 (HHV), 1816 tissue infections, 1027 description of, 1163–1164 Cardiovirus, 1592 typing systems, 1036–1037 epidemiology and transmission, 1164, Carini, Antonio, 2087 Campylobacter coli, 321 1166–1168 Cary-Blair transport medium, 345 source attribution, 182 features of human and veterinary interest, Caspofungin susceptibility testing, 1362 1165 clinical breakpoints for Candida spp., 2352 testing conditions, 1351 neighbor-joining phylogenetic tree, 1164 clinical use, 2325 Campylobacter gracilis neoehrlichiosis, 1168 spectrum of activity, 2320, 2324 resistance patterns of, 1385 Canibacter genus, description, 492 susceptibility testing, 2359 Campylobacter jejuni, 321 Canine Bartonella species, 897 Catalase-negative, Gram-positive cocci source attribution, 182 Capillaria philippinensis antimicrobial susceptibilities, 444–445 susceptibility testing, 1362 clinical significance, 2610 clinical significance, 438–439 testing conditions, 1351 description of agent, 2610 collection, transport, and storage of speci- Campylobacter selective medium, Blaser- direct examination and microscopy, 2610 mens, 439 Wang, 345 epidemiology, transmission, and preven- description of genera, 437–438 Campylobacter thioglycolate medium, 345 tion, 2610 direct examination, 439 Canadian Human Pathogens and Toxins Act, microscopy of, 2607 epidemiology and transmission, 438 460, 980 serologic tests, 2610–2611 evaluation, interpretation, and reporting of Canavanine-glycine-bromthymol blue agar, taxonomy, 2610 results, 445 mycology, 2030 treatment, 2611 identification, 440–444 Cancer Capillary electrophoresis, postamplification isolation procedures, 439 human papillomavirus (HPV) and, 1850, analysis, 101 serologic tests, 444 1852–1853 Capnocytophaga genus taxonomy, 436–437 vaccine for HPV, 1853 antimicrobial susceptibility, 665 typing systems, 444 Candida chromogenic media, mycology, biochemical reactions of, 663 Catalase-positive cocci 2030 clinical significance, 658 antimicrobial susceptibilities, 387–389 Candida spp. direct examination, 659–660 clinical significance, 377–378 anamorphic/teleomorph combinations, identification of, 662–663 collection, transport, and storage of speci- 2057 isolation procedures, 661 mens, 379 antibody detection, 2041 taxonomy, 656 description of families, 367, 369, 374 antifungal susceptibilities, 2068 typing, 665 epidemiology and transmission, 374–377 antifungal susceptibility testing, 2351–2354 Capnodiales order evaluation, interpretation, and reporting of antigen detection, 2047, 2070–2071 Cladosporium genus, 2239–2240 results, 389–390 antimicrobial susceptibilities, 2077 Hortaea genus, 2240 identification, 380–386 chromogenic agars, 2073–2074 overview of genera in, 2235 isolation procedures, 379–380 clinical breakpoints for, 2352 phaeohyphomycosis, 2247, 2248 microscopy, 379 clinical significance, 2065–2066 taxonomy and description of, 2239–2240 nucleic acid detection, 379 CLSI and EuCAST breakpoints for, Capreomycin (CAP), 1401 serologic tests, 386–387 2359–2360 Carbapenem taxonomy, 367 conventional (Sanger) DNA sequencing, resistance, 1306 typing systems, 386 2074–2075 susceptibility testing for Pseudomonas, Catalase test, 332 cultural and biochemical characteristics 798–799 Catheter(s) of, 2061 Carbapenemases processing recommendations for central description of, and its teleomorphs, 2059 detection among Gram-negative bacilli, venous, 319–320 echinocandin resistance, 2341 1333, 1335–1336 specimen collection and transport, 303 epidemiology and transmission, 2064–2065 laboratory detection of Enterobacterales Catheter tips epidemiology of azole resistance, producing, 740–741 collection and transport, 2017 2335–2336 resistance mediators, 737 processing and culture guidelines, evaluation, interpretation, and reporting of Carbapenems 2020–2021 results, 2077–2078 adverse effects, 1207 Cation-adjusted Mueller-Hinton broth germ tube test, 2074 Bacteroides spp., 1384 (CAMHB), 1284 (1,3)-b-d-glucan detection, 2048 chemical structures of, 1202 Cat scratch disease (CSD), 893, 894, 896 historical approaches to identification, detection of colonization with carbapenem- agents of, 896 2072–2073 resistant organisms, 1336–1337 lymph node histopathology of, 897

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CD101 (rezafungin), 2327–2328 Centipedes, stinging and biting for envenom- Chancroid, Haemophilus ducreyi, 673 CDC anaerobe 5% sheep blood agar, 345 ation, 2636 Chapare virus (arenavirus), 271 CDC National Nosocomial Infections Central-line-associated bloodstream infec- Characterization, 292 Surveillance, 141 tions (CLABSI), 141, 143 Chemical disinfection, 228–230 C. Diff Banana Broth, 345 Central nervous system Chemotaxonomy, 293–294 Cefiderocol, 1205 infectious syndromes, 318 cellular fatty acid analysis, 293 Cefoperazone, 1205 parasites, 2390 cell wall composition, 293–294 Cefotaxime, 1204 specimen preparation and procedures, polar lipids, 294 Cefotetan, 1204, 1383 2393–2394 respiratory quinones, 294 Cefoxitin, 1204 CEN Workshop Agreement, 209 Chickenpox activity against Clostridium spp., 987 Cephalosporin(s) varicella, 1757–1759 Bacteroides spp., 1383 adverse effects, 1205–1206 See also Varicella-zoster virus (VZV) Cefsulodin Irgasan Novobiocin (CIN) Agar, Bacteroides spp., 1383–1384 Chikungunya virus 345 chemical structures of, 1202 commercial diagnostic tests, 1692 Ceftaroline, 1205 Cutibacterium spp., 1388 laboratory techniques, 161 Ceftobiprole, 1205 mechanism of action, 1203 Chilomastix genus Ceftolozane, 1205 pharmacology, 1203–1204 classification, 2382 Ceftriaxone, 1204 spectrum of activity, 1204–1205 detection in humans, 2381 Ceftriaxone-resistant Neisseria gonorrhoeae, Cephalosporinases Chilomastix mesnili 1426 laboratory detection of Enterobacterales flagellate, 2507 Cell cultures producing, 739–740 key features of trophozoites and cysts of, centrifugation-enhanced rapid cell culture, resistance mediators, 737 2509 1467 Cephalotheca foveolata, microscopy, 2145, 2146 nonpathogenic flagellate, 2516 Chlamydia isolation medium, 1470 Cerebrospinal fluid trophozoite, 2516 cocultured cell lines, 1468, 1469 collection and processing of virus speci- Chilopoda, 2638, 2639 cytotoxicity assays, 1467, 1469 mens, 1454 Chimpanzee strain, MTBC, 579 ELVIS, 1466, 1467 processing recommendations, 320 Chlamydia spp. EMEM pH 2 to 3, 1470 specimen collection and transport, 304 antigen detection, 1142 growth medium with 10% fetal bovine specimen for parasite detection, 2427, antimicrobial susceptibilities, 1145 serum, 1469 2429–2430 biosafety considerations, 1142–1143 HAD test, 1466–1467 Cervical cancer, human papillomavirus CF (complement fixation) test, 1144 maintenance medium, 1469–1470 (HPV) and, 1852 clinical significance, 1138–1139 media, 1469–1470 Cestoda, classification, 2384, 2385 collection, transport and storage of speci- proprietary media, 1470 Cestodes, 2582 mens, 1140 RPMI 1640 medium, 1470 alveolar hydatid disease (Echinococcus commercially available reagents for, susceptibility profiles, 1468, 1469 multilocularis), 2588 1464 traditional, 1465–1466 characteristics, 2582, 2583 description of genus, 1084 transport media and collection swabs, coenurosis (Taenia multiceps or T. serialis), diagnostic tests for, 1112 1469–1490 2588 direct examination, 1140–1142 virology, 1463, 1465–1469 cysticercosis (Taenia crassiceps), 2588 enzyme immunoassays (EIAs), 1142, Cellobiose arginine lysine (CAL) agar, cysticercosis (Taenia solium), 2587–2588 1144–1145 345–346 cystic hydatid disease (Echinococcus granu- epidemiology, 1138–1139 Cellular fatty acid analysis, 293 losus), 2588 epidemiology and clinical diseases associ- Cellulitis, 325 Diphyllobothrium latum, 2582–2584 ated with, 1110 Cellulomonadaceae family helminth recovery and identification, 2423 evaluation, interpretation, and reporting of Cellulomonas genus, 490 Hymenolepis nana, 2586–2587 results, 1145 identification, 512 larval, infecting human host, 2587–2588 identification, 1144 Oerskovia genus, 490, 492 sparganosis (Spirometra mansonoides), 2588 isolation procedures, 1142–1144 Cellulomonas genus Taenia saginata, 2584–2585 microimmunofluorescence test, 1144 description, 490 Taenia solium, 2585–2586 nucleic acid detection, 1140–1142 identification, 512 Cetrimide agar, non-uSP, 346 serologic tests, 1144–1145 Cellulosimicrobium genus Cetrimide agar, uSP, 346 taxonomy, 1137–1138 description, 492 Cetylpuridium chloride-sodium chloride typing systems, 1144 identification, 513 (CPC-NaCl), 335 Chlamydiae, 289 Cell wall composition, 293–294 Chaetomium genus, 2245 Chlamydia pneumoniae Center for Applied Microbiology and Chaetothyriales order clinical significance, 1139 Research, 1728 Anthopsis genus, 2240 collection, transport, and storage of speci- Centers for Disease Control and Prevention Arthrocladium genus, 2241 mens, 1140 (CDC), 5, 139, 213, 459, 460, 559, Cladophialophora genus, 2241 epidemiology, 1139 760, 971, 1242, 1677, 1926, 2389 Cyphellophora genus, 2241 nucleic acid detection, 1142 biothreat agents, 243–244 Exophiala genus, 2241 serologic tests, 1144 Chlamydia trachomatis, 1138 Fonsecaea genus, 2241 taxonomy, 1137, 1138 decontamination of instruments for prion Knufia genus, 2241 Chlamydia psittaci diseases, 235 overview of genera in, 2235–2236 clinical significance, 1139 disease surveillance, 156 phaeohyphomycosis, 2247, 2248, 2249 collection, transport, and storage of speci- hantaviruses, 1713 Phialophora genus, 2242 mens, 1140 Infectious Diseases Pathology Branch of, Rhinocladiella genus, 2242 cytological testing, 1142 1728 taxonomy and description, 2240–2242 epidemiology, 1139 malaria, 2438–2440 typing systems, 2253 nucleic acid detection, 1142 penicillin breakpoints, 1349 Veronaea genus, 2242 taxonomy, 1137–1138 Tick-Borne Rickettsial Disease Case Chagas, Carlos, 2087 Chlamydia trachomatis, 2620 Report, 1174 Chagas’ disease antigen detection, 1142 Centers for Medicare and Medicaid Services commercially available kits for diagnosis, 2392 antimicrobial susceptibilities, 1145 (CMS), 5, 114, 115, 142 Trypanosoma cruzi, 2622 cell culture, 1143–1144

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characteristics of commercial amplified Chromobacterium violaceum Cladophialophora bantiana, laboratory-acquired assays for, 1141 antimicrobial susceptibility, 665 infection, 215 clinical significance, 1138–1139 biochemical reactions of, 664 Cladophialophora carrionii, morphology by collection, transport, and storage of speci- direct examination, 661 direct examination, 2039 mens, 1140 epidemiology and transmission, 658 Cladorrhinum genus, 2246, 2248 detection of, 322 identification of, 663 Cladosporium genus, 2239–2240, 2248 epidemiology, 1138–1139 isolation procedures, 661 Clarithromycin, 1212–1214 identification, 1144 taxonomy, 657 Classification, 292 immunofluorescence detection of, 1465 Chromoblastomycosis Clavulanic acid, 1207–1208 laboratory-acquired infection, 216 antifungal susceptibilities, 2254 Cleaning, 225 nucleic acid detection, 1140–1142 clinical significance, 2250 approach to, 226–227 point-of-care tests (POCTs), 1142 epidemiology and transmission, 2246–2247 importance of, 227 reagents for detection, 1464 in vivo in animal models, 2254 laboratory, 236–239 serologic tests, 1144–1145 microscopy, 2251 Spaulding classification, 227 taxonomy, 1137–1138 Chromogenic Listeria agar, 348 Cleavage-invader technology, 88–89, 90 Chlamydophila psittaci, laboratory-acquired Chromosomal abnormalities, azole resistance, Climate change, mycotoxins and, 2284 infection, 216 2340 Clindamycin, 1215–1216 Chloramphenicol Chronic aspiration syndrome, rapidly growing activity against Clostridium spp., 987 acetyltransferases, 1259 mycobacteria, 616–617 Bacteroides spp., 1384 adverse effects, 1225 Chronic lung infection, rapidly growing detection of inducible resistance in staphy- decreased accumulation of, 1259–1260 mycobacteria, 616 lococci and streptococci, 1326–1327 mechanism of action, 1224 Chronic wasting disease (CWD), 1923 inducible resistance, 1305 pharmacology, 1224 public health concern, 1925 Clinical and Laboratory Standards Institute resistance, 1259–1260 See also Prion diseases (CLSI), 760, 1037, 1316, 1348, 1377, spectrum of activity, 1224 Chronic wound infections, Pseudomonas, 789 1378, 1424 Chloramphenicol acetyltransferases (CATs), Chryseobacterium Bartonella species, 900 1244 characteristics of, 843 reference standards, 1284 Chlorine dioxide identification, 832, 844–845 susceptibility recommendations, 1278 disinfection with, 238 MALDI-TOF mass spectrometry, 833 susceptibility testing methods, 955 Chloroquine, mechanism of resistance, 2670, taxonomy, 829 Clinical Laboratory Improvement Act of 1967 2671 Chrysosporium (CLIA ’67), 5, 6 Chocolate agar, 346 clinical significance, 2152 Clinical Laboratory Improvement Chocolate tellurite agar, 346 hyphomycetes, 2149 Amendments, 116, 1348, 1515 Cholera medium base with tellurite and Cidofovir Clinical microbiology laboratory, 72 blood, 346 against herpesviruses, 1952 automated specimen processing, 76–77 Cholera medium TCBS (thiosulfate citrate cytomegalovirus resistance to, 1788 automation, history of, 76 bile salt sucrose), 346 drug interactions, 1953 bacteriological media, 341–359 Chopped meat broth, 346 herpes viruses, 1962–1964 batch vs. immediate testing, 74–75 Christensen agar, 346 human adenovirus (HAdV), 1840–1841 criteria for evaluation and selection of Christensen’s urea agar, mycology, 2030 human herpesvirus 6 (HHV-6), 1817, 1819 automation system, 82–83 CHROMagar, mycology, 2030 human herpesvirus 7 (HHV-7), 1820 current systems for automation, 76–83 CHROMagar Acinetobacter, 346 mechanism of resistance, 1963 digital imaging, 80 CHROMagar COL–APSE, 346 pharmacology, 1953 geography of, 72–73 CHROMagar CTx, 346 spectrum of activity, 1953 infectious disease testing in, 73 CHROMagar ECC, 346 Ciliates, 2498 limitations of automated system, 80, 82 CHROMagar E. coli, 346 Neobalantidium coli, 2516–2518 location of testing, 73 CHROMagar ESBL, 346 Cimex lectularius (bed bugs), 2623 molecular automation, 76 CHROMagar KPC, 346 Cinchona alkaloids organism banking and storage, 148 CHROMagar Listeria, 346 adverse effects, 2654 preanalytical microbiology, 73–74 CHROMagar MRSA, 346 mechanism of action, 2654 role in infection prevention, 145–151 CHROMagar O157, 346 pharmacokinetics, 2654 role of process improvement, 75–76 CHROMagar Orientation, 347 spectrum of activity, 2654 screening environmental sources, 150 CHROMagar Pseudomonas, 347 Cionorchis sinensis screening patients and health care workers, CHROMagar Salmonella, 347 eggs of, 2599 149 CHROMagar Salmonella Plus, 347 life cycles of, 2595 staffing models, 74 CHROMagar STEC, 347 Citrinin staff training level, 74 CHROMagar StrepB, 347 classification and biosynthesis of, 2281 surveillance cultures of patient, hospital CHROMagar Vibrio, 347 common food substrates, 2282 personnel, and environment, 148–150 CHROMagar Y. enterocolitica, 347 genetic structure, 2280 total laboratory automation, 78, 80 chromID candida agar, mycology, 2030 pathological effects and toxicological refer- workflow in, 74–76 chromID CARBA agar, 347 ence values, 2283 Clinical Microbiology Procedures Handbook chromID C. difficile, 347 structure of, 2279 (4th ed.), 302 chromID CPS, 347 See also Mycotoxins Clinical resistance, 2334 chromID ESBL, 347 Citrobacter genus, 724 Clofazimine, 1401 chromID MRSA, 347 biochemical characterization of, 732 Clonality, factors impacting, 184–185 chromID P. aeruginosa, 347 epidemiology, transmission and clinical Clostridia class, taxonomy and description, chromID Salmonella, 347 significance, 730 940–941 chromID S. aureus, 347 identification, 736 Clostridial agar, 348 chromID Strepto B, 347 nomenclature and source of species, 726 Clostridial myonecrosis, 972–973 chromID Vibrio, 347 See also Enterobacterales order Clostridioides difficile, 287, 970, 922 chromID VRE, 347–348 CLABSI (central line-associated bloodstream activities of drugs against, 987 Chromobacterium spp. infections) antibiotic-associated diarrhea (AAD), 972 clinical significance, 658 interpretive criteria for, 32 antigen detection of GDH enzyme, 978 epidemiology and transmission, 657 Cladophialophora genus, 2241, 2247, 2248, 2249 characteristics of, 984

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Clostridioides difficile (continued) Clostridium sordellii Comamonas, 808 common tests for diagnosis of disease, 979 activities of drugs against, 987 antimicrobial susceptibility, 820 decontamination, 211 extracellular toxins of, 974 characteristics of, 818 infection (CDI), 971–972 gynecologic infections, 973 clinical significance, 811 isolation and identification of, 981–982 Clostridium tetani, 970 description of, 808 methods for detection in clinical samples, characteristics of, 984 epidemiology and transmission, 808 978–980 suspected infection, 980–981 identification, 818–819 methods to detect toxins, 979 Coagulase mannitol agar, 348 typing systems, 819 nucleic acid amplification methods, 978–979 Coagulase test, 332 Combination assays, 53 PCR ribotyping, 173 COBA (colistin oxolinic acid blood agar), Committee for Clinical and Laboratory resistance patterns of, 1386 348 Standards (CLSI), 2351–2352 suspected CDI, 978 Cobicistat broth microdilution guidelines for molds, testing algorithms for, 980 drug interactions, 1943 2364–2365 toxin immunoassays for diagnosis of CDI, pharmacology, 1943 broth microdilution guidelines for yeasts, 979–980 Coccidioides spp. 2355–2357 typing of, 985–986 antibody detection, 2041 Community-acquired respiratory distress See also Clostridium genus antigen detection, 2047, 2195 syndrome (CARDS), 1118 Clostridium genus, 287 antimicrobial susceptibilities, 2200, 2201 Competency assessment, 209 activities of drugs against, 987 biosafety, 2196 Compliance, 7–13 antimicrobial susceptibilities, 986 clinical significance, 2193 competency assessment, 11–12 botulism, 974–975 clinical specimens, 2194 complaint and error investigation, 12–13 carbohydrate fermentation, 983 coccidioidomycosis, 2192, 2193, 2196, plan-do-check-act (PDCA) cycle, 13 C. difficile infection, 971–972 2199–2200 quality assurance (QA), 9–13 characteristics of commonly encountered description of, 2190 quality control (QC), 8–9 clostridia, 984–985 epidemiology and transmission, 2192 quality management, 7–8 characteristics of species, 969 evaluation, interpretation, and reporting of training, 11 clinical microbiology of clostridial diseases, results, 2202 Computerized expert systems, 1309 976–981 identification, 2197–2198 Confirmatory tests, 1281 clinical significance, 969, 970–976 microscopy, 2194 Congenital rubella syndrome (CRS), 1561 clostridial bacteremia, 970–971 mycelial phase of, 2190 Congenital syphilis description of, 968, 970 nucleic acid detection, 2196 clinical and laboratory criteria for diagno- enteric infections, 971 serologic tests, 2199–2200 sis, 1088 epidemiology and transmission, 970 spherule and endospores, 2190 tests for, 1102 evaluation, interpretation, and reporting of taxonomy, 2188 Congenital Zika syndrome (CZS), 1694 results, 986, 988 typing systems, 2198–2199 Congo red acid morpholinepropanesulfonic histotoxic clostridial skin and soft tissue Coccidioides immitis acid pigmentation (CRAMP) agar, infections, 972–974 H&E stain, 2046 348 identification of clostridial species, 982–985 laboratory-acquired infection, 215 Congo red BHI agarose medium, 348 isolation procedures, 981–982 morphology by direct examination, 2038 Conidiobolus genus MALDI-TOF MS identification, 984, 988 Coccidioides posadasii antifungal susceptibilities, 2179 serologic tests, 986 laboratory-acquired infection, 215 identification, 2178–2179 taxonomy, 968 morphology by direct examination, 2038 microscopy of C. coronatus, 2179 tetanus, 975–976 Cockroaches, arthropods as scalars, Coniochaeta typing systems, 985–986 2630–2631 clinical significance, 2151 See also Clostridioides difficile Coelomycetes hyphomycetes, 2147 Clostridium botulinum (botulism), 970 clinical significance, 2152 Conjunctivitis, human adenovirus (HAdV), biothreat agent, 247 description of, 2149, 2151 1834, 1835 suspected infection, 980–981 key phenotypic features of, 2140 Contamination control, laboratory practice, Clostridium difficile Ribotyping Network, 985 Coenurosis, Taenia multiceps or T. serialis, 112–113 Clostridium perfringens, 970 2582, 2588 Cooked meat medium, 348 activities of drugs against, 987 Cokermyces genus Coppe Labs, human herpesvirus 6 (HHV-6) on blood agar, 977 identification, 2172 testing, 1818 characteristics of, 984 unbranched sporangiophores, 2173 Coriobacteriia class enteritis necroticans, 971 COLA (Commission of Office Laboratory clinical significance, 945–946 extracellular toxins of, 973 Accreditation), 6 taxonomy and description, 939–940 food poisoning, 971 Colistin Corneal infections, rapidly growing mycobac- resistance patterns of, 1386–1387 screen tests detecting resistance among teria, 617 suspected foodborne illness, 976–978 Gram-negative bacilii, 1338–1339 Cornmeal agar with dextrose, mycology, 2030 traumatic gas gangrene due to, 972–973 susceptibility testing for Pseudomonas, 799 Cornmeal agar with Tween 80, mycology, Clostridium ramosum Colistin (polymyxin E) resistance, 1257–1259 2030–2031 activities of drugs against, 987 College of American Pathologists (CAP), 6, Cornybacterium spp., susceptibility testing, characteristics of, 984 114, 116, 1743 1362–1363 Gram stain of, 976, 977 Collinsella spp. Coronaviridae family, 1606 Clostridium ramosum, C. innocuum, biochemical characteristics of, 953 Coronavirinae subfamily, 1606 C. clostridioforme (RIC group), 1387 clinical significance, 945–946 Coronaviruses (CoVs) Clostridium septicum Colloidal carbon wet mounts, mycology, 2027 antigen detection, 1611 activities of drugs against, 987 Colonic microbiome, 258–260 clinical significance, 1610–1611 on blood agar, 977 See also Gastrointestinal microbiome collection, transport, and storage of speci- characteristics of, 984 Colorimetric microtiter plate (CMP) systems, mens, 1611 extracellular toxins of, 974 postamplification analysis, 101, 103 commercial assays incorporating detection Gram stain of, 977 Colorimetric redox (reduction/oxidation) of, 1615–1616 spontaneous, nontraumatic gas gangrene methods, 1409 description, 1606–1608 due to, 973 Columbia blood agar, 348 detection and identification methods, suspected neutropenic enterocolitis, 980 Columbia CNA agar, 348 1473

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detection frequency by month and age C. singulare, 509 collection, transport, and storage of speci- band, 1609 C. sputi, 509 mens, 1182 direct detection, 1611–1612, 1617 C. stationis, 509 complement fixation test, 1184 discovery of, 1607–1608 C. striatum, 502, 509 description of agent, 1180 electron micrograph, 1607 C. sundsvallense, 509 diagnostic tests for, 1112 epidemiology and transmission, 1608–1610 C. thomssenii, 509 direct examination, 1182 evaluation, interpretation, and reporting of C. timonense, 509 enzyme-linked immunosorbent assays, 1184 results, 1618 C. tuberculostericum, 510 epidemiology and clinical diseases associ- isolation procedures, 1617 C. tuscaniense, 510 ated with, 1110 MERS-CoV detection, 1610, 1617, 1618 C. ulcerans, 510 epidemiology and transmission, 1180–1181 microscopy, 1611 C. urealyticum, 510 evaluation, interpretation, and reporting of nucleic acid detection, 1611–1612, 1617 C. ureicelerivorans, 510 results, 1185–1186 origin, 1606–1607 C. xerosis, 510 19F-fluorodeoxyglucose positron emission phylogenetic relationships among members, description, 489–490 tomography/computed tomography, 1607 diphtheria toxin testing, 504–505 1182, 1183 real-time PCR assays, 1612, 1613–1614 epidemiology and transmission, 493 indirect fluorescent antibody (IFA) tests, SARS-CoV detection, 1610, 1617, 1618 identification, 501–510 1184 serologic tests, 1617–1618 identification of medically relevant species, isolation procedures, 1182–1184 structure of, 1606 498–499 laboratory-acquired infection, 215–216 taxonomy, 1606 MALDI-TOF MS systems, 497, 499 microscopy, 1182 Corticicoccus genus, 368, 377 morphologic characteristics, 528 nucleic acid detection, 1182 Corynebacteriaceae family sequence-based identification, 499–500 scanning electron micrograph of, 1181 Corynebacterium genus, 489–490, 501–510 testing conditions, 1351 serologic tests, 1184 identification, 501–511 whole-genome sequencing as identification special considerations, 1186 Turicella genus, 401, 510–511 tool, 500–501 taxonomy, 1180 Corynebacterium genus See also Coryneform bacteria typing systems, 1184 biochemical testing, 496–497 Corynebacterium diphtheriae CPC (cetylpyridinium chloride), digestion C. accolens, 501 algorithm for processing, 496 and decontamination method, 563, C. afermentans subsp. afermentans, 501 collection, transport, and storage of speci- 571–572 C. afermentans subsp. lipophilum, 501 mens, 494 CRE, media for detection of, 338 C. amycolatum, 501, 502 evaluation, 515 Creutzfeldt-jakob disease (CjD), 1923 C. appendicis, 501 isolation procedures, 494–495 clinical significance, 1926 C. aquatimens, 501, 503 Corynebacterium pseudotuberculosis iatrogenic CjD (iCjD), 1925 C. argentoratense, 503 algorithm for processing, 496 sporadic, 1924 C. atypicum, 503 evaluation, 515 variant (vCjD), 1924, 1925 C. aurimucosum, 503 isolation procedures, 495 See also Prion diseases C. auris, 503 Corynebacterium ulcerans CRISPR (clustered regularly interspaced short C. auriscanis, 503 algorithm for processing, 496 palindromic repeats) analysis, method, C. bovis, 503 evaluation, 515 176 C. canis, 503 isolation procedures, 494–495 Crohn’s disease, 754–755 C. confusum, 503 Coryneform bacteria Cronobacter genus, 724 C. coyleae, 503–504 antimicrobial susceptibilities, 514 differentiation of Cedecea, 734 CDC Group F-1 bacteria, 504 clinical significance, 493–494 epidemiology, transmission, and clinical C. diphtheriae, 502, 504 collection, transport, and storage of speci- significance, 729 C. durum, 505 mens, 494 identification, 735–736 C. falsenii, 505 description of genera within families, nomenclature and source of species, 726 C. freiburgense, 505 489–493 See also Enterobacterales order C. freneyi, 505 direct examination, 494 Crustacea, 2621, 2638 C. glucuronolyticum, 505 disease associations in humans, 489 Cryptococcus spp. C. hansenii, 505 epidemiology and transmission, 493 antibody detection, 2041 C. imitans, 505–506 evaluation, interpretation, and reporting of antigen detection, 2047, 2071 C. jeikeium, 506 results, 514–515 clinical significance, 2066 C. kroppenstedtii, 506 genus and species assignment, 495–496 cultural and biochemical characteristics C. kutscheri, 506 Gram stain morphologies, 491 of, 2061 classification, 526 identification, 495–497, 499–501, 501–514 description, 2059 clinical significance, 493–494 identification of Corynebacterium species, epidemiology and transmission, 2065 C. lipophiloflavum, 506 498–499 (1,3)-b-d-glucan detection, 2048 C. lowii, 506 identification of medically relevant, 500 morphology by direct examination, 2038 C. macginleyi, 507 isolation procedures, 494–495 taxonomy and nomenclature, 2058 C. massiliense, 507 serologic tests, 514 typing systems, 2076–2077 C. matruchotii, 507 susceptibility testing, 1362–1363 See also Yeasts C. minutissimum, 507 taxonomy, 488–489 Cryptococcus neoformans C. mucifaciens, 502, 507 testing conditions, 1351 antifungal susceptibilities, 2068 C. oculi, 507 typing systems, 514 on cornmeal agar, 2063 collection, transport, and storage of speci- Cowpox virus (CPxV), epidemiology, cultural and biochemical characteristics, mens, 494 1892 2061 C. pilbarense, 507–508 Coxiella genus, taxonomy, 1180 Diff-Quik stain, 2045 C. propinquum, 508 Coxiella burnetii Gram stain, 2042, 2043 C. pseudodiphtheriticum, 508 acute Q fever, 1185 India ink preparation, 2045, 2063 C. pseudotuberculosis, 508 antigen detection, 1182 isolation procedures, 2072 C. pyruviciproducens, 508 antimicrobial susceptibility, 1185 Cryptosporidium genus, 2536 C. resistens, 508 biothreat agent, 252 anthroponotic vs. zoonotic transmission, C. riegelii, 508 chronic Q fever, 1185 2538–2539 C. simulans, 509 clinical significance, 1181–1182 antigen detection, 2540–2541

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Cryptosporidium genus (continued) Cutaneous specimens Cystoisospora belli, 2526 C. hominis oocysts and Giardia duodenalis collection and transport, 2017 clinical significance, 2529–2530 cysts, 2542 processing and culture guidelines, 2021 direct examination, 2530–2531 classification, 2383 virus detection methods, 1447 epidemiology, transmission, and preven- clinical significance, 2539–2540 Cutaneous ulcers tion, 2528–2529 collection, transport, and storage of speci- parasites, 2390 evaluation, interpretation, and reporting of mens, 2540 specimen preparation and procedures, results, 2533 commercial enteric panel assays for DNA 2394 life cycle of, 2526 detection, 2543 Cutaneous warts, human papillomavirus line drawings of, 2527 commercial immunochromatography assays (HPV), 1851 microscopy, 2530–2531 for antigen detection, 2543 Cutibacterium spp. nucleic acid detection, 2531 commercial immunofluorescence assays for biochemical characteristics of, 952 serologic tests, 2531–2532 microscopy, 2541 clinical significance, 944–945 stain demonstrating oocysts, 2527 commercially available kits for detection, resistance patterns of, 1388–1389 structural data for, 2529 2391 Cyclopiazonic acid treatment, 2532 description of agent, 2536–2537 classification and biosynthesis of, 2281 Cystoisospora natalensis, 2526 detection in humans, 2381 common food substrates, 2282 life cycle of, 2527 direct examination, 2540–2541 genetic structure, 2280 structural data for, 2529 epidemiology, transmission, and preven- pathological effects and toxicological refer- Cytomegalovirus (CMV), 1962 tion, 2538–2539 ence values, 2283 antigen detection, 1776–1778 evaluation, interpretation, and reporting of structure of, 2279 antiviral drug resistance, 1964–1965 results, 2544 See also Mycotoxins antiviral susceptibility testing, 1787–1788 foodborne transmission, 2539 Cycloserine (CS), 1401 cell cultures, 1782 isolation procedures, 2542 Cycloserine cefoxitin egg yolk fructose agar, clinical significance, 1771–1772 life cycle of, 2537 348 collection, transport, and storage of speci- microscopy, 2540 Cyclospora genus mens, 1772–1776 oocysts of C. hominus, C. muris, Cyclospora classification, 2383 commercial immunoassay systems for, 1784 cayetanensis, and Cystoisospora belli, detection in humans, 2381 conventional tube culture, 1782 2541 Cyclospora cayetanensis, 2526 description of agent, 1770 PCR detection, 2541 clinical significance, 2530 detection and identification methods, 1473 prevention, 2539 culture, 2531 direct examination, 1776–1782 susceptible populations, 2538 epidemiology, transmission, and preven- enzyme immunoassays, 1783, 1785 taxonomy, 2536 tion, 2529 epidemiology and transmission, 1770–1771 treatment, 2543–2544 evaluation, interpretation, and reporting of evaluation, interpretation, and reporting of typing systems, 2541–2542 results, 2533 results, 1788–1790 waterborne transmission, 2539 laboratory techniques, 161 fetus and newborn infant, 1771 Culture, mycobacteria, 565–568 life cycle of, 2527–2528 gene targets for antiviral resistance, 1989, Culture-based methods line drawings of oocysts, 2527 1990 automated blood culture systems, 34 microscopy, 2530–2531 histopathologic testing, 1776 BacT/ALERT, 34, 35 serologic tests, 2531–2532 IgG avidity assay, 1785–1786 Bactec 9000 Series, 35 stain demonstrating oocysts, 2527 IgM antibody measurements, 1785 manual blood culture systems, 33–34 structural data for, 2529 immunocompetent host, 1771 pediatric blood culture bottles, 36 treatment, 2532 immunocompromised host, 1771–1772 VersaTREK blood culture system, 36 Cyphellophora genus, 2241 immunofluorescence assays, 1785 Culture media Cysteine albumin broth, 348 immunologic assays for CMV-specific im- bacteriological media, 341–359 Cystic echinococcosis, commercially available mune monitoring, 1787 commercial sources for chromogenic agar kits for diagnosis, 2392 isolation procedures, 1782–1783 media for bacteria, 340–341 Cysticercosis laboratory methods for diagnosis and moni- composition of media, 339 commercially available kits for diagnosis, toring infections, 1773–1774 detection of emerging antibiotic-resistant 2392 measurement of CMV-specific cell-mediat- pathogens, 338 Taenia crassiceps, 2582, 2588 ed immunity, 1786–1787 preparation of media, 339, 341 Cystic fibrosis, rapidly growing mycobacteria, mechanisms and mutations of antiviral drug Cunninghamellaceae family 616 resistance, 1963 genus Cunninghamella, 2175 Cystic hydatid disease, Echinococcus granulo- nucleic acid detection, 1778–1782 human mucormycosis, 2164 sus, 2588 PCR molecular assays for qualitative and spherical sporangiospore, 2176 Cystine heart agar, 348 quantitative detection, 1781 Cupriavidus Cystine tellurite blood agar, 348 prognosis, 110 clinical significance, 811 Cystine tryptic agar, 348 serologic tests, 1783–1787 description of, 808 Cystic fibrosis (CF), 788 specimens for direct detection, 1774–1775 epidemiology and transmission, 808 colony morphologies of P. aeruginosa from specimens for measurement of cell- identification of, 816–817 CF sputum, 789 mediated immunity, 1776 species, 807 endogenous vs. exogenous infection, 788 specimens for serologic testing, 1776 Curtobacterium genus epidemiological considerations of patients specimens for virus isolation, 1775–1776 description, 492 with, 788 spin amplification shell vial assay, 1782–1783 identification, 513 P. aeruginosa infection in patients with, taxonomy, 1770 Curvularia genus, 2244, 2245, 2250 788–789 treatment and prevention, 1772 morphology by direct examination, 2040 patient exposure to inanimate reservoirs, Czapek-Dox agar, mycology, 2031 Curvularia geniculata, microscopy of grains, 788 2267 specimens from patients with, 324 Cutaneotrichosporon spp. susceptibility of P. aeruginosa CF isolates, Daclatasvir antifungal susceptibilities, 2068 799–800 drug interactions, 1949 description, 2064 Cystoisospora genus HCV therapy, 1947 white piedra, 2230 classification, 2383 mechanism of resistance, 1971, 1973 Cutaneous anthrax, 458, 460, 461, 462 detection in humans, 2381 pharmacology, 1949

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Dalbavancin, 1218–1220 Arthroderma spp., 2227 Didanosine lipoglycopeptide resistance, 1262 characteristics of clinically isolated, drug interactions, 1940 D’Antoni’s iodine, parasitology, 2409 2209–2215 HIV therapy, 1938 Dangerous Goods Regulations (DGR), 1457 clinical significance, 2216–2217 pharmacology, 1940 Daptomycin, 1218–1220 collection, transport, and storage of speci- Dientamoeba genus resistance, 1260–1261 mens, 2217–2218 classification, 2382 as resistance target, 1426 description of etiologic agents, 2222–2227 detection in humans, 2381 Dark-field illumination, 21 direct examination, 2218–2219 Dientamoeba fragilis Darunavir epidemiology and transmission, 2216 clinical significance, 2512 drug interactions, 1943 evaluation, interpretation, and reporting culture, 2512 HIV therapy, 1939 laboratory results, 2227 description of agent, 2511–2512 mechanism of resistance, 1967 grouping on basis of host and habitat, direct detection, 2512 pharmacology, 1943 2216 epidemiology, transmission, and preven- Dasabuvir hair invasion by, 2219 tion, 2512 drug interactions, 1949 identification, 2220–2222 evaluation, interpretation and reporting of HCV therapy, 1947 isolation procedures, 2219–2220 results, 2513 mechanism of resistance, 1970, 1971 laboratory testing of specimens, 2218–2220 flagellate, 2507 pharmacology, 1949 Lophophyton gallinae, 2226 key features of trophozoites and cysts of, Dassie bacillus, 579 morphology by direct examination, 2039 2509 Databases for microbiologists, 290 Nannizzia spp., 2226 microscopy, 2512 DCLS agar, Hajna, 348 nucleic acid detection, 2220 taxonomy, 2511 Decarboxylase tests, 332 Paraphyton spp., 2226 treatment, 2512–2513 Decontamination, 225 procedures for phenotypic identification trophozoites of, 2513 DEET (diethyltoluamide), 2622 of, 2226 Dietzia genus Delafield’s hematoxylin stain, parasitology, 2411 strain typing system, 2227 classification, 526 Delamanid, 1401 taxonomy, 2208, 2216 clinical significance, 534, 537 Delftia, 808 See also Superficial mycoses description, 527 antimicrobial susceptibility, 820 Desmospora genus morphologic characteristics, 528 characteristics of, 818 classification, 526 recovered from human specimens, 535 clinical significance, 811 description, 527 See also Actinomycetes description of, 808 morphologic characteristics, 528 Diethylcarbamazine (DEC) epidemiology and transmission, 808 recovered from human specimens, 535 adverse effects, 2651 identification, 818–819 See also Actinomycetes major indications for, 2651 typing systems, 819 Desulfovibrio genus, 998 mechanism of action, 2651 Deltapolyomavirus, 1863, 1864 characteristics of, 997 pharmacokinetics, 2651 Dematiaceous fungi, morphology by direct clinical importance, 1003 spectrum of activity, 2651 examination, 2039 identification, 1005–1006 See also Anthelmintic agents Dengue virus, commercial diagnostic tests, phenotypic characteristics of, 1012 Differential agar for group D streptococci, 349 1690 Detection methods, viruses, 1473–1475 Diff-Quik, fungi detection, 2036 Density gradient media, 1462 Detection of antibacterial drug resistance Digestion-decontamination methods, Deoxycholate agar, 348 aminoglycosides, 1426 562–563 Deoxycholate citrate agar, 348 anaerobic bacteria, 1426 CPC method, 571–572 Deoxycholate citrate agar, Hynes, 348 beta-lactamases in Gram-negative bacteria, NALC-NaOH method, 570–571 Deoxycholate citrate lactose sucrose (DCLS) 1424 oxalic acid method, 571 agar, 349 beta-lactam-resistant pneumococci, 1426 sodium hydroxide method, 571 Department of Health and Human Services ceftriaxone-resistant Neisseria gonorrhoeae, sulfuric acid method, 572 (HHS), Laboratory Response Network 1426 Digital PCR (polymerase chain reaction), (LRN), 243–245 daptomycin, 1426 95–96 Dermabacter genus FDA-cleared molecular assays for, 1423, Diloxanide furoate description, 492 1425, 1427 adverse effects, 2658 identification, 502, 512 fluoroquinolones, 1426 mechanism of action, 2658 Dermabacteraceae family linezolid, 1426–1427 pharmacokinetics, 2658 description, 491–492 macrolides, 1427 spectrum of activity, 2658 identification, 512 methicillin-resistant Staphylococcus aureus Dilution testing Dermacoccaceae family (MRSA), 1420, 1421–1422 agar method, 1290–1291 clinical significance, 378–379 mupirocin, 1427 batch and lot quality control, 1292 description of, 374 mycobacteria, 1427 broth macrodilution (tube) method, epidemiology and transmission, 377 polymyxins, 1427 1289–1290 identification, 385–386 targets of PCR-based assays for MRSA, broth microdilution method, 1286–1289 key tests for identification, 375 1422 frequency of testing, 1292–1293 taxonomy of, 368 technology, 1420–1421 MIC ranges, 1292 See also Catalase-positive cocci trimethoprim, 1427 quality control for, 1291–1293 Dermatophilus genus vancomycin-resistant enterococci, 1422, strain selection, 1292 classification, 526 1424 Dimorphic fungi, laboratory-acquired infec- clinical significance, 534 Diabetic foot infections, Pseudomonas, 789 tion, 215 description, 527 Dialister genus, 996 Dimorphic fungi causing systemic mycoses microscopic morphology, 532 characteristics of, 997 antigen detection, 2195 morphologic characteristics, 528 clinical importance, 1002 antimicrobial susceptibilities, 2200 recovered from human specimens, 535 Diaporthales order clinical significance, 2192–2193 See also Actinomycetes Diaporthe genus, 2242, 2248 collection, transport, and storage of speci- Dermatophyte test medium, mycology, 2031 overview of genera in, 2236 mens, 2193–2194 Dermatophytes phaeohyphomycosis, 2248 description of agents, 2188–2191 anatomic specificity, 2217 taxonomy and description, 2242 direct examination, 2194–2196 antimicrobial susceptibilities, 2227 Dicrocoeliidae family, 2592, 2601 epidemiology and transmission, 2191–2192

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Dimorphic fungi causing systemic mycoses routine response of laboratory, 159 phenotypic differentiation, 441 (continued) steps in investigation, 158, 163 See also Catalase-negative, Gram-positive evaluation, interpretation, and reporting of surveillance, 156 cocci results, 2200–2202 surveillance and investigation, 162 Dolutegravir identification, 2197–2198 Disinfectants, selection for laboratory, drug interactions, 1946 in vitro susceptibilities to antifungal agents, 211–212 HIV therapy, 1940 2201 Disinfection, 224 mechanism of resistance, 1965, 1968 isolation procedures, 2196–2197 approach to, 226–227 pharmacology, 1946 microscopy, 2194 biosafety cabinets, 237 Doxycycline nucleic acid detection, 2195–2196 chlorine dioxide, 238 Rickettsia spp., 1157 serologic tests, 2199–2200 classification of chemical disinfectants, 225 treatment of rickettsial infections, 1173 taxonomy, 2187–2188 heat surface, 230 Dracunculus medinensis, 2628 typing systems, 2198–2199 label, 225 clinical significance, 2610 Diphtheria virulence agar base, 349 laboratory, 236–239 description of agent, 2609 Diphyllobothrium latum large area, 237–238 direct examination and microscopy, 2610 characteristics of, 2583 medical and laboratory equipment, 231 epidemiology, transmission, and preven- clinical significance, 2583–2584 paraformaldehyde and formaldehyde, 238 tion, 2609–2610 collection, transport, and storage of speci- peracetic acid (PAA), 238 microscopy of, 2607 mens, 2584 principles and definitions, 224–225 serologic tests, 2610 description of agent, 2582 selection of agents, 237 taxonomy, 2609 direct examination, 2584 single-use devices, 230–231 treatment, 2610 epidemiology, transmission, and preven- Spaulding classification, 227 Dried blood spots, collection and processing tion, 2582–2583 surface, 227–230 of virus specimens, 1454 evaluation, interpretation, and reporting of uV germicidal irradiation surface, 230 Drug efflux transporters, azole resistance, results, 2584 vapor-phase hydrogen peroxide, 238 2339 taxonomy, 2582 work surfaces, 237 Drug resistance treatment, 2584 Disk diffusion methods evolution of, 2343 Diplopoda, 2638, 2639 inhibition zone diameter distributions for, principles of hepatitis C virus, 1971–1972 Diptera, 2639 1280–1281 Drug susceptibility testing (DST), 1398 arthropods as vectors, 2620–2622, 2631 susceptibility testing, 1382–1383 Drug susceptibility testing of Mycobacterium summary of, 2621 Disk diffusion testing, 1293–1295 tuberculosis complex Dipylidium caninum advantages and disadvantages, 1295 agar proportion method, 1405–1406 clinical significance, 2617 agar medium for, 1293–1294 alternative approaches, 1408–1409 description of agent, 2617 antimicrobial agent disks, 1293 antimycobacterial agents test concentra- direct examination and microscopy, 2617 antimicrobial disks, 1294 tions, 1404 epidemiology, transmission, and preven- frequency of testing, 1295–1296 critical concentrations, 1403 tion, 2617 incubation, 1294 drug resistance, 1403 microscopy, 2613 inoculation procedure, 1294 low vs. high drug concentrations, 1403 serologic tests, 2617 interpretation and reporting of results, methods of, 1404–1406 taxonomy, 2617 1294–1295 MGIT 960 System for, 1406–1408 treatment, 2617 quality control for, 1295–1296 MODS system (Microscopic Observation Direct fluorescent-antibody (DFA) testing, semiautomated instrumentation for, Drug Susceptibility), 1408–1409 reagents, 1463, 1464 1301–1302 molecular methods, 1409 Dirofilaria immitis special disk tests, 1296 service referral, 1403–1404 clinical significance, 2614 strain selection, 1295 TB features affecting DST, 1403 description of agents, 2612 zone-of-inhibition diameter ranges, 1295 TREK Sensitive MYCOTB MIC plate direct examination, 2614–2615 Dithiothreitol (Sputolysin), mycology method, 1408 epidemiology, transmission, and preven- reagent, 2026 VersaTREK, 1408 tion, 2612, 2614 DNA when to perform, 1404 microscopy, 2613, 2614–2615 acquired resistance by DNA transfer, 1244 when to report, 1404 serologic tests, 2615 quantitative methods, 106–107 Drug target modification, azole resistance, taxonomy, 2612 DNA-DNA hybridization (DDH) studies, 2336–2337 treatment, 2615 289, 295 Drug therapy, anti-HBV (hepatitis B virus), Dothideales order DNA microarrays, method, 179–180 1969 Aureobasidium genus, 2242 DNase-SISPA (sequence-independent single Dubos broth, 349 Hormonema genus, 2242 primer amplification), 274 Dulbecco’s phosphate-buffered saline (PBS), overview of genera in, 2236 DNase test agar with toluidine blue, 349 1462 phaeohyphomycosis, 2247, 2249 DNA target sequencing, genotypic identifica- Dyes, 335 taxonomy and description, 2242 tion, 63 Dysgonomonas spp. typing systems, 2253 Dobrava-Belgrade virus (DOBV), 1707, 1708 antimicrobial susceptibility, 665 Disaster preparedness, 204 Docosanol biochemical reactions of, 663 Discriminatory power, 168, 170 against herpesviruses, 1952 clinical significance, 658 Disease cluster detection, 181–182 drug interactions, 1954 direct examination, 660, 661 Disease outbreaks, 155 pharmacology, 1954 epidemiology and transmission, 658 definitions, 155–156 Dolosicoccus genus identification of, 663 detection of, 157–158 cellular morphology, 437 isolation procedures, 661 epidemic curves, 159 clinical significance, 438 taxonomy, 657 epidemiological approach, 159–160 identification, 440 D-zone test, 1326–1327 examples of, 162–164 phenotypic differentiation, 442 high-consequence pathogens, 159–160 See also Catalase-negative, Gram-positive infectious diseases, 157 cocci Ears key agencies, 156 Dolosigranulum genus infectious syndromes, 318 laboratory detection methods, 160–162 cellular morphology, 437 specimen collection and transport, 304 resource information for global, 164–165 clinical significance, 438 Eastern encephalitis virus, commercial diag- role of laboratory in, 159–162 identification, 441 nostic tests, 1692

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Ebola virus, 183 Egg yolk agar, 349 emergomycosis, 2192, 2193, 2196, 2200, 2202 animal inoculation, 1730 Ehrlichia spp. epidemiology and transmission, 2192 antigens in infected pig, 1727 antimicrobial susceptibilities, 1173 evaluation, interpretation, and reporting of clinical significance, 1725–1726 clinical significance, 1168–1169 results, 2202 diagnostic testing, 160 collection, transport, and storage of speci- identification, 2198 electron microscopy of infected liver, 1726 mens, 1169–1170 microscopy, 2194 geography and associated human diseases, description of, 1163–1164 nucleic acid detection, 2196 1723 diagnostic tests for, 1113 serologic tests, 2200 inactivation of, 2435 direct examination, 1170–1171 taxonomy, 2188 laboratory techniques, 161 E. chaffeensis ehrlichiosis, 1169 typing systems, 2199 nucleic acid amplification for detection of, E. ewingii ehrlichiosis, 1169 Emmonsia spp. 1730, 1731 E. muris eauclairensis, 1169 adiaspiromycosis, 2192, 2193, 2196 taxonomy and description, 1720 epidemiology and clinical diseases associ- antigen detection, 2195 ultrastructural characteristics of, 1728 ated with, 1110 biosafety, 2196 West African outbreak (2013–2016), 217, epidemiology and transmission, 1164, clinical significance, 2193 1719 1166–1168 clinical specimens, 2194 See also Filoviridae family evaluation, interpretation, and reporting of culture for yeast phase, 2196 Echinocandins results, 1173–1174 description of, 2191 acquired resistance, 2324 features of human and veterinary interest, epidemiology and transmission, 2192 anidulafungin, 2320, 2324–2325 1165 evaluation, interpretation, and reporting of antifungal drugs, 2340–2341 immunochemistry for antigen detection, results, 2202 biofilms, 2342 1171 identification, 2198 caspofungin, 2320, 2325 isolation procedures, 1171–1172 microscopy, 2194 clinical and microbiological resistance, laboratory confirmation, 1170–1173 nucleic acid detection, 2196 2335 microscopy, 1170–1171 typing systems, 2199 drug interactions, 2324 neighbor-joining phylogenetic tree, 1164 Empedobacter brevis epidemiology of resistance, 2341 nucleic acid detection of E. chaffeensis, characteristics of, 843 FKS mechanism of resistance, 2341, 2342 1171 identification, 845 hot spot polymorphisms, 2341–2342 serologic tests, 1172–1173 Emtricitabine mechanism of action, 2324 taxonomy, 1163 drug interactions, 1940, 1951 mechanisms of resistance, 2340–2342 treatment and prevention, 1173 HBV therapy, 1950 micafungin, 2320, 2325 See also Anaplasmataceae family HIV therapy, 1938 pharmacokinetics, 2324 Eikenella corrodens mechanism of resistance, 1965, 1967 spectrum of activity, 2320, 2324 antimicrobial susceptibility, 666 pharmacology, 1940, 1951 therapeutic drug monitoring, 2324 biochemical reactions of, 664 Encephalitis, VZV infection, 1758–1759, 1761 toxicity and adverse effects, 2324 clinical significance, 658–659 Encephalitozoon spp. Echinococcus granulosus, cystic hydatid disease, direct examination, 660, 661 antimicrobial susceptibilities, 2312 2582, 2588 epidemiology and transmission, 657 clinical significance, 2309 Echinococcus multilocularis, alveolar hydatid identification of, 663 description, 2305–2306 disease, 2582, 2588 isolation procedures, 661 detection, 2311 Echinostoma hortense, life cycles of, 2595 reporting results, 666 identification, 2312 Echinostomatidae family typing, 665 life cycle of microsporidia, 2307 clinical significance, 2601 Elbasvir serologic tests, 2312 description of agents, 2601 drug interactions, 1948 Endemic treponematoses diagnosis, 2601 HCV therapy, 1947 clinical significance, 1088 epidemiology, transmission, and preven- mechanism of resistance, 1971, 1973 epidemiology and transmission, 1085 tion, 2601 pharmacology, 1948 Endo agar, 349 geographic distribution, hosts and egg Elizabethkingia, taxonomy, 829 Endocarditis morphology of, 2593 Elizabethkingia anophelis agents of, 896–897 treatment, 2601 characteristics of, 843 anthroponotic bartonelloses, 896 Echoviruses, 1576 detection, 161 choice and use of antibiotics for, 900–901 E. coli O157:H7 MuG agar, 349 identification, 845 Endolimax genus Edwardsiella genus Elizabethkingia meningoseptica, 848, 1261 classification, 2383 epidemiology, transmission, and clinical characteristics of, 843 detection in humans, 2381 significance, 731 clinical significance, 829 Endolimax nana See also Enterobacterales order identification, 832, 845 intestinal amebae of humans, 2500 Efavirenz, 1965 MALDI-TOF mass spectrometry, 833 key features, 2499 drug interactions, 1942 Elizabethkingia miricola, identification, 845 nonpathogenic, 2504–2505 HIV therapy, 1938 Ellinghausen-McCullough-johnson-Harris Endoreticulatus spp., description, 2306 mechanism of resistance, 1965, 1967 medium, 349 Enfuvirtide pharmacology, 1942 Elvitegravir drug interactions, 1945 Efflux pumps drug interactions, 1946 HIV therapy, 1939 Pseudomonas, 796 HIV therapy, 1940 mechanism of resistance, 1968 resistance mechanism, 1245–1246 mechanism of resistance, 1965, 1968 pharmacology, 1945 Eflornithine pharmacology, 1946 Entamoeba genus adverse effects, 2661 Emarellia grisea and E. paragrisea, taxonomy classification, 2383 mechanism of action, 2661 and description, 2263 detection in humans, 2381 mechanism of resistance, 2670 Emerging infection, 183 Entamoeba coli pharmacokinetics, 2661 Emergomyces spp. intestinal amebae of humans, 2500 spectrum of activity, 2661 antigen detection, 2195 key features, 2499 Eggerthella spp. biosafety, 2196 nonpathogenic, 2504 antimicrobial susceptibilities, 955 clinical significance, 2193 Entamoeba hartmanni biochemical characteristics of, 953 clinical specimens, 2194 intestinal amebae of humans, 2500 clinical significance, 946 culture for yeast phase, 2196–2197 key features, 2499 resistance patterns of, 1389 description of, 2191 nonpathogenic, 2504–2505

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Entamoeba histolytica Pseudocitrobacter genus, 730 nucleic acid detection, 422–423 antigen detection, 2502 resistance in miscellaneous, 741–742 phenotypic characteristics for identification clinical significance, 2501 resistance mediators, 737 of, 425–426 commercially available kits for detection, Serratia genus, 730 phenotypic tests for detecting resistance, 2391 taxonomy, 724–725 1317–1319 commercially available molecular amplifi- typing systems, 738 phylogenetic tree of species, 419 cation panels, 2503 Enterobacteriaceae family, 724 resistance to glycopeptides among members description of agent, 2498–2500 carbapenem resistance, 1306 of, 430 direct examination, 2501 description of genera, 725 serologic tests, 428 epidemiology, transmission, and preven- detection of ESBL-producing, 1328, 1331 taxonomy, 418 tion, 2500 detection of plasmid-mediated AmpC-type tetracycline specific resistance determinant evaluation, interpretation, and reporting of b-lactamases among, 1332–1333 in, 1256 results, 2504 ESBL-producing, 1306 typing systems, 427–48 infection, 2497 nonautomated identification system, 52 vancomycin resistance in, 1422, 1424 intestinal amebae of humans, 2500 phenotypic tests for detecting resistance, Enterocytozoon bieneusi key features of, 2499 1317–1319 antimicrobial susceptibilities, 2312 microscopy, 2501–2502 properties of genus, 776 clinical significance, 2309 nucleic acid detection techniques, reportable organisms for MALDI-TOF description, 2306 2502–2503 MS, 55 detection, 2310, 2311 serologic tests, 2503–2504 Enterobius vermicularis (pinworm or thread- life cycle of microsporidia, 2307 treatment, 2504 worm), 2559 Enterohepatic helicobacters Entamoeba polecki, intestinal amebae of adult worms of, 2556 characteristics of, 1046 humans, 2500 clinical significance, 2559–2560 clinical significance, 1048 Entecavir description of agent, 2558 epidemiology and transmission, 1047 drug interactions, 1951 direct examination, 2560–2561 hosts and disease spectra, 1045 HBV therapy, 1950 eggs of, 2553 identification, 1051 mechanism of resistance, 1969 epidemiology and transmission, 2558–2559 susceptibility testing of, 1054 pharmacology, 1951 life cycle completion time, 2558 See also Helicobacter spp. Enteric adenoviruses life cycle of, 2560 Enteromonas genus clinical features, 1659 macroscopic examination, 2561 classification, 2382 clinical significance, 1660–1661 microscopy, 2560–2561 detection in humans, 2381 description of, 1658 relative sizes of eggs, 2552 Enteromonas hominis epidemiology and transmission, 1660 taxonomy, 2558 flagellate, 2507 molecular assays for detection, 1664 transmission and life cycle, 2559 key features of trophozoites and cysts of, taxonomy of, 1656, 1657 treatment, 2561 2509 See also Gastroenteritis viruses See also Nematodes nonpathogenic flagellate, 2516 Enteric infections, Clostridium spp., 971 Enterococci Enterovirus genus, 1437 Enteritis necroticans detection of high-level aminoglycoside- Enteroviruses Clostridium perfringens, 971 resistant (HLAR), 1325–1326 affecting humans, 1577 suspected, C. perfringens type C, 978 b-lactamase testing for, 1320–1321 antiviral susceptibilities, 1585 Enterobacter genus, 724 linezolid resistance in, 1305 clinical significance, 1578–1580 differentiation of Cedecea, 734 vancomycin resistance detection in, clinical syndromes associated with, 1579 differentiation of Pantoea agglomerans, 733 1323–1324 description, 1576–1578 epidemiology, transmission, and clinical vancomycin resistance in, 1304 detection and identification methods, 1473 significance, 728–729 Enterococcosel agar, 349 direct examination, 1581–1583 identification, 735 Enterococcosel agar with vancomycin, 349 diseases and specimen selection, 1580 nomenclature and source of species, 726 Enterococcosel broth, 349 epidemiology and transmission, 1578 tetracycline specific resistance determinant Enterococcus genus, 295 evaluation, interpretation, and reporting of in, 1256 antimicrobial susceptibilities, 428–429 results, 1585 See also Enterobacterales order clinical significance, 421–422 identification, 1584 Enterobacter cloacae, 162 collection, transport, and storage of speci- isolation procedures, 1583–1584 Enterobacterales order mens, 422 nucleic acid detection, 1581–1583 antimicrobial susceptibility, 738–742 commercially available agar-based media serologic test, 1585 Citrobacter genus, 730 for isolation of vancomycin-resistant taxonomy, 1576 collection, transport, and storage of speci- enterococci (VRE), 424 typing systems, 1584–1585 mens, 732 description of, 418–420 Entomophthoromycosis Cronobacter, 729 direct examination, 422–423 antifungal susceptibilities, 2179 differentiation of unusual genera, 735, 736 epidemiology and transmission, 420–421 clinical manifestations, 2177–2178 Edwardsiella genus, 731 evaluation, interpretation, and reporting of collection, transport, and storage of speci- epidemiology, transmission, and clinical results, 429, 431 mens, 2178 significance, 725–732 health concern of VRE infections, 420–421 direct examination, 2178 Erwinia, Enterobacter, and Pantoea, 728–729 HLSR (high-level streptomycin resistance) epidemiology and transmission, 2177 evaluation, interpretation, and reporting of in, 1304–1305 evaluation, interpretation, and reporting of results, 742 identification by commercial systems, 424, results, 2179 genera and species within, 726–727 426 family Ancylistaceae, 2178–2179 Hafnia genus, 731 identification by conventional physiologi- family Basidiobolaceae, 2179 identification, 732–738 cal testing, 424 identification, 2178–2179 isolation procedures, 732 identification by MALDI-TOF MS, 426 isolation procedures, 2178 Klebsiella and Raoultella, 727–728 identification by molecular methods, nucleic acid detection, 2178 Lelliottia, Pluralibacter, and Kosakonia, 729 426–427 phenotypic identification, 2178–2179 nucleic acid-based identification, 738 isolation procedures, 423–424 serologic tests, 2179 Plesiomonas shigelloides, 731 microscopy, 422 taxonomy, 2163 Proteus, Providencia, and Morganella, molecular assays for detecting vancomycin treatment and outcome, 2178 730–731 resistance, 1423 typing systems, 2179

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Entomophthoromycotina structure of, 2279 tetracycline specific resistance determinant subphylum of kingdom Fungi, 2009, 2010 See also Mycotoxins in, 1256 taxonomy, 2163 Ertapenem, resistant breakpoint differences, typing systems, 711–713 Entry inhibitors, HIV therapy, 1939, 1945 1378 uropathogenic E. coli, 691–692 Envenomation, stinging and biting for, Erwinia genus virulence testing and identification of 2635–2637 epidemiology, transmission, and clinical EPEC, ETEC, EAEC, and EIEC, 706 Environmentally acquired resistance, azoles, significance, 728–729 Esculin azide broth, 349 2337–2338 nomenclature and source of species, 726 Esculin hydrolysis, 332, 411 Environmental Protection Agency (EPA), See also Enterobacterales order Esophageal microbiome, 258 225, 226 Erysipelothrix genus See also Gastrointestinal microbiome Enzyme Commission, 263 antimicrobial susceptibilities, 484 ESP Myco medium, 349 Enzyme immunoassays (EIAs) clinical significance, 483 Ethambutol (EMB), 1400 antibody interference, 133–134 collection, transport, and storage of speci- Ethionamide (ETH), 1402 antiviral susceptibility testing, 1988 mens, 483 Etravirine, 1965 biotin interference, 134 description of agent, 482–483 drug interactions, 1942 categorization of, 126 direct examination, 483 HIV therapy, 1938 competitive, 131 epidemiology and transmission, 483 mechanism of resistance, 1965, 1970 diagram of IgM capture, 133 evaluation, interpretation, and reporting of pharmacology, 1942 hook effect, 132–133 results, 484 Eubacterium genus measurement of IgM, 133 identification, 483–484 antimicrobial susceptibilities, 955 noncompetitive, 131, 132 isolation procedures, 483 biochemical characteristics of, 953 plate variability, 132 serologic tests, 484 clinical significance, 947 quantification of, 127 taxonomy, 482 resistance patterns of, 1389 See also Immunoassays typing systems, 484 taxonomy and description, 940 Eosin-methylene blue agar, Levine, 349 Erysipelothrix rhusiopathiae Eubacterium lenta, resistance patterns of, 1389 Eosin-methylene blue agar, modified, Holt- susceptibility testing, 1363 EuCAST. See European Committee on Harris and Teague, 349 testing conditions, 1351 Antimicrobial Susceptibility Testing Epidemics, influenza viruses, 1510–1511 Erysipelotrichia class (EuCAST) Epidemiology. See Molecular epidemiology clinical significance, 948 Eugonic agar, 349 Epidemiological cutoff values, susceptibility taxonomy and description, 941 Eugonic LT100 medium base without Tween testing, 2353–2354 Erythromycin, 1212–1214, 1230 80, 349 Epidermophyton spp. ESBLs. See Extended-spectrum b-lactams Eukaryotes anatomic specificity, 2217 Escherichia genus, 292 classification of parasitic protists, characteristics of dermatophytes and der- antigenic typing of, 711–712 2382–2384 maphytoids, 2209 antimicrobial susceptibilities, 713–715 classification of parasitic worms and arthro- description of, 2224, 2226 biochemical reactions of species, 690 pods, 2384–2387 grouping of dermatophytes on host and cefazolin as surrogate for oral cephalospo- diagram of classification, 2380 habitat, 2216 rins in urinary isolates in, 1337–1338 modern classification of, 2380–2382 taxonomy, 2208, 2216 clinical significance, 691–696 parasites of medical importance, 2379 See also Dermatophytes collection, transport, and storage of speci- protist and parasites detected in humans, Epstein-Barr virus (EBV), 1797 mens, 701–702 2381 antigen detection, 1801–1802 common media for isolation of, 704 supergroups, 2380 chronic active EBV infection, 1806 description of, 689 Eumycetoma (eumycotic mycetoma), 2261 clinical significance, 1798–1800 detecting resistance, 1316 antigen detection, 2268 collection, transport, and storage of speci- diarrheagenic E. coli, 692, 693, 696, antimicrobial susceptibilities, 2271 mens, 1800–1801 714–715 assimilation patterns, 2269–2270 commercial products for EBV diagnosis, differentiation of Shigella and, 697 clinical significance, 2265 1803 direct examination, 702 collection, transport, and storage of speci- description of agent, 1797–1798 EAEC, 695–696 mens, 2266 direct examination, 1801–1802 EIEC, 695 cultures of mycetoma-causative agents, EBV DNA load in critically ill patients, EPEC, 694–695 2264 1806 epidemiology and transmission, 689, 691 direct examination, 2266–2268 EBV DNA load in CSF, 1806 ETEC, 694 epidemiology and transmission, 2263, 2265 EBV-specific antibodies, 1803–1805 extraintestinal E. coli, 713–714 evaluation, interpretation, and reporting of epidemiology and transmission, 1798 extraintestinal pathogenic E. coli, 691 results, 2271 evaluation, interpretation, and reporting of general medium growth requirements, 703 identification, 2268–2270 results, 1805–1806 identification of, 706 in vitro susceptibilities of mycetoma-caus- future perspectives, 1806–1807 isolation procedures, 703–706 ative fungi, 2272 heterophile antibodies, 1803 laboratory-acquired infection, 216 isolation procedures, 2268 infectious mononucleosis, 1805 meningitis- and sepsis-associated E. coli, microscopy, 2266–2267 isolation, identification, and typing, 1802 692 molecular identification, 2270 microscopy, 1801 NAAT and antigen detection from non- morphological identification, 2268–2269 nasopharyngeal carcinoma, 1805 stool specimens, 711 nucleic acid detection, 2268 nucleic acid amplification techniques, 1802 next-generation sequencing (NGS)-based overview of species causing, 2262 oncogenic potential of, 1799–1800 typing, 713 serologic tests, 2270–2271 serologic tests, 1803–1805 nucleic acid amplification tests (NAATs) taxonomy and description of agents caus- taxonomy, 1797 for, 707–710 ing, 2261, 2263 transplantation, 1806 plating media for, 703–705 typing systems, 2270 Ergot alkaloids role of sequencing to differentiate, 711 European Aspergillus PCR Initiative, 2049 classification and biosynthesis of, 2281 sequencing of 16S rRNA, 271 European Centre for Disease Prevention and common food substrates, 2282 specimen enrichment for stool culture, 703 Control, 422, 725 genetic structure, 2280 STEC and EHEC, 692–694 European Commissioner for Health and Food pathological effects and toxicological refer- stool toxin testing for STEC, 705–706 Safety, 725 ence values, 2283 taxonomy, 688–689 European Committee for Standardization, 209

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European Committee on Antimicrobial morphological identification, 2268 Federal Select Agent Program, 203, 245, 875, Susceptibility Testing (EuCAST), morphology by direct examination, 1183–1184 798, 1037, 1348, 1377, 1378, 1424, 2040 select non-Tier 1 agents, 251–253 2351–2352 taxonomy and description, 2261 Tier 1 select agents, 245–250 Bartonella species, 900 Famciclovir Feeley-Gorman agar, 349 broth microdilution guidelines for molds, against herpesviruses, 1952 Feline Bartonella species, 897 2364–2365 antiviral therapy for herpes simplex virus Fetus, cytomegalovirus (CMV) infection, broth microdilution guidelines for yeasts, (HSV), 1742 1771 2355–2357 drug interactions, 1954 Fidaxomicin, 1214 reference standards, 1284 herpes viruses, 1962–1964 Filamentous fungi selecting methods, 1278 mechanism of resistance, 1963 MALDI-TOF MS identification of, 61–63 susceptibility testing methods, 955 pharmacology, 1954 preservation methods, 202, 203 European Molecular Biology Laboratory- spectrum of activity, 1954 reportable organisms for MALDI-TOF European Bioinformatics Institute, 296 Fasciolidae MS, 57 European Organization for Research and clinical significance, 2602 Filarial nematodes Treatment of Cancer (EORTC), 2050, description of agent, 2601–2602 clinical significance, 2571, 2573 2111, 2112 diagnosis, 2602 diagnosis, 2573–2574 European Society for Clinical Microbiology epidemiology, transmission, and preven- Loa loa, 2576–2577 and Infectious Diseases (ESCMID), tion, 2602 lymphatic filarial parasites, 2570–2575 114, 980, 1388, 2048 treatment, 2602 Mansonella species, 2577–2578 European Society for Clinical Virology, 114 Fasciolidae family Onchocerca volvulus, 2575–2576 Excavata supergroup clinical significance, 2601 taxonomy, 2570 eukaryotes, 2380 description of agents, 2600 treatment and prevention, 2574–2575 parasitic protists, 2382–2383 diagnosis, 2601 Filarial worms, 2570 Exiguobacterium genus epidemiology, transmission and prevention, Filariasis, commercially available kits for description, 493 2600–2601 diagnosis, 2392 identification, 513 geographic distribution, hosts and egg Fildes enrichment agar, 350 Exophiala genus, 2241, 2248, 2249 morphology of, 2593 Filoviridae family, 1719 Exophiala jeanselmei geographic distribution, hosts and histories animal inoculation, 1730 Gram stain, 2042, 2043 of, 2592 antiviral susceptibilities, 1733 in vitro susceptibility, 2272 treatment, 2601 cell culture, 1730 microscopy of grains, 2267 Fasciolopsis buski clinical significance, 1725–1726 morphology by direct examination, 2040 eggs of, 2599 collection, transport, and storage of speci- Exserohilum genus, 2244–2245, 2249 life cycles of, 2595 mens, 1727–1728 Exserohilum rostratum, 2049 Fastidious bacteria, 1348 current filoviruses and associated human Extended-spectrum b-lactams (ESBLs) Abiotrophia spp., 1360 diseases, 1723 laboratory detection of Enterobacterales Aerococcus spp., 1360–1361 description of agents, 1720 producing, 739 Aeromonas spp., 1361 direct examination, 1728–1730 media for detection of Enterobacteriaceae, 338 Bacillus spp., 1361–1362 Ebola virus antigens, 1727 resistance mediators, 737 BMD MIC testing conditions, 1350 Ebola virus hemorrhagic fever, 1726 Extracellular polysaccharide production, 411 Campylobacter spp., 1362 electron microscopy, 1728–1729 Eye(s) CLSI and EuCAST disk diffusion and epidemiology and transmission, 1720, collection and processing of virus speci- MIC testing, 1349 1723–1724 mens, 1454 Corynebacterium spp., 1362–1363 evaluation and interpretation of results, infectious syndromes, 318 disk diffusion and MIC testing conditions, 1733–1734 parasites, 2390 1351–1353 identification of virus, 1730, 1732 pathogenic fungi recovery, 2019 Erysipelothrix rhusiopathiae, 1363 isolation procedures, 1730 processing and culture guidelines, 2021 Gemella spp., 1363 nucleic acid detection, 1730, 1731 specimen collection and transport, Granulicatella spp., 1360 postmortem specimens, 1728 304–305; 2017 HACEK group, 1363–1364 safety and security, 1727 specimen for parasite detection, 2428, 2430 Haemophilus influenzae, 1355–1357 safety and security of agents, 1727 specimen preparation and procedures, 2394 Helicobacter pylori, 1364–1365 serologic diagnosis, 1732–1733 trematodes of, 2602–2603 Lactobacillus spp., 1365 shipping, 1728 Leuconostoc spp., 1365 taxonomy, 1720 Listeria monocytogenes, 1365 ultrastructural characteristics of Ebola virus, F901318 (F2G Ltd.), 2327 Micrococcus spp., 1365 1728 Facklamia genus Moraxella catarrhalis, 1366 Filoviruses antimicrobial susceptibilities, 445 Neisseria gonorrhoeae, 1357–1358 detection and identification methods, 1473 cellular morphology, 437 Neisseria meningitidis, 1358–1359 See also Filoviridae family identification, 440, 441 Pasteurella spp., 1366 Finegoldia spp. phenotypic differentiation, 442 Pediococcus spp., 1365 biochemical features, 930 See also Catalase-negative, Gram-positive potential bacterial agents of bioterrorism, flow scheme for identification of, 931 cocci 1359–1360 taxonomy, 925 Falciformispora senegalensis, 2262 Rothia mucilaginosa, 1366 Finegoldia magna assimilation patterns, 2269 streptococci other than pneumococci, antimicrobial susceptibilities, 933 cultures of, 2264, 2265 1355 changes in classification, 926 in vitro susceptibility, 2272 Streptococcus pneumoniae, 1349–1350, clinical significance, 927–928 microscopy of grains, 2267 1354–1355 epidemiology, 927 morphological identification, 2268 Vibrio spp., 1366–1367 resistance patterns of, 1390 morphology by direct examination, 2040 Fastidious Gram-negative bacteria, Firmicutes phylum, 289, 996 taxonomy and description, 2261 reportable organisms for Bacilli class, 940 Falciformispora tompkinsii MALDI-TOF MS, 56 biochemical characteristics of, 953 assimilation patterns, 2269 Fatal familial insomnia (FFI), 1923 clinical significance, 942–943, 946–948 microscopy of grains, 2267 Feces. See Stool Clostridia class, 940–941

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Erysipelotrichia class, 941 trematodes of the liver, 2600–2601 epidemiology, 874 predominant phyla in humans, 256 See also Trematodes taxonomy, 871 taxonomy and description, 940–941 Foodborne Diseases Active Surveillance Francisella philomiragia Fish tank granuloma, 1411 Network (FoodNet), 163–164, 761, characteristics of, 873 Flagellates, 2498 1028 clinical significance, 871, 875 collection, transport, and storage of Foodborne Diseases Active Surveillance epidemiology, 874 specimens, 2508 Program, 1028 taxonomy, 871 description of agents, 2508 Foodborne illnesses, outbreak, 163–164 Francisella tularensis Dientamoeba fragilis, 2511–2513 Foodborne Outbreak Online Database Tool antimicrobial susceptibilities, 879 direct examination, 2508 (FOOD Tool), 459 bioterrorism potential, 1359 epidemiology, transmission, and FoodNet, 163–164, 761, 1028 biothreat agent, 249–250 prevention, 2508 Food poisoning, Clostridium perfringens, 971 characteristics of, 873 evaluation, interpretation, and reporting of Forensic microbiology, 184 clinical significance, 871, 874–875 results, 2508 Formaldehyde, disinfection with, 238 differentiation from Gram-negative Giardia duodenalis, 2508, 2510–2511 Formalin for cell culture preservation, 1463 bacteria, 872 key features of trophozoites and cysts of, Fosamprenavir direct fluorescent antibody (DFA) staining 2509 drug interactions, 1943–1944 of, 876, 878 microscopy, 2508 HIV therapy, 1939 epidemiology and transmission, 872, 874 nonpathogenic, 2516 pharmacology, 1943 Gram stain of, 876 taxonomy, 2507 Foscarnet laboratory-acquired infection, 214 Flaviviridae family, 1640, 1685, 1686 against herpesviruses, 1952, 1962–1964 laboratory safety issues for handling Flaviviruses cytomegalovirus (CMV) resistance to, 1788 cultures, 876 characteristics of, 1686 drug interactions, 1953 testing conditions, 1350 clinical significance, 1693 Epstein-Barr virus (EBV), 1798 Free-living amebae commercial diagnostic tests, 1690–1691 human herpesvirus 6 (HHV-6), 1817, 1819 animal inoculation, 2493 genome, 1688 human herpesvirus 7 (HHV-7), 1820 antigen detection, 2491 Fleas, arthropods as vectors, 2623–2624 mechanism of resistance, 1963 clinical and laboratory diagnosis, Fletcher medium, 350 pharmacology, 1953 2490–2491 Flu. See Influenza viruses spectrum of activity, 1953 clinical significance, 2488–2490 Flubendazole. See Benzimidazoles Fosfomycin, 1230 clinical syndromes caused by, 2488 Fluconazole adverse effects, 1228 collection, handling, and storage of acquired resistance, 2321 mechanism of action, 1227 specimens, 2490 clinical breakpoints for Candida spp., pharmacology, 1227 concept of, 2486 2352 spectrum of activity, 1227–1228 description of agents, 2486–2488 clinical use, 2321 Fox, George, 288 direct examination, 2490–2491 spectrum of activity, 2320, 2321 Francisella genus epidemiology, 2488 therapeutic drug monitoring, 2321 antigen detection, 876 evaluation, interpretation, and reporting of toxicity and adverse effects, 2321 antimicrobial susceptibilities, 879 results, 2493–2494 Flucytosine characteristics of species, 873 isolation, 2491–2493 acquired resistance, 2326 clinical significance of, 874–875 nucleic acid detection, 2491 clinical use, 2326 collection, transport, and storage of speci- permanently stained preparations, 2491 drug interactions, 2326–2327 mens, 875–6 serology, 2493 mechanism of action, 2326 description of, 872 taxonomy, 2486 mechanisms of resistance, 2343 differentiation of F. tularensis from Gram- treatment, 2493 pharmacokinetics, 2326 negative bacteria, 872 Freeze-drying storage, microorganisms, spectrum of activity, 2326 direct examination, 876 200–201 therapeutic drug monitoring, 2327 epidemiology and transmission, 872, 874 Fumonisins toxicity and adverse effects, 2327 evaluation, interpretation, and reporting of classification and biosynthesis of, 2281 Fluids, specimen collection and transport, results, 879 common food substrates, 2282 305 F. hispaniensis, 875 genetic structure, 2280 Fluorescent microscope, 20–21 F. novicida, 875 pathological effects and toxicological Fluoroquinolones, 1209–1211 F. philomiragia, 875 reference values, 2283 bacterial resistance against, 1254–1256 F. tularensis, 874–875 structure of, 2279 pefloxacin as surrogate for, inSalmonella identification, 877–878 See also Mycotoxins enterica, 1338 isolation procedures, 876–877 Fungal meningitis, 163, 2048–2049 as resistance target, 1426 microscopy, 876 Fungemia targets of, 1255 nucleic acid detection, 876 diagnostic importance, 28 See also Quinolones serologic tests, 878–879 interpretation of blood culture, 31–33 Folliculitis, Pseudomonas, 789 taxonomy, 871–872 See also Laboratory detection of bacteremia Fonsecaea genus, 2241 typing systems, 878 and fungemia Fonsecaea compacta, morphology by direct Francisella halioticida Fungi examination, 2039 characteristics of, 873 antibody detection, 2037, 2041 Fonsecaea pedrosoi taxonomy, 871 antigen detection, 2041–2048 microscopy, 2252 Francisella hispaniensis characteristic morphology by direct morphology by direct examination, 2039 characteristics of, 873 examination, 2038–2040 muriform cells, 2045 clinical significance, 873, 875 classification and identification of Fontana-Masson, fungi detection, 2036 epidemiology, 874 anamorphic molds, 2011–2012 Fontana-Masson stain, mycology, 2027–2028 taxonomy, 871 classification of kingdom, 2163 Foodborne digeneans Francisella noatunensis common mycological terms, 2013–2015 life cycles of, 2595 characteristics of, 873 direct microscopic examination, 2035, trematodes of respiratory system taxonomy, 871 2037 (Paragonimus), 2598–2599 Francisella novicida fungal-specific metabolite detection, trematodes of the eyes, 2602–2603 characteristics of, 873 2049 trematodes of the intestine, 2601–2602 clinical significance, 875 (1,3)-b-d-glucan detection, 2048–2049

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Fungi (continued) drug interactions, 1953 Genetic shift, 183 identification by nucleic acid sequencing, Epstein-Barr virus (EBV), 1798 Genetic Testing Reference Material 109–110 human adenovirus (HAdV), 1840–1841 Coordination Program, CDC, 113 identification of molds, 2012 human herpesvirus 6 (HHV-6), 1817, 1819 Genital fluids identification of yeasts, 2011 human herpesvirus 7 (HHV-7), 1820 processing recommendations, 322–323 key to main groups of medically important, mechanism of resistance, 1963 specimen collection and transport, 306–307 2010 pharmacology, 1953 Genital specimens, collection and processing kingdom Fungi, 2009–2011 spectrum of activity, 1953 of virus, 1454–1455 mass spectrometry, 2049 Gardnerella genus, 515–516 Genital tract, infectious syndromes, 318 methods and stains for direct microscopic Gardnerella selective agar, 350 Genitourinary infections, Mollicutes, and histological detection, 2036 Gas gangrene, 972–973 1120–1121 morphological characteristics of, suspected, 976 Genome, age of, 296 2007–2008 Gastroenteritis viruses Genomes OnLine Database, 419 nomenclature of, 2008 antigen detection assays, 1662–1663 Genome Trakr database, 187 nucleic acid detection, 2049–2050 antigenic and genetic typing systems, Genotypic assays phylum Ascomycota, 2010–2011 1667 antiviral susceptibility testing, 1988–1993 phylum Basidiomycota, 2009–2010 cell culture, 1666–1667 applications, 1991–1993 phylum Microsporidia, 2011 clinical significance, 1660–1661 gene targets for antiviral resistance testing, phylum Zygomycota, 2009 collection, transport, and storage of speci- 1989 polyphasic identification, 2012–2013 mens, 1661–1662 interpretation of, 1994, 1997 subphylum Entomophthoromycotina, 2009 description of, 1657–1658 protocol for Sanger sequence-based, 1991 subphylum Mucoromycotina, 2009 direct detection, 1662–1666 Genotypic methods, 294–295, 794–795 taxonomy and classification of, 2008–2011 electron micrographs of, 1658 16S rRNA sequencing studies, 294–295 See also Dimorphic fungi causing systemic electron microscopy, 1662 advantages and disadvantages of, 1320 mycoses; Melanized fungi epidemiology and transmission, 1658–1660 DNA-DNA hybridization studies, 289, 295 Fusarium spp. evaluation, interpretation, and reporting of DNA target sequencing, 63 antigen detection, 2143 results, 1668 G1C content, 294 antimicrobial susceptibilities, 2144–2145 human adenovirus (HAdV), 1833, 1834 sequence analysis of protein-encoding classification of infections, 2133 isolation procedures, 1666–1667 genes, 295 clinical significance, 2142–2143 molecular detection assays, 1663–1665 viruses, 181 collection, transport, and storage of speci- PCR and RT-PCR assays, 1663–1665 whole-genome sequence-based methods, mens, 2143 serologic tests, 1667–1668 295, 795 description of, 2142 taxonomy of, 1656–1657 Gentamicin, 1212 direct examination, 2143–2144 Gastrointestinal anthrax, 458, 461, 462 Gentamicin-amphotericin B solution, 1463 epidemiology and transmission, 2142 Gastrointestinal Bacteria Reference unit Geobacillus spp., characters for differentiating evaluation, interpretation, and reporting of (GBRu), 977 species, 468 results, 2145 Gastrointestinal microbiome Geotrichum candidum (1,3)-b-d-glucan detection, 2048 colonic, 258–260 cultural and biochemical characteristics, identification, 2144 esophageal, 258 2062 isolation procedures, 2144 gastric, 258 morphological features of, 2063 key phenotypic features of clinically signifi- microbial composition, 255 Gerstmann-Sträussler-Scheinker disease cant, 2135–2136 predominant phyla, 256 (GSS), 1923 microscopy, 2141, 2143 small intestinal, 258 Giardia genus microscopy of grains, 2267 See also Human microbiome classification, 2382 morphology by direct examination, 2039 Gastrointestinal tract commercially available kits for detection, nucleic acid detection, 2143–2144 infection by curved and spiral-shaped 2391 serologic tests, 2144 bacteria, 1024, 1026 Giardia duodenalis taxonomy, 2134, 2140, 2142 infectious syndromes, 318 antigen detection, 2510–2511 typing systems, 2144 processing recommendations, 321–322 clinical significance, 2510 See also Hyaline molds virus detection methods, 1447 description of agent, 2508 Fusidic acid, resistance, 1264 GC agar, 350 detection in humans, 2381 Fusion inhibitor resistance, HIV–1, 1968 GCII agar, 350 direct examination, 2510–2511 Fusobacterium genus, 996 GC-Lect agar, 350 epidemiology, transmission, and preven- antimicrobial activities of potential agents, Gel analysis, postamplification detection and, tion, 2508, 2510 1013 99, 101 infection, 2497 characteristics of, 997 Gemella genus key features of trophozoites and cysts of, 2509 clinical importance, 1001–1002 cellular morphology, 437 microscopy, 2510 direct examination, 1003 clinical significance, 438 nucleic acid detection techniques, 2511 epidemiology and transmission, 998 epidemiology and transmission, 438 taxonomy, 2508 molecular detection, 1004 evaluation, interpretation, and reporting of treatment, 2511 phenotypic characteristics of, 1011 results, 445 Giardia lamblia, flagellate, 2507 resistance patterns of, 1385 identification, 440, 441 Giemsa stain molecular methods for identification, blood, 2434 443–444 blood films for malaria diagnosis, b-Galactosidase, 332 phenotypic differentiation, 441–442 2441–2443 Gammapapillomavirus sp., nucleotide sequence susceptibility testing, 1363 fungi detection, 2036 of L1 gene, 1848 testing conditions, 1351 mycology, 2028 Gammapolyomavirus, 1863 See also Catalase-negative, Gram-positive parasitology, 2410–2411 Ganciclovir cocci Plasmodium spp. in thin blood films, against herpes B virus, 1750 GeneMark, gene-finding algorithm, 263 2445–2447 against herpesviruses, 1952 Gene sequencing Gimenez stain, 337 cytomegalovirus (CMV), 1964–1965 characteristics and application, 169 Gingivitis, 1086 cytomegalovirus (CMV) resistance to, method, 174–175 Glanders and melioidosis, biothreat agent, 1788 Genetic drift, 183 250–251

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Glecaprevir characteristics of genera representing, 997 detection of plasmid-mediated AmpC-type drug interactions, 1948 clinical significance, 998–1003 b-lactamases among Enterobacteriaceae, HCV therapy, 1947 collection, transport, and storage of speci- 1332–1333 pharmacology, 1948 mens, 1003 penicillinases detection in aerobic and Glimmer, gene-finding algorithm, 263 common genera in human infection, 999 anaerobic, 1328 Global Polio Eradication Initiative, 1578 direct examination, 1003–1004 phenotypic detection of b-lactam resistance Global Public Health Intelligence Network epidemiology and transmission, 998 among, 1327–1338 (GPHIN), 164 evaluation, interpretation, and reporting of resistance in, 1306–1307 Globicatella genus results, 1015 Gram-negative rods antimicrobial susceptibilities, 445 Fusobacterium and related genera, algorithm for identification of curved, cellular morphology, 437 1001–1002 1025 clinical significance, 438 genetic identification methods, 1012–1013 curved and spiral-shaped, 1024 identification, 440 identification, 1005–1013 curved bacilli in clinical specimens, phenotypic differentiation, 442 isolation procedures, 1004 1026–1027 See also Catalase-negative, Gram-positive MALDI-TOF MS, 1012 Gram-positive anaerobic cocci (GPAC) cocci molecular detection, 1004 antimicrobial susceptibilities, 933 (1,3)-b-d-Glucan detection, fungi, phenotypic characteristics of, 1012 biochemical features of different species, 2048–2049 Porphyromonas and related genera, 1000 930 Glucose fermenters, 633 presumptive identification, 1005–1006 changes in classification of species, 926 b-Glucuronidase, 332–333 Prevotella and related genera, 1000–1001 clinical significance, 927–928 test for streptococci, 408 taxonomy and description of group, collection, transport, and storage of speci- Glycine-buffered saline, 335 995–998 mens, 928 Glycopeptides unculturable, 1013 description of group, 925–926 adverse effects, 1220 Gram-negative bacilli direct examination, 928 mechanism of action, 1218–1219 nonautomated identification system, 52 epidemiology, 927 pharmacology, 1219 resistance patterns of, 1383–1385 evaluation, interpretation, and reporting of reduced susceptibility in staphylococci, Gram-negative bacteria results, 934 1305 b-lactamases in, 1424 identification, 929, 931–933 resistance, 1261–1262 molecular assays for detection of isolation procedures, 928–929 spectrum of activity, 1219–1220 b-lactamase resistance in, 1425 MALDI-TOF MS method, 932–933 types of resistance to, 430 pefloxacin as surrogate for fluoroquinolone taxonomy, 925 Glycylcyclines, 1216–1218 susceptibility, 1338 Gram-positive bacilli, nonautomated identifi- Gnathostoma spp. phenotypic detection of non-b-lactam cation system, 52 clinical significance, 2611 resistance in, 1338–1339 Gram-positive bacteria description of agents, 2611 phenotypic tests for detecting resistance, catalase-negative, 436–437 direct examination and microscopy, 2611 1317, 1319 preservation methods, 201, 202 epidemiology, transmission, and preven- preservation methods, 201, 202 reportable organisms for MALDI-TOF tion, 2611 reportable organisms for MALDI-TOF MS, MS, 55 serologic tests, 2611 55–56 resistance in, 1306 taxonomy, 2611 screen tests for colistin resistance detection, resistance to agents against, 1260–1264 treatment, 2611 1338–1339 See also Agents against Gram-positive GN broth, Hajna, 350 See also Aerobic Gram-negative bacteria bacteria; Enterococcus genus Gomori methenamine silver (GMS), fungi Gram-negative, nonfermentative bacteria Gram-positive cocci detection, 2035, 2036 (GNF) features and availability of taxons in Gonococcal Antimicrobial Surveillance antimicrobial susceptibilities, 848 MALDI-TOF MS databases, 363–364 Program, 1357 characteristics of genus Acinetobacter, 830 general approaches to identification, Gonococcal Isolate Surveillance Program clinical significance, 829, 831 362–365 (GISP), 1357 epidemiology and transmission, 829 MALDI-TOF MS for routine identifica- Gonorrhea evaluation, interpretation, and reporting of tion, 365 Neisseria gonorrhoeae, 640–641 results, 848 nonautomated identification system, 52 See also Neisseria gonorrhoeae identification, 831–834 See also Catalase-negative, Gram-positive Gordonia genus, 1413, 1414 isolation procedures, 831 cocci classification, 526 oxidase-negative, 834–836 Gram-positive organisms clinical significance, 537 oxidase-positive, indole-negative, trypsin- cefoxitin as surrogate for oxacillin, 1322 colonial morphology, 530 negative, 836–839 detection of heteroresistant VISA, description, 527 oxidase-positive, indole-negative, trypsin- 1324–1325 epidemiology and transmission, 533 positive, 839–844 detection of inducible clindamycin resis- microscopic morphology, 532 oxidase-positive, indole-positive, 844–846 tance in staphylococci and strepto- morphologic characteristics, 528 pink-pigmented, 846–848 cocci, 1326–1327 recovered from human specimens, 535 taxonomy, 829 detection of oxacillin resistance among See also Actinomycetes Gram-negative organisms staphylococci, 1321–1323 Gradient diffusion method, manual, 1301 carbapenem resistance mechanisms, 1334 detection of penicillin resistance in pneu- Gram, Hans Christian joachim, 336 cefazolin as surrogate for oral cephalospo- mococci, 1321 Gram-negative anaerobic cocci (GNAC) rins in urinary isolates, 1337–1338 D-zone test, 1326–1327 characteristics of genera of, 932 detection of b-lactamase-producing, high-level aminoglycoside resistance clinical significance, 928 1329–1330 (HLAR) detection among entero- description of group, 926–927 detection of carbapenemases among, 1333, cocci, 1325–1326 epidemiology, 927 1335–1336 high-level mupirocin resistance detection identification, 929 detection of colonization with carbapenem- in staphylococci, 1327 taxonomy, 925 resistant organisms, 1336–1337 b-lactamase testing for enterococci, Gram-negative anaerobic rods detection of colonization with ESBL- 1320–1321 antimicrobial susceptibilities, 1013–1015 producing, 1331–1332 b-lactamase testing for staphylococci, 1320 Bacteroides and related genera, 999–1000 detection of ESBL-producing oxacillin-salt agar supplemental test for S. biochemical testing, 1006–1012 Enterobacteriaceae, 1328, 1331 aureus, 1322

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Gram-positive organisms (continued) H5N1 influenza A, 1511 Haematobacter spp., identification, 836–837 phenotypic detection of resistance among, H7N9 influenza A, 1511 Hafnia genus 1320–1327 HACEK organisms (Haemophilus spp., epidemiology, transmission, and clinical single-well broth dilution method, 1327 Aggregatibacter spp., Cardiobacterium significance, 731 vancomycin resistance detection in spp., Eikenella corrodens, and Kingella H. alvei, 690 Enterococcus and Staphylococcus, spp.), 656 nomenclature and source of species, 726 1323–1325 antimicrobial susceptibility, 665–666 See also Enterobacterales order Gram-positive rods clinical significance, 658–659 Hair algorithm for identification of, 452–453 epidemiology and transmission, 657 collection and transport, 2017 identification of aerobic, 451–454 identification, 662 pathogenic fungi recovery, 2019 Listeria and Erysipelothrix, 477 isolation procedures, 661 processing and culture guidelines, 2021 See also Actinomycetes; Coryneform susceptibility testing, 1363–1364 Halofantrine bacteria testing conditions, 1352 adverse effects, 2655 Gram-positive rods (non-spore-forming Haemophilus spp. mechanism of action, 2655 bacilli) antigen detection, 675 pharmacokinetics, 2655 antimicrobial susceptibilities, 955–956 antimicrobial susceptibilities, 682–683 spectrum of activity, 2655 biochemical testing, 950, 952 biotypes of H. influenzae and H. parainflu- Hand hygiene, laboratory, 236–237 clinical significance, 941–948 enzae, 672 Hantaan virus (HTNV), 1707 collection, transport, and storage of speci- capsular serotyping and biotyping, 681 Hantaviruses mens, 948 clinical significance, 672–673 animal models, 1709 dendrogram of bacterial genera, 939 collection, transport, and storage of speci- antigen detection, 1711 direct examination, 948–949 mens, 673–674 antivirals for, 1709–1710 DNA sequence analysis, 952–953 colony appearance, 677–678 clinical significance, 1708–1710 epidemiology and transmission, 941 commercial biochemical identification collection, transport, and storage of speci- evaluation, interpretation, and reporting of systems, 679 mens, 1710 results, 956–957 conventional biochemical tests, 679 description of agents, 1706–1707 features of, 942–943 description of genus, 670–671 detection and identification methods, 1473 identification, 949–955 differential characteristics of, 671 direct examination, 1710–1711 identification by MALDI-TOF MS, direct examination, 674–675 epidemiology and transmission, 1707–1708 953–955 epidemiology and transmission, 671–672 evaluation, interpretation, and reporting of isolation procedures, 949 evaluation, interpretation, and reporting of results, 1713 presumptive identification, 949–950 results, 683 identification, 1711–1713 taxonomy and description of agents, H. aegyptius, 673, 678 microscopy, 1710–1711 938–941 H. ducreyi, 323, 673 nucleic acid detection, 1711–1712 See also Agents against Gram-positive H. haemolyticus, 673 serologic tests, 1712 bacteria identification, 678–681 species associated with human disease, 1707 Gram stain, 336, 2036, 2037, 2043 isolation procedures, 675–678 taxonomy of, 1706 Granulicatella genus mass spectrometry, 679–680 therapy for, 1709 antimicrobial susceptibilities, 444–445 media, 675–677 vaccines for, 1710 cellular morphology, 437 microscopy, 674–675 virus isolation, 1712–1713 clinical significance, 438 molecular identification, 680 Hantavirus pulmonary syndrome (HPS), 1706 epidemiology and transmission, 438 molecular techniques, 675 antivirals for, 1709 evaluation, interpretation, and reporting of problems in identification, 680–681 clinical significance, 1708–1709 results, 445 resistance rates, 682 criteria for diagnosis, 1713 identification, 440 serologic tests, 682 microscopy, 1710–1711 molecular methods for identification, susceptibility testing algorithm, 683 treatment of, 1709 443–444 susceptibility test methods, 682–683 HardyCHROM BluEcoli, 350 phenotypic differentiation, 440–441 taxonomy, 670–671 HardyCHROM carbapenemase agar, 350 susceptibility testing, 1360 test medium, 350 HardyCHROM EEC agar, 350 taxonomy, 436 tetracycline specific resistance determinant HardyCHROM ESBL agar, 350 testing conditions, 1351 in, 1256 HardyCHROM MRSA, 350 See also Catalase-negative, Gram-positive typing systems, 681–682 HardyCHROM Salmonella, 350 cocci x and V factor growth requirements, HardyCHROM SS, 350 Grazoprevir 678–679 HardyCHROM Staphylococcus aureus, 350 drug interactions, 1946 Haemophilus influenzae, 1348 Hartley’s Digest broth, 351 hepatitis C virus (HCV) therapy, 1947 biotypes of, 672 Hashimoto’s thyroiditis, human herpesviruses pharmacology, 1946 clinical significance, 672–673 (HHV), 1816 Great Plate Count, 291 colony appearance, 677–678 H broth, 350 GreenChip, 180, 273 colony growth, 677 Health care-associated infections (HAIs) Grimontia, properties of genus, 776 colony morphologies, 676 definition, 139 Grimontia hollisae, 775, 777, 779 commercial test methods, 1356 distribution of most common, 140 Griseofulvin determining growth factor, 678 identification and susceptibility testing of clinical use, 2327 electron micrographs, 672 HAI pathogens, 145–146 drug interactions, 2327 Gram stain of, 674 infection prevention committee, 141–142 mechanism of action, 2327 incidence of resistance, 1355–1356 infection rates, sites, and predominant pharmacokinetics, 2327 reference test methods, 1349, 1356 pathogens, 139–141 spectrum of activity, 2327 satellite phenomenon, 677 laboratory information systems, 146 toxicity and adverse effects, 2327 strategies for testing and reporting of morbidity, mortality, and cost, 140–141 Group A streptococci (GAS), sequencing, results, 1356–1357 outbreak recognition and investigation, 175 Haemophilus parainfluenzae 147–148 Gulf War Syndrome, 1122 biotypes of, 672 rapidly growing mycobacteria, 617–618 Gum Listeria medium, 350 clinical significance, 673 specimen collection and transport, 145 Gymnascella hyalinospora, microscopy, 2141, colonies of, 678 steps in outbreak investigations, 147 2142, 2145, 2146 determining growth factor, 678 surveillance, 142–144

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terms, 140 Helicobacter pylori evaluation, interpretation, and reporting of See also Invention prevention program antibiotic therapy, 1052–1053 results, 1633–1634 (IPP) characteristics of, 1046 genome organization, 1626 Health care-related pneumonia, Pseudomonas, clinical significance, 1047–1048 geographic distribution, 1628 789 commercial test methods, 1364–1365 identification, 1632 Health care setting, transmission of prions in, detection of antibody in blood, 1052 isolation procedures, 1632 1925–1926 epidemiology and transmission, 1047 nucleic acid detection, 1631 Healthcare Infection Control Practices fecal specimens, 1048 person-to-person transmission, 1627 Advisory Committee, 2105 gastric biopsy specimens, 1048 serologic tests, 1632–1633 Health Protection Agency, united Kingdom, genotypic susceptibility testing of, 1053 taxonomy, 1625 985 identification of, 1051 transmission, 1627–1628 Healthcare Infection Control Practices incidence of resistance, 1364 typing systems, 1632 Advisory Committee (HICPAC), 150 isolation of, 1050 vaccines and antiviral agents, 1629–1630 Heart infusion agar, 351 microscopic examination of gastric biopsy virus detection, 1633 HealthMap, 164 specimens, 1048–1049 water- and foodborne transmission, 1627 “Healthy People 2020,” u.S. Department of nucleic acid detection, 1049–1050 Hepatitis B virus (HBV) Health and Human Services, 580 phenotypic susceptibility testing, 1053 agents against, 1950–1951 Hektoen enteric agar, 351 reference test method, 1364 antigen, 1910, 1912–1913 Helcobacillus genus stool antigen detection, 1049 anti-HBV drug therapy, 1969 description, 492 strategies for testing and reporting of antiviral susceptibility testing, 1915–1916 identification, 512 results, 1365 bioinformatics-based sites for resistance Helcococcus genus susceptibility testing, 1364–1365 analysis, 1995, 1996 antimicrobial susceptibilities, 445 testing conditions, 1351 blood-borne pathogen, 217 cellular morphology, 437 typing of, 1051–1052 clinical significance, 1909–1910 clinical significance, 438–439 urease testing of gastric biopsy specimens, collection, transport, and storage of speci- epidemiology and transmission, 438 1049 mens, 1910 identification, 441 Helminth eggs, relative sizes of, 2552 description of agent, 1905–1907 molecular methods for identification, Helminths diagrammatic representation of coding 443–444 Anisakis and related species, 2606–2608 regions, 1906 phenotypic differentiation, 442 Baylisascaris procyonis, 2615–2616 direct detection, 1910, 1912–1913 See also Catalase-negative, Gram-positive Capillaria philippinensis, 2610–2611 electron micrograph of serum, 1906 cocci commercially available kits for diagnosis, epidemiology and transmission, 1907, 1909 Helicase-dependent amplification (HDA), 2392 evaluation, interpretation, and reporting of process, 99, 101 Dipylidium caninum, 2617 results, 1916–1917 Helicobacter spp. Dirofilaria immitis and other Dirofilaria spp., gene targets for antiviral resistance testing, algorithm for identification of, 1025 2612, 2614–2615 1989 antimicrobial susceptibility, 1052–1054 Dracunculus medinensis, 2609–2610 genetic mechanisms of resistance to inhibi- bacteremia, 1027 Gnathostoma spp., 2611 tors of, 1969 characteristics of, 1046 less common cestodes, 2616–2618 genotypes and geographic circulation, 1914 clinical significance, 1047–1048 less common nematodes, 2606–2616 genotyping application, 1992–1993 collection, transport, and storage of speci- Parastrongylus (Angiostrongylus) spp., HBV reverse transcriptase (RT) resistance, mens, 1048 2611–2612 1969–1970 description of agents, 1044–1045, 1047 Spirometra spp., 2617–2618 identification, 1913 direct examination, 1048–1050 Toxocara spp., 2609 intact infectious virion, 1906 enterohepatic helicobacters, 1047, 1048 Trichinella spp., 2608–2609 isolation procedures, 1913 epidemiology and transmission, 1047 Hematologic, virus detection methods, 1447 markers in stages of infection and convales- evaluation, interpretation, and reporting of Hematoxylin and eosin (H&E), fungi detec- cence, 1907 results, 1054 tion, 2035, 2036 mechanisms of resistance, 1969–1970 gastrointestinal tract infections, 1024, 1026 Hemiptera, 2639 microscopy, 1910 “H. heilmannii”-like organisms (HHLO), arthropods as vectors, 2622–2623 molecular assays for nucleic acid detection, 1047, 1048 bed bugs, 2623 1913 hosts and diseases, 1045 reduviid bug, 2622–2623 nucleoside/nucleotide analogues, H. pylori, 1047, 1048 summary of, 2621 1950–1951 H. pylori stool antigen detection, 1049 Hemorrhagic fever viruses, 217 nucleoside RT inhibitor (NRTI) resistance, identification, 1051 biothreat agent, 249 1969–1970 isolation procedures, 1050–1051 criteria for diagnosis, 1713 schematic representation of HBV life cycle microscopy, 1048–1049 Hemorrhagic fever with renal syndrome in hepatocytes, 1908 nucleic acid detection, 1049–1050 (HFRS), 1706 serologic tests, 1914–1915 serologic tests, 1052 animal models, 1709 taxonomy, 1905 taxonomy, 1044 antivirals for, 1709 typing systems, 1913 typing systems, 1051–1052 clinical significance, 1708 worldwide distribution of genotypes, 1908 urea breath test, 1049 treatment of, 1709 Hepatitis C virus (HCV) urease testing of gastric biopsy specimens Hepatitis A virus (HAV) acute results, 1651 for H. pylori, 1049 antigen detection, 1630 agents against, 1946–1950 “Helicobacter heilmannii”-like organisms clinical presentation and course, 1629 analysis of, 182 (HHLO) clinical significance, 1629–1630 antigen detection, 1644 clinical significance, 1048 collection, transport, and storage of speci- anti-HCV therapy, 1970–1971 detection in gastric biopsy specimens, 1050 mens, 1630 antiviral susceptibility, 1649–1651 epidemiology and transmission, 1047 commercial immunoassays available for, bioinformatics-based sites for resistance evaluation, interpretation, and reporting of 1632 analysis, 1995, 1996 results, 1054 commercial molecular assays for detection, blood-borne pathogen, 217 isolation of, 1050 1631 chronic results, 1651 susceptibility testing of gastric, 1053 description, 1625–1626 clinical features of acute, 1642 See also Helicobacter spp. direct examination, 1630–1631 clinical significance, 1641–1642

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Hepatitis C virus (HCV) (continued) transmission, 1627 mechanisms and mutations of antiviral drug collection, transport, and storage of speci- typing systems, 1632 resistance, 1963 mens, 1643 vaccines and antiviral agents, 1630 resistance to antiviral agents, 1962–1965 commercially available antigens in serology virus detection, 1633 varicella-zoster virus, 1964 tests, 1649 zoonotic genotypes, 1629 Heterophyes heterophyes DAA (direct-acting antiviral) classes, 1641 Hepatitis viruses, detection and identification eggs of, 2599 DAA regimens for treatment, 1642, 1643 methods, 1473–1474 life cycles of, 2595 description, 1640–1641 Hepatovirus genus, 1625 Heterophyidae direct detection, 1643–1646 HEPES, reagent, 1463 clinical significance, 2602 discovery of, 271 Hepeviridae family, 1625 description of agent, 2602 epidemiology and transmission, 1641 Herpes B virus diagnosis, 2602 evaluation, interpretation, and reporting of clinical significance, 1750 epidemiology, transmission, and preven- results, 1651 collection, transport, and storage of speci- tion, 2602 gene targets for antiviral resistance testing, mens, 1750 geographic distribution, hosts and egg 1989 description of, 1750 morphology of, 2593 genome and protein coding scheme, 1641 identification of virus, 1751 Hexapoda, 2638 genotyping, 1646–1647 reverence laboratories for, 1751 HiChrome Aureus Agar Base with egg tel- genotyping application, 1993 serodiagnosis, 1751 lurite, 351 isolation procedures, 1646 Herpes simplex virus (HSV), 1962, 1985 HiChrome Listeria Agar Base, 351 microscopy, 1643–1644 antigen detection, 1745 HiCrome MeReSa Agar with methicillin, 351 NS3/4A protease inhibitors, 1946–1948 antiviral drug resistance, 1963–1964 HiCrome RajHans Medium, 351 NS5A inhibitors, 1948–1949, 1972–1973 antiviral susceptibilities, 1747–1749 HiCrome Salmonella Agar, 351 NS5B RNA-dependent RNA polymerase antiviral therapy, 1742 HiCrome uTI Agar, 351 inhibitors, 1949–1950 asymptomatic or subclinical infection, 1741 HiFluoro Pseudomonas Agar Base, 351 nucleic acid detection, 1644–1646 clinical significance, 1741–1742 High-level aminoglycoside resistance nucleotide and nonnucleoside RdRp collection, transport, and storage of speci- (HLAR) inhibitor resistance, 1972 mens, 1742–1743 agar dilution screening method for, 1325 principles of HCV drug resistance, description of agent, 1740–1741 broth microdilution screening method for, 1971–1972 detection and identification methods, 1325 protease inhibitors (PIs), 1972 1474 detection among enterococci, 1325–1326 recommendations for screening chronic, diagnostic tests for, 1746 disk diffusion screening method for, 1648 direct detection, 1743–1745 1325–1326 recommended testing algorithm for detec- DNA amplification, 1743–1745 Enterococcus spp., 1304–1305 tion, 1645 epidemiology and transmission, 1741 Highly active antiretroviral therapy ribavirin, 1973 evaluation, interpretation, and reporting of (HAART), 1866 serologic tests, 1647–1649 results, 1749–1750 Hippurate hydrolysis, 333 taxonomy, 1640 FDA-cleared molecular amplification tests test for streptococci, 408 tests for diagnosis and management of for, 1744 Histoplasma capsulatum infection, 1643 genotyping application, 1991–1992 antibody detection, 2041 Hepatitis D virus (HDV) herpes CNS disease in immunocompetent antigen detection, 2047–2048, 2195 clinical significance, 1918 host, 1742 antimicrobial susceptibilities, 2200, 2201 collection, transport, and storage of speci- herpes in immunocompromised host, 1742 biosafety, 2196 mens, 1918–1919 identification, 1745–1746 blastoconidia of, 2189 description of agent, 1917–1918 interpretation of type-specific serology, clinical significance, 2192 direct detection, 1919 1749–1750 clinical specimens, 2194 epidemiology and transmission, 1918 interpretation of virus detection tests, 1749 culture for yeast phase, 2196 evaluation, interpretation, and reporting of isolation of HSV in infected cells, 1747 description, 2188–2189 results, 1919 isolation procedures, 1745 epidemiology and transmission, 2191 schematic representation of life cycle in latency and recurrent disease, 1741 evaluation, interperation, and reporting of hepatocytes, 1908 mechanisms and mutations of antiviral drug results, 2200–2202 serologic course of infection, 1918 resistance, 1963 Gomori methenamine silver (GMS) stain, serologic tests, 1919 microscopy, 1745 2046 taxonomy, 1917 monoclonal antibodies for HSV-1 and histoplasmosis, 2191, 2192, 2195, 2199, typing, 1919 HSV-2 detection, 1748 2200–2202 Hepatitis E virus (HEV) neonatal herpes, 1742 identification, 2197 antigen detection, 1630–1631 ocular herpes infections, 1742 microscopy, 2194 clinical presentation and course, 1629 primary infection, 1741 morphology by direct examination, 2038 clinical significance, 1629–1630 proposed guidelines for phenotypic antiviral mycelial phase of, 2188 commercial immunoassays available for, susceptibility, 1987 nucleic acid detection, 2195 1632 serologic tests, 1746–1747 serologic tests, 2199 commercial molecular assays for detection, systemic HSV infection in hospitalized taxonomy, 2187–2188 1631 adults, 1742 typing systems, 2198 description, 1626–1627 taxonomy of types, 1740 HIV. See Human immunodeficiency virus epidemiology, 1628–1629 typing, 1745–1746 (HIV) evaluation, interpretation, and reporting of Western blot, 1746 Homothallic ascomycetes results, 1633–1634 Herpesviridae family, varicella-zoster virus clinical significance, 2151 genome organization, 1626 (VZV), 1757 description, 2145, 2147 genotypes 1 and 2, 1628 Herpesviruses key phenotypic features of, 2137 geographic distribution, 1628 agents against, 1951–1954 Hongkongmyces genus, 2245 identification, 1632 cytomegalovirus (CMV), 1964 Hookworms isolation procedures, 1632 detection and identification methods, 1474 clinical significance, 2562 nucleic acid detection, 1631–1632 gene targets for antiviral resistance testing, culture, 2563 serologic tests, 1633 1989 description of, 2561 taxonomy, 1625 herpes simplex virus, 1963–1964 direct examination, 2562–2563

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eggs, 2554, 2561 evaluation, interpretation, and reporting of evaluation, interpretation, and reporting of epidemiology and prevention, 2561 results, 1819–1820 results, 1490–1492 helminth recovery and identification, 2423 future directions, 1821 fusion inhibitor resistance, 1965, 1968 larvae, 2561 Hashimoto’s thyroiditis, 1816 genotyping application, 1992 life cycle completion time, 2558 identification, 1817 genotyping assays, 1488–1489 macroscopic examination, 2563 immunosuppressed populations, 1816 historical perspective and origin, 1477 microscopy, 2562–2563 isolation procedures, 1817 HIV-1 genotyping application, 1985, relative sizes of eggs, 2552 laboratories offering testing, 1818 1992 summary of, 2559 latency, persistence, and transmission, 1815 HIV-1 prognosis, 110 taxonomy, 2561 primary infection, 1815–1816 HIV-1 replication cycle showing antiretro- transmission and life cycle, 2561–2562 serologic tests, 1818–1819 viral drug action, 1966 treatment, 2563 taxonomy, 1814 immunoassays, 1485–1486, 1490–1491 worms, 2561 therapy, 1816–1817 infection, 2669 See also Nematodes tissue distribution, 1814–1815 INI (integrase inhibitors) resistance, 1965, Horie arabinose ethyl violet broth, 351 transplant recipients, 1816 1968 Hormonema genus, 2242 typing systems, 1817–1818 initial screening tests, 1484–1487 Hortaea genus, 2240, 2247 Human herpesvirus 7 (HHV-7) integrase strand transfer inhibitors, 1938, Hortaea werneckii antiviral susceptibilities, 1821 1945–1946 microscopy, 2238 clinical significance, 1820 intersubtype variation, 1968–1969 tinea nigra, 2228–2229 collection, transport, and storage of speci- isolation procedures, 1484 Hoyle medium, 351 mens, 1820 mechanisms of resistance to antiviral HPVs. See Human papillomaviruses (HPVs) description of agent, 1820 agents, 1965–1969 Human(s) direct examination, 1820–1821 NNRTI (nonnucleoside reverse transcrip- characteristics differentiating virus families epidemiology, 1820 tase inhibitors) resistance, 1965, 1967 infecting, 1442 evaluation, interpretation, and reporting of nonnucleoside reverse transcriptase inhibi- lung and hepatic digeneans of, 2592 results, 1821 tors, 1938, 1941–1942 major schistosomes infecting, 2591 future directions, 1821 NRTI (nucleoside reverse transcriptase in- protistan parasites detected in, 2381 identification, 1821 hibitors) resistance, 1965, 1966–1967 taxonomic classification of viruses infect- isolation procedures, 1821 nucleoside and/or NRTI, 1937, 1938, ing, 1440–1441 laboratories offering testing, 1818 1940–1941 Human adenovirus (HAdV), 1831 serologic tests, 1821 p24 antigen assays, 1482 See also Adenoviruses taxonomy, 1814, 1820 phenotyping assays, 1489 Human Adenovirus Working Group, 1831 therapy, 1820 protease inhibitors, 1938, 1942–1945 Human bocaviruses tissue distribution, 1820 protease inhibitors (PI) resistance, 1965, antigen detection, 1885 transmission, 1820 1967 clinical significance, 1885 typing systems, 1821 replication cycle, 1478 description of agent, 1885 Human herpesvirus 8 (HHV-8), 271 resistance assays, 1489, 1491–1492 direct examination, 1885–1886 antigen detection, 1827–1828 RNA and DNA assays, 1491 epidemiology and transmission, 1885 antimicrobial susceptibilities, 1829 RNA and DNA qualitative assays, 1482 evaluation, interpretation, and reporting of clinical significance, 1826–1827 RNA viral load assays, 1483–1484 results, 1886 collection, transport, and storage of speci- screening for atypical and HIV-2 infections, isolation procedures, 1886 mens, 1827 1487 microscopy, 1885 commercial diagnostic tests for, 1828 serologic tests, 1484–1488 nucleic acid detection, 1885–1886 description of agent, 1826 specimen collection, storage, and transport, serologic tests, 1886 direct examination, 1827–1828 1481–1482 taxonomy, 1880 epidemiology and transmission, 1826 specimens for antibody testing, 1486–1487 typing systems, 1886 evaluation, interpretation, and reporting of structure and genomic organization, Human bufavirus (BuV), 1880, 1886 results, 1829 1477–1478 Human cytomegalovirus (CMV) identification and typing systems, 1828 supplemental assays for, 1487–1488 genotyping application, 1991 isolation procedures, 1828 taxonomy of, 1477 human herpesvirus 5 (HHV-5), 1770 Kaposi’s sarcoma (KS), 1826–1827 therapy and vaccination, 1481 proposed guidelines for phenotypic antiviral nucleic acid detection, 1828 time course for appearance of laboratory susceptibility, 1987 serologic tests, 1828–1829 markers for, 1480 See also Cytomegalovirus (CMV) taxonomy, 1826 transmission, 1479 Human ehrlichiosis, epidemiology and trans- Human immunodeficiency virus (HIV) tropism assays, 1489–1490 mission, 1167–1168 acute retroviral syndrome, 1479–1480 viral load assays, 1491 Human enterovirus C, 1437 antiviral agents against, 1937–1946 virologic parameters during course of infec- Human granulocytic anaplasmosis (HGA) antiviral susceptibilities, 1488–1490 tion, 1479 clinical significance, 1168–1169 bioinformatics-based sites for resistance Human intestinal spirochetosis epidemiology and transmission, 1166–1167 analysis, 1995 epidemiology and transmission, 1086 Human herpesvirus 6 (HHV-6A and blood-borne pathogen, 217 microscopy, 1085 HHV-6B) CCR5 inhibitor (maraviroc) resistance, Human metapneumovirus (HMPV), 273–274 antiviral susceptibilities, 1819 1965, 1968 antigen detection, 1553 assays for detection, 1818 classification, 1477 clinical significance, 1552 cardiomyopathy, 1816 clinical latency, 1480 collection, transport, and storage of speci- cardiovascular disease, 1816 clinical significance, 1479–1481 mens, 1552–1553 clinical significance, 1815–1817 description of agents, 1477–1478 commercially available rapid antigen tests, collection, transport, and storage of speci- detection and identification methods, 1546 mens, 1817 1474 description, 1551 description of agent, 1814 diagnostic testing algorithms, 1490 detection and identification methods, 1474 direct examination, 1817 direct detection, 1482–1484 direct examination, 1553–1554 drug-induced hypersensitivity syndromes, disease progression to AIDS, 1480–1481 direct fluorescent antibody (DFA) reagents, 1816 entry inhibitors, 1938, 1945 1548 epidemiology, 1814 epidemiology, 1478–1479 epidemiology and transmission, 1551–1552

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Human metapneumovirus (HMPV) diagnostic methods, 1531 hyphomycetes, 2147, 2149 (continued) direct examination, 1530–1531 identification, 2153 evaluation, interpretation, and reporting of evaluation, interpretation, and reporting of isolation procedures, 2152–2153 results, 1554 results, 1535 key phenotypic features of, 2137–2140 identification, 1554 immunofluorescence staining, 1534 serologic tests, 2153 isolation procedures, 1553–1554 isolation and identification, 1532–1534 taxonomy, 2145 microscopic detection, 1547 molecular viral respiratory panels, 1533 taxonomy and identification, 2132–2134 microscopy, 1553 nucleic acid detection, 1532 typing systems, 2153 serologic tests, 1554 serologic tests, 1534–1535 See also Fusarium spp. taxonomy, 1551 taxonomy, 1528, 1529 Hyaluronidase production, streptococci, 411 typing systems, 1554 See also Parainfluenza viruses Hybrid capture assays, 88, 89 Human microbiome Human parvovirus 4 (PARV 4), 1880, 1886 Hybridization arrays beginnings of Human Microbiome Project Human pathogens, taxonomy of, 1439 high-density, 104–105 (HMP), 254–255 Human polyomaviruses (HPyVs) low- to moderate-density, 105–106 gastrointestinal, 258–260 antigen detection, 1868 Hydrogen peroxide, disinfection with, 238 methods for studying, 255–256 antiviral susceptibilities, 1872 Hymenolepis diminuta microbial composition by body habitat, 255 clinical significance, 1865–1867 human infection, 2616 oral, 256–258 collection, transport, and storage of speci- microscopy, 2613 placental, 260 mens, 1867 Hymenolepis nana predominant phyla by body site, 256 description of agents, 1863–1864 characteristics of, 2583 reference strain genomes, 262–263 direct examination, 1867–1871 clinical significance, 2586 relative cell numbers of human cell types diseases associated with, 1865 collection, transport, and storage of speci- and bacteria in, 255 epidemiology and transmission, 1864–1865 mens, 2587 of respiratory tract, 260–261 evaluation, interpretation, and reporting of description of agent, 2586 skin, 261–262 results, 1872–1784 epidemiology, transmission, and preven- studies of, 256–262 isolation and culture procedures, 1871 tion, 2586 vaginal, 260 Merkel cell carcinoma, 1867 evaluation, interpretation, and reporting of Human Microbiome Project (HMP), nucleic acid amplification methods, results, 2587 254–255, 271 1870–1871 human infection, 2616 HMP Consortium, 262–263 nucleic acid detection, 1868, 1870 serologic tests, 2587 reference strain genomes, 262–263 polyomavirus-associated nephropathy taxonomy, 2586 Human Oral Microbe Identification (PVAN), 1866 treatment, 2587 Microarray, 257 positive controls and standards, 1870 Hymenoptera, 2635, 2639 Human papillomaviruses (HPVs) progressive multifocal leukoencephalopathy Hyphomycetes adjunctive/triage tests, 1858–1859 (PML), 1865–1866 clinical significance, 2151–2152 amplification strategies and targets, 1855, serologic tests, 1871–1872 description, 2147, 2149 1857 taxonomy, 1863 key phenotypic features of, 2138–2140 anogenital warts (AGWs), 1851 template extraction, 1870 Hypersensitivity pneumonitis, rapidly growing antigen detection, 1854 trichodysplasia spinulosa, 1867 mycobacteria, 617 approaches to molecular testing, 1856 Human T-cell lymphotropic viruses (HTLV) cancer and, 1852–1853 clinical significance, 1500–1501 clinical significance, 1851–1853 collection and storage of specimens, Identification, 292 collection, transport, and storage of speci- 1501–1502 Identification systems mens, 1853–1854 description of, 1498 criteria for selecting instrumented systems, considerations for selecting assay, 1857 direct examination, 1502–1503 63 cutaneous warts, 1851 epidemiology and transmission, 1498–1501 genotypic, 63 description of, 1847, 1849–1850 evaluation, interpretation, and reporting of laboratory verification for performance, 64 direct examination, 1854–1859 results, 1504–1506 limitations of microorganisms, 64 epidemiology and transmission, 1850–1851 genomic organization of, 1499 organism, 45–47 evaluation, interpretation, and reporting of identification, 1503 phenotypic, 47–51 results, 1859–1860 isolation, 1503 technologies for microorganism identifica- genomic organization of, 1847, 1849 PCR detection of nucleic acids, 1502–1503 tion, 46 genotyping, 1857–1858 serologic testing algorithm for, 1499 See also Phenotypic identification systems; indications for clinical testing, 1855 serologic tests, 1503–1504 Proteomic identification systems isolation procedures, 1859 taxonomy, 1498 Ignavigranum genus level of automation and technical complex- typing systems, 1503–1504 clinical significance, 439 ity, 1858 Western blot (WB) analysis, 1499, 1501, 1504 phenotypic differentiation, 442 microscopy, 1854 Human T-cell virus, detection and identifica- See also Catalase-negative, Gram-positive natural history of cervical, 1850 tion methods, 1474 cocci next-generation sequencing assays, 1858 Human viruses, next-generation sequencing Illusory parasitosis, 2637 nucleic acid detection, 1854–1855 (NGS), 275 Imipenem, activity against Clostridium spp., oral papillomatosis, 1852 Hyaline molds 987 prognosis, 110 antimicrobial susceptibilities, 2153 Immune reconstitution inflammatory syn- prophylactic vaccines, 1853 ascomycetes, 2145, 2147 drome (IRIS), 2091 quality monitoring, 1859–1860 basidiomycetes, 2147 Immunization, laboratory staff, 212 recurrent respiratory papillomatosis (RRP), clinical significance, 2134, 2151–2152 Immunoassays, 127–136 1851–1852 coelomycetous fungi, 2149, 2151 agglutination reactions, 128–129 serologic tests, 1859 collection, transport, and storage of speci- automated platforms, 134, 135 taxonomy, 1847 mens, 2134, 2152 basic principles of, 125 validation metrics, 1859–1860 description of agents, 2145, 2147, 2149, 2151 categorization of, 126 Human parainfluenza viruses (HPIVs) direct examination, 2152 chemiluminescent (CIAs), 132 antigen detection, 1531–1532 epidemiology and transmission, 2151 complement fixation, 129 collection, transport, and storage of speci- evaluation, interpretation, and reporting of enzyme immunoassays (EIAs), 126, 131, mens, 1530 results, 2153 132

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general concepts of, 125–127 source attribution, 182 Integrase strand transfer inhibitors, HIV historic perspective on development, transmission, 183 therapy, 1940, 1945–1946 124–125 See also Laboratory-acquired infections Integrated Microbial Genomes with immunodiffusion (ID) technique, 128 Infectious Diseases Pathology Branch of Microbiome Samples (IMG/M), 263 immunofluorescence assays, 129–130 CDC, 1728 Intermediate, breakpoint definitions, 1285 lateral-flow (LFA), 135–136 Infectious Diseases Society of America International Agency for Research on Cancer limit of detection for select, 125 (IDSA), 302, 597, 980, 1217, 1386, (IARC), 1849 multiplex, 134–135 1993, 2042, 2048, 2078 International Air Transport Association neutralization assays, 129 Infectious keratitis, Pseudomonas, 789 (IATA), 1457 precipitation reactions, 127–128 Infectious mononucleosis International Coalition of Medicines quantification of EIAs, 127 Epstein-Barr virus (EBV), 1797, 1798– Regulatory Authorities (ICMRA), rapid, 135–136 1799, 1805 2662 screening versus diagnostic assays, 125–126 methods for prevention, diagnosis, and International Code of Botanical specimen sources for serologic evaluation, monitoring, 1801 Nomenclature, 2087 126 Influenza viruses International Code of Nomenclature for technical challenges of EIAs, 132–134 agents against, 1954–1955 Algae, Fungi and Plants, 2103 use of serologic analysis, 126–127 antigen detection, 1512, 1514–1515 International Code of Nomenclature (ICN) Western blot and immunoblot, 130 antiviral susceptibilities, 1523 fungi, 2008 See also Enzyme immunoassays (EIAs) bioinformatics-based sites for resistance International Code of Nomenclature for Immunocompetent host analysis, 1996 Prokaryotes (ICNP), 291–292 cytomegalovirus (CMV) infection, 1771 cell culture, 1520–1521 International Code of Nomenclature of herpes CNS disease, 1742 clinical significance, 1511–1512 Bacteria (The Bacteriological Code), human adenovirus (HAdV), 1840 collection, transport, and storage of speci- 291 Immunocompromised host mens, 1512 International Committee on Systematic cytomegalovirus (CMV) infection, commercially available antigen-based rapid Bacteriology (ICSB), 291 1771–1772 detection kits, 1514 International Committee on Systematics of Epstein-Barr virus (EBV), 1800 commercially available kits for detection, Prokaryotes (ICSP), 292, 631 herpes in, 1742 1513 International Commission on the Taxonomy human adenovirus (HAdV) infection, description of agents, 1510 of Fungi (ICTF), 2008, 2056 1835, 1840 detection and identification methods, 1474 International Committee on Taxonomy of human herpesvirus 7 (HHV-7), 1820 direct detection, 1512, 1514–1515, 1520 Viruses (ICTV), 1435–1436, 1439, Immunofluorescent antibody stain, 337–338 epidemiology and transmission, 1510–1511 1706, 1770, 1831, 1847, 1863, 1880 Immunosuppressed host evaluation, interpretation, and reporting of International HPV Reference Center, 1847 human herpesviruses (HHV), 1816 results, 1523–1524 International Journal of Systematic and Mycoplasma and Ureaplasma spp., 1122 FDA-cleared molecular detection assays for, Evolutionary Microbiology (IjSEM) Immunotherapy, human adenovirus (HAdV), 1516–1519 (journal), 290, 291 1841 gene targets for antiviral resistance testing, International Organization for Imperial College London, 187 1989 Standardization (ISO) Inactivated influenza vaccines (IIVs), 1512 genetic mechanisms of resistance to inhibi- accreditation, 7 Incineration, sterilization, 233 tors, 1974 breakpoints, 1281 India ink, nigrosin, fungi detection, 2036 genotyping application, 1993 reference, 1284 Indinavir identification and typing systems, International Society for Human and Animal drug interactions, 1944 1521–1522 Mycology (ISHAM), 2103, 2132 HIV therapy, 1939 isolation from embryonated chicken eggs, International Society of Travel Medicine pharmacology, 1944 1521 (ISTM), 164 Indirect fluorescent-antibody (IFA), reagents, isolation procedures, 1520–1521 International Working Group on the 1463, 1464 laboratory-acquired infection, 217 Classification of Staphylococcal Indole test, 333 M2 channel blockers, 1973–1974 Cassette Chromosome Elements, Infant botulism, 975 M2 protein inhibitors, 1954 175 Infant Botulism Treatment and Prevention methods to identify and characterize Intestinal amebae, 2498 Program, California Department of isolates, 1522 Intestinal spirochetosis, 1086 Public Health, 975, 980 microscopy, 1512 clinical significance, 1088–1089 Infection prevention program (IPP), 139 neuraminidase inhibitors, 1954–1955 collection, transport, and storage of speci- antimicrobial stewardship, 144–145 neuraminidase inhibitors (NAIs), mens, 1089 committee, 141–142 1974–1975 microscopy of human, 1085 emerging issues and trends in health care, nucleic acid analyses, 1515, 1520 term, 1088 150–151 proposed guidelines for phenotypic antiviral Intestinal tract HAI surveillance, 142–144 susceptibility, 1987 direct parasite detection, 2400–2401 hospital, 141–145 serologic tests, 1522–1523 duodenal capsule technique, 2426 process surveillance, 144 taxonomy, 1510 duodenal contents, 2425–2426 reporting laboratory data, 146–147 Inhalational anthrax, 458, 461, 462 examination for pinworm, 2424 role of clinical microbiology laboratory, Inhibitory mould agar, mycology, 2031 parasite recovery from specimens, 2425 145–151 Injectional anthrax, 458, 461, 462 parasites, 2390 structure, personnel and responsibility, 141 Innate resistance, selection of bacterial patho- sigmoidoscopy material, 2424 See also Health care-associated infections gens with, 1243 specimen preparation and procedures, (HAIs) Inquilinus limosus 2394–2395 Infectious disease(s) characteristics of, 840 trematodes of, 2601–2602 dynamics of, 182–183 identification, 839 Intrasporangiaceae family, description, 493 epidemiology of, 167 InSTEDD (Innovative Support to Intrinsic resistance, Pseudomonas, 795–796 etiologies of syndromes, 318 Emergencies Diseases and Disasters), Invasive meningococcal disease (IMD), 641 forensic microbiology, 184 164 Investigational methods geographic spread, 183 Institut Pasteur, 1728 antimicrobial susceptibility testing, laboratory testing, 73 Instrumentation, molecular assays, 107–108 1308–1309 pathogen evolution, 182–183 Integrase inhibitors (INIs), HIV–1, 1968 Smarticles technology, 1308

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Iodamoeba genus description of, 859–860 morphologic characteristics, 528 classification, 2383 epidemiology and transmission, 860–861 recovered from human specimens, 535 detection in humans, 2381 identification, 864 See also Actinomycetes Iodamoeba bütschlii isolation procedures, 863 intestinal amebae of humans, 2500 taxonomy, 858 key features, 2499 Ketoconazole, 2322–2322 Labcorp, human herpesvirus 6 (HHV-6) test- Iodine, parasitology, 2409 acquired resistance, 2323 ing, 1818 Iodoquinol clinical use, 2323 Laboratory adverse effects, 2658 spectrum of activity, 2323 change in, 296 mechanism of action, 2658 toxicity and adverse effects, 2323 hand hygiene, 236–237 pharmacokinetics, 2658 Ketolides outbreak detection methods, 160–162 spectrum of activity, 2658 adverse effects, 1215 See also Clinical microbiology laboratory; Ion sequencing, 104 mechanism of action, 1214–1215 Microbiology laboratory automation Iron hematoxylin stain, parasitology, 2411 pharmacology, 1215 Laboratory-acquired infections IS6110 fingerprinting, RFLP method, resistance, 1263–1264 disinfectant selection, 211–212 172–173 spectrum of activity, 1215 gloves, 211 Isavuconazole Kidneys and bladder, specimens for parasite handwashing, 210–211 acquired resistance, 2322 detection, 2428, 2430 immunization and screening, 212 azole, 2321–2322 Kingdom Fungi, 2009–2011 investigation and management of, 218–220 clinical use, 2322 phylum Ascomycota, 2010–2011 laboratory coats, gowns, scrubs, and foot- spectrum of activity, 2320, 2322 phylum Basidiomycota, 2009–2011 wear, 211 therapeutic drug monitoring, 2322 simplified taxonomic scheme illustrating, laboratory exposures, 218–219 toxicity and adverse effects, 2322 2010 laboratory infections, 219 Isoniazid, 1399 subphylum Entomophthoromycotina, 2009 masks and respirators, 211 Itraconazole subphylum Mucoromycotina, 2009 potential pathogens, 213–218 acquired resistance, 2322 See also Fungi preparedness, 210 clinical breakpoints for Candida spp., 2352 Kingella spp. reporting requirements, 219–220 clinical use, 2322 antimicrobial susceptibility, 666 risk assessment and mitigation of risk, spectrum of activity, 2320, 2322 biochemical reactions of, 664 207–209 therapeutic drug monitoring, 2322 clinical significance, 659 safety implications of MALDI-TOF MS, toxicity and adverse effects, 2322 direct examination, 661 212 Ivermectin, 2649–2651 epidemiology and transmission, 657 safety initiatives, 210–213 adverse effects, 2650–2651 identification of, 663 use of personal items and electronic major indications for, 2650 taxonomy, 657 devices, 213 mechanism of action, 2650 Kingella kingae Laboratory detection of bacteremia and pharmacokinetics, 2650 biochemical reactions of, 664 fungemia, 28, 40 spectrum of activity, 2650 isolation procedures, 661 critical factors, 29–31 See also Anthelmintic agents Klebsiella genus, 724 culture-based methods, 33–36 Ixodes ricinus, gradual engorgement of feeding, biochemical characterization, 733 diagnostic importance, 28 2640 cefazolin as surrogate for oral cephalospo- interpretation of blood culture results, Ixodes scapularis (tick) rins in urinary isolates in, 1337–1338 31–33 babesiosis, 2451–2452 epidemiology, transmission, and clinical microorganisms in blood, 28 life cycle of, 2451 significance, 727–728 non-culture-based methods, 36–37 identification, 735 prognostic importance, 29 nomenclature and source of species, 726 quality audits and benchmarks, 39–40 Janibacter genus, description, 493 phenotypic tests for detecting resistance, rapid identification of microbial isolates, janssen, Hans and Zacharias, 16 1318 37–39 japanese encephalitis virus, commercial tetracycline specific resistance determinant specimen collection, 31 diagnostic tests, 1691 in, 1256 Laboratory-developed tests (LDTs), 113, jC polyomavirus (jCPyV), 1863 See also Enterobacterales order 115–116 commercial nucleic acid amplification Klebsiella oxytoca, detecting resistance, 1316 FDA oversight and, 13–14 products, 1871 Klebsiella pneumoniae Laboratory practice disease associated with, 1865 carbapenem resistance, 1306 contamination control, 112–113 serologic tests, 1871–1872 detecting resistance, 1316 credentials, 116 See also Human polyomaviruses (HPyVs) Klebsiella pneumoniae carbapenemases (KPCs), quality control and assurance, 113–114 Jeotgalicoccus genus, 368, 377 1420 regulatory and reimbursement issues, joint fluid, pathogenic fungi recovery, 2019 Kligler iron agar, 351 115–116 Kluyvera genus, differentiation of, 735 reporting and interpretation of results, Knoellia genus, description, 493 114–115 Kanamycin esculin azide agar, 351 Knoxdaviesia genus, 2243 specimen collection, transport, and process- Kaposi’s sarcoma (KS), 271 Knufia genus, 2241 ing, 111–112 human herpesvirus 8 (HHV-8), 1826–1827 Koch, Robert, 206, 269, 270, 278, 457 Laboratory preparedness, 210, 211 KS-associated herpesvirus (KSHV), 1826, Köhler, August, 16 Laboratory Response Network (LRN), 1827 Köhler illumination, 19–20, 26 243–245, 756 Karolinska Institute, 1847, 1863 Kocuria spp., identification tests, 375 bioterrorism-related specimens, 460 Keratitis, rapidly growing mycobacteria, 617 Kosakonia genus structure of, 245 Keratoconjunctivitis, human adenovirus differentiation of Pantoea agglomerans, 733 Laboratory safety (HAdV), 1833 epidemiology, transmission, and clinical bacterial pathogens, 316–317 Kersch, Gil, 1153 significance, 729 engineering controls, 317 Kerstersia nomenclature and source of species, 726 Lacazia loboi, 2292 antimicrobial susceptibilities, 865 See also Enterobacterales order antimicrobial susceptibilities, 2294 clinical significance, 861 Kroppenstedtia genus clinical significance, 2293–2294 collection, transport, and storage of speci- clinical significance, 537 collection, transport, and storage of specimens, 862 description of, 527 mens, 2294

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description of, 2293 identification, 2300 Legionellaceae group, 905 direct examination, 2294 isolation procedures, 2300 Legionella pneumophila outbreak, 162 epidemiology and transmission, 2293 microscopy, 2299–2300 Legionnaires’ disease (LD), 905, 908 evaluation, interpretation, and reporting of serologic and DNA tests, 2300 laboratory diagnosis, 917 results, 2294 taxonomy, 2299 See also Legionella genus isolation procedures, 2294 typing systems, 2300 Leifsonia genus serologic tests, 2294 Lamivudine description, 492 taxonomy, 2291–2292 drug interactions, 1941, 1951 identification, 513 typing systems, 2294 HBV therapy, 1950 Leishmania genus b-Lactam(s) HIV therapy, 1938 animal inoculation, 2462 antimicrobial susceptibility of Aeromonas, mechanism of resistance, 1965, 1967, characteristics of agents of trypanosomiasis, 770, 772 1969 2459 Bacteroides spp., 1383 pharmacology, 1940–1941, 1951 classification, 2382–2383 Pseudomonas resistance to, 796 LAP test, 333 clinical significance, 2461 resistance to, 1247–1250 Lasiodiplodia genus, 2234, 2247, 2248, 2249 collection of specimens, 2461–2462 b-Lactamase(s) Lasiodiplodia theobromae, 2234, 2238 culture, 2462 Aeromonas species, 770, 772 Lassa virus detection in humans, 2381 AmpC, 1252–1253 antigens in liver of infected patients, 1725 diagnosis, 2461 broad-spectrum, 1250–1251 geography and human diseases, 1721 features of Leishmania spp. organisms infect- Bush-jacoby-Medeiros Group 2b, 1252 neutralization tests, 1733 ing humans, 2459 carbapenemases, 1253–1254 See also Arenaviridae family life cycle, 2458, 2460 characteristics of, 1251 Lateral flow technology, 2112 microscopic detection, 2462 classification of, 1250, 1251 Lawrence Livermore Microbial Detection morphology, 2458, 2460 extended-spectrum (ESBL), 1243, Array, 180, 273 nucleic acid detection, 2462 1251–1252 Lawrence Livermore National Laboratory, 180 serologic and antigen tests, 2463 inhibitor-resistant class A, 1252 Lawsonella genus skin testing, 2462–2463 metallo-b-lactamases, 1254 clinical significance, 537 treatment and prevention, 2463 oxacillin-hydrolyzing class D, 1253 description of, 527 Leishmaniae, techniques for parasite recovery Pseudomonas resistance to, 796 morphologic characteristics, 528 and identification, 2436 resistance mechanisms, 1250–1254 See also Actinomycetes Leishmaniasis serine carbapenemases, 1253–1254 Ledipasvir commercially available kits for diagnosis, by spectrum, 1250–1254 drug interactions, 1948 2392 b-Lactamase testing HCV therapy, 1947 mechanisms of resistance, 2673–2674 for enterococci, 1320–1321 mechanism of resistance, 1971, 1973 proposed mechanisms of resistance for drugs for staphylococci, 1320 pharmacology, 1948 against, 2670 susceptibility testing, 1382 Lederberg, joshua, 164 selected antiparasitic agents and suscepti- b-Lactamase inhibitors Leeming and Notman medium, mycology, bility testing method, 2683 avibactam, 1208 2031 susceptibility test methods, 2685–2686 clavulanic aid, 1207–1208 Legionella genus, 1348 Lelliottia genus relebactam, 1209 advanced identification, 915–916 differentiation of Pantoea agglomerans, 733 sulbactam, 1208 antibody determination, 916–917 epidemiology, transmission, and clinical vaborbactam, 1208–1209 antigen detection, 909–910 significance, 729 Lactobacillus spp. antimicrobial susceptibilities, 917 nomenclature and source of species, 726 antimicrobial susceptibilities, 955 basic identification, 913–915 See also Enterobacterales order clinical significance, 946–947 clinical significance, 908 Lemierre syndrome, 1385 resistance patterns of, 1389 collection, transport, and storage of speci- Lepidoptera, 2635, 2639 susceptibility testing, 1365 mens, 908 Leptospira genus taxonomy and description, 940 composition and selectivity of media for antibiotic susceptibilities, 1062 testing conditions, 1352 growing, 911 antigen detection, 1060 Lactococcus genus culture media, 911–912 bacteremia, 1027 cellular morphology, 437 description of agent, 905, 907 clinical significance, 1060 clinical significance, 439 direct examination, 909–910 collection, transport, and storage of speci- identification, 440 epidemiology and transmission, 907–908 mens, 1060 phenotypic differentiation, 442 evaluation, interpretation, and reporting of description of family, 1058 taxonomy, 436 results, 917 direct examination, 1060 testing conditions, 1352 flow scheme for basic identification, 914 epidemiology and transmission, 1059–1060 See also Catalase-negative, Gram-positive identification from bacterial colonies, evaluation, interpretation, and reporting of cocci 913–916 results, 1062 Lacto-fuchsin, mycology, 2028 inoculation of plates, 911 genotypic classification, 1058 Lactophenol cotton blue, mycology, 2028 isolation procedures, 910–913 identification, 1061 Lactophenol cotton blue and potassium Legionnaire’s disease, 323 isolation procedures, 1060–1061 hydroxide, 2028 medium incubation, 912 microscopy, 1060 Lactritmel agar (Borelli’s medium), mycology, microscopy, 909 nucleic acid detection, 1060 2031 morphology of L. pneumophila, 909 organisms in urine, 1027 Lagenidium and Paralagenidium spp., 2292 nucleic acid detection, 910 serologic classification, 1058 antimicrobial susceptibilities, 2300 pathogenesis, 907–908 serologic tests, 1061–1062 clinical significance, 2299 photographs of L. pneumophila colonies, 912 species of, 1059 collection, transport, and storage of speci- plate inspection, 912–913 taxonomy, 1058 mens, 2299 specimen plating, 910–911 typing systems, 1061 description of, 2299 susceptibility testing, 917 Leptotrichia genus, 996 direct examination, 2299–2300 taxonomy, 905 clinical importance, 1002 epidemiology and transmission, 2299 typing systems, 916 phenotypic characteristics of, 1011 evaluation, interpretation, and reporting of workup of suspect colonies and look-alike Leptotrichia buccalis, direct examination, results, 2300 bacteria, 913 659–660

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Letermovir Liver, trematodes of, 2600–2601 ultrastructural characteristics of, 1728 against herpesviruses, 1954 Liver and spleen See also Arenaviridae family mechanism of resistance, 1963 parasites, 2390 Lymphogranuloma venereum (LGV), 1137, Leucobacter genus, description, 492 specimen for parasite detection, 2428, 1139, 1143 Leuconostoc genus 2430–2431 Lysozyme test, 333 antimicrobial susceptibilities, 444 specimen preparation and procedures, 2395 Lyophilization, 200–201 cellular morphology, 437 Liver infusion agar, 351 Lyssavirus clinical significance, 439 L. mono Confirmatory Agar Base, 351–352 diagram of morphology and structural evaluation, interpretation, and reporting of Loa loa protecins, 1676 results, 445 clinical significance, 2576 diversity, 1675 identification, 440 description of, 2576 See also Rabies phenotypic differentiation, 442 diagnosis, 2576 susceptibility testing, 1365 diagrammatic representation of extremities, testing conditions, 1352 2573 M2 protein inhibitors, against influenza virus, See also Catalase-negative, Gram-positive direct examination, 2577 1954, 1955 cocci epidemiology and transmission, 2576 Macacine herpesvirus 1. See Herpes B virus Libraries, molecular epidemiology, 186–188 microfilariae in humans, 2572 McBride Listeria agar, 352 Lice, arthropods as vectors, 2624–2626 parasite of humans, 2571 MacConkey agar, 352 Lichtheimia genus taxonomy, 2576 MacConkey agar, Fluorocult, 352 culture variability and branching, 2169 treatment and prevention, 2577 MacConkey agar with sorbitol, 352 identification, 2168, 2170 Lobo, jorge de Oliveira, 2291 McFarland standards, 335–336 Lichtheimiaceae family Lobomycosis, 2291 Macrococcus genus, epidemiology and trans- genus Lichtheimia, 2168, 2169 Loeffler medium, 352 mission, 377 genus Rhizomucor, 2168, 2169 Lombard-Dowell agar, 352 Macrolides, 1402 human mucormycosis, 2164 Lombard-Dowell egg yolk agar, 352 adverse effects, 1214 LIM broth, 351 Lomentospora genus, 2243, 2249 fidaxomicin, 1214 Lincomycin, 1215 Lomentospora prolificans mechanism of action, 1212–1213 Lincosamides antifungal susceptibilities, 2254 pharmacology, 1213 adverse effects, 1216 microscopy, 2251, 2252 resistance, 1263–1264 mechanism of action, 1215 Loop-mediated amplification (LAMP), 99, 100 as resistance target, 1427 pharmacology, 1215–1216 Lophophyton spp., taxonomy, 2208 spectrum of activity, 1213–1214 spectrum of activity, 1216 Lophophyton gallinae, description of, 2226 Macrophomina genus, 2234 Linezolid Lopinavir, mechanism of resistance, 1965, 1967 Macrophomina phaseolina, 2234 resistance, 1263 Lopinavir-ritonavir Madurella spp., taxonomy and description, resistance in enterococci and staphylococci, drug interactions, 1944 2261 1305 HIV therapy, 1939 Madurella mycetomatis as resistance target, 1426–1427 pharmacology, 1944 assimilation patterns, 2269 Linnaeus, Carolus, 292 Lowenstein-Gruft medium, 352 cultures of, 2264, 2265 Lipoglycopeptide, resistance, 1262–1263 Lowenstein-jensen medium, 352 in vitro susceptibility, 2272 Lipopeptides Lower respiratory tract specimens microscopy of grains of, 2266–2267 adverse effects, 1220 collection and transport, 2018 morphological identification, 2268 mechanism of action, 1218–1219 pathogenic fungi recovery, 2019 morphology by direct examination, 2040 pharmacology, 1219 pretreatment, 2020 taxonomy and description, 2261 spectrum of activity, 1219–1220 processing and culture guidelines, 2022 Maggots, endoparasitic arthropods, 2633–2635 Listeria genus Lugol’s iodine, parasitology, 2409 Malachite green broth, 352 antimicrobial susceptibilities, 482 Lujo virus Malaria biochemical differentiation of species, 480 antigens in liver of infected patients, 1725 Centers for Disease Control and Prevention CAMP (Christie, Atkins, Munch-Petersen) geography and human diseases, 1721 (CDC), 2438–2440 test, 479, 480, 481 See also Arenaviridae family comparison of diagnostic direct methods clinical significance, 478 Lumefantrine for, 2448 collection, transport, and storage of speci- adverse effects, 2655 immunochromatographic tests for, 2435 mens, 478 mechanism of action, 2655 mechanisms of P. falciparum resistance to description of agent, 477 pharmacokinetics, 2655 antimalarials, 2670–2672 direct examination, 478–479 spectrum of activity, 2655 overview of, 2669–2670 epidemiology and transmission, 477–478 Lungs proposed mechanisms of resistance for drugs evaluation, interpretation, and reporting of bronchoscopy aspirates, 2431 against, 2670 results, 482 direct wet mount, 2431 selected antiparasitic agents and suscepti- identification, 479, 481 expectorated and induced sputum, 2431 bility testing method, 2683 isolation procedures, 479 permanent stained smears, 2431 susceptibility test methods, 2682–2685 macroscopic view of colonies, 480 specimen for parasite detection, 2429, 2431 techniques for parasite recovery and identi- serologic tests, 482 Lyme borreliosis fication, 2436 taxonomy, 477 Borrelia species, 1067 Malassezia spp. typing systems, 481–482 See also Borrelia burgdorferi sensu lato (Lyme antifungal susceptibilities, 2068 Listeria Oxford medium base with antibiotic Borrelia group) clinical significance, 2066 inhibitor, 351 Lymph nodes, 325 description, 2059, 2064 Listeria transport enrichment medium, 351 Lymph nodes and lymphatics, specimen for epidemiology and transmission, 2065 Listeria monocytogenes parasite detection, 2428, 2431–2432 isolation procedures, 2072 susceptibility testing, 1365 Lymphocytic choriomeningitis (LCM) virus, morphological features of, 2063 subtyping, 174 1719 morphology by direct examination, 2038 List of Prokaryotic Names with Standing in animal inoculation, 1730 Parker ink stain, 2042, 2043 Nomenclature (LPSN), 289, 525 antigens in liver of infected patients, 1725 taxonomy and nomenclature, 2058 Littman oxgall agar, mycology, 2031 cell culture, 1730 Malassezia furfur Live attenuated influenza virus (LAIV) geography and human diseases, 1721 culture, 2228 vaccine, 1512 neutralization tests, 1733 microscopy, 2229

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skin scrapings, 2228 Measles virus evaluation, interpretation, and reporting of tinea versicolor, 2227–2228 clinical significance, 1561–1562 results, 2254–2255 MALDI-TOF MS. See Matrix-assisted laser collection, transport, and storage of speci- identification, 2252–2253 desorption ionization–time of flight mens, 1562–1563 isolation procedures, 2251–2252 mass spectrometry cytologic examination, 1563 overview of clinically relevant species, Malt extract agar, mycology, 2031 description, 1560 2235–2237 Mannitol egg yolk polymyxin agar, 352 detection and identification methods, serologic tests, 2254 Mannitol lysine crystal violet-brilliant green 1474 taxonomy and description of agents, agar, 352 direct examination, 1563 2234–2246 Mannitol salt agar, 352 enzyme-linked immunosorbent assays typing systems, 2253–2254 Mannitol salt broth, 352 (ELISAs), 1564–1565, 1566 Melarsoprol Mannitol selenite broth, 352 epidemiology and transmission, 1560–1561 adverse effects, 2661 Mansonella spp. evaluation, interpretation, and reporting of mechanism of action, 2661 clinical significance, 2577 results, 1565–1566 mechanism of resistance, 2670 description of, 2577 genotyping, 1564 pharmacokinetics, 2661 diagnosis, 2577–2578 identification, 1563–1564 spectrum of activity, 2661 epidemiology, 2577 immunofluorescence assay, 1563 Melting-curve analysis, real-time PCR, 95 microfilariae in humans, 2572 isolation, 1563–1564 Meningeal anthrax, 461, 462 parasite of humans, 2571 nucleic acid detection, 1563 Meningitis, varicella-zoster virus infection, taxonomy, 2577 plaque reduction neutralization (PRN) 1758–1759, 1761 treatment and prevention, 2578 assay, 1565 Merkel cell carcinoma, MCPyV virus, 1865, Maraviroc serologic diagnosis, 1564–1565 1867 drug interactions, 1945 taxonomy, 1560 Merkel cell polyomavirus (MCPyV), 1863 HIV therapy, 1939 Mebendazole, 2645, 2648 Mesocestoides spp., human infection, 2616 mechanism of resistance, 1968 Mechanisms of resistance Metarrhizium pharmacology, 1945 African trypanosomiasis, 2674–2675 clinical significance, 2152 Marburg virus antiretroviral (ARV) drugs and HIV, hyphomycetes, 2149 animal inoculation, 1730 1965–1969 Methanosarcinales, 294 clinical significance, 1725–1726 drugs for hepatitis B virus (HBV), Methenamine silver stain, mycology, 2028 geography and associated human diseases, 1969–1970 Methicillin-resistant Staphylococcus aureus 1723 drugs for hepatitis C virus (HCV), (MRSA), 1242–1243 taxonomy and description, 1720 1970–1973 FDA-cleared molecular assays for detection, See also Filoviridae family drugs for herpes viruses, 1962–1965 1423 Maribavir, mechanism of resistance, 1963 drugs for influenza, 1973–1974 media for detection of, 338 Martin-Lewis agar, 352 future perspectives, 2675 molecular detection of, 1421–1422 Marvinbryantia, taxonomy and description, 940 leishmaniasis, 2673–2674 targets of PCR-based assays to detect, 1422 Mass spectrometry (MS), 294 malaria, 2669–2672 Methicillin-susceptible Staphylococcus aureus characteristics and application, 169 schistosomiasis, 2675 (MSSA), 1421–1422 post-amplification analysis, 106 summary of proposed, 2670 Methylene blue stain, 336 Matrix-assisted laser desorption ioniza- trichomoniasis, 2672–2673 Methylobacterium spp. tion–time of flight mass spectrometry Media, 2025–2026 characteristics of, 846 (MALDI-TOF MS), 76, 296, 291, additives, 359–360 identification, 847 833–834, 1421 commercial manufacturers of fungal, Methyl red Voges-Proskauer medium, 352 aerobic Gram-negative bacteria, 630, 2032–2033 Metronidazole, 955 633–634 mycology laboratory, 2029–2032 activity against Clostridium spp., 987 application, 3 parasitology, 2412, 2413 adverse effects, 1225 bacteria and fungi identification, 109 See also Culture media mechanism of action, 1225 blood cultures, 38–39 Medical College of Wisconsin, 1682 mechanism of resistance, 2670 characteristics and application, 169 Medical devices pharmacology, 1225 characteristics and availability of taxons in, collection and transport, 2017 resistance, 1264–1265 databases of catalase-negative Gram- disinfection, 230–231 resistant breakpoint differences, 1378 positive cocci, 363 processing and culture guidelines, 2021 spectrum of activity, 1225 features and availability of taxons in, data- Medical laboratory technician (MLT), defini- M’Fadyean stain, 336 bases of Gram-positive cocci, 364 tion, 74 MGIT 960 System, 1406–1408 Gram-positive rods, 451 Medicopsis romeroi inoculum and incubation, 1406–1407 identification of Gram-positive bacteria, assimilation patterns, 2269 pyrazinamide (PZA) testing, 1407–1408 953–955 in vitro susceptibility, 2272 quality control, 1407 identifying aerobic Gram-positive cocci, microscopy of grains, 2267 reading and interpreting results, 1407 362–365 morphological identification, 2268–2269 Micafungin infection prevention, 142 morphology by direct examination, 2040 clinical breakpoints for Candida spp., 2352 introduction in clinical microbiological taxonomy and description, 2263 clinical use, 2325 laboratory, 922–923 Mefloquine spectrum of activity, 2320, 2324 method, 180 adverse effects, 2655 Microascales order microbiology lab method, 1336 mechanism of action, 2654 Knoxdaviesia genus, 2243 reportable organisms, 55–57 mechanism of resistance, 2670 Lomentospora genus, 2243 resistance for antimicrobial susceptibility, pharmacokinetics, 2654–2655 Microascus genus, 2243 1308 spectrum of activity, 2655 overview of genera in, 2236 safety implications of, 212 Melanized fungi phaeohyphomycosis, 2234, 2247, 2249 streptococci, 406–407 antifungal susceptibilities, 2254 Scedosporium genus, 2243, 2263 target plate, 54 clinical significance, 2247–2250 Scopulariopsis genus, 2243 turnaround time for, 54, 57 collection, transport, and storage of speci- taxonomy and description, 2242–2243, workflow, 53 mens, 2250 2263 Mayo Medical Labs, human herpesvirus 6 direct examination, 2250–2251 Triadelphia genus, 2243 (HHV-6) testing, 1818 epidemiology and transmission, 2246–2247 typing systems, 2253

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Microascus genus, 2243 light, with labeled components, 17 Middlebrook ADC Enrichment, 353 Microbiological resistance, 2334–2335 maintenance, 25 Middlebrook OADC Enrichment, 353 susceptibility testing, 2353–2354 objective lenses, 19 MIDI (Microbioal ID Inc.), 293 Microfilariae, techniques for parasite recovery objective lens labeling, 19 MIDI, Inc., phenotypic identification system, and identification, 2436 phase contrast, 21 51 Microarray approaches, pathogen discovery stereoscopic/dissecting, 21 Millipedes, stinging and biting for envenom- and microbial genomics, 272–273 types and applications, 20–21 ation, 2636 Microbacteriaceae family Microscopic Observation Drug Susceptibility Miltefosine description, 492 (MODS) system, 1408–1409 adverse effects, 2659 identification, 513 Microscopy mechanism of action, 2659 Microbacterium genus brief history of, 16 pharmacokinetics, 2659 description, 492 common techniques, 22 spectrum of activity, 2659 identification, 513 contrast, 18 Minimum inhibitory concentration (MIC) Microbial diversity, 290 correlation of findings to culture, 22–23 dilution methods for, 1284 Microbial genomics documentation of, competency, 23–24 distributions, 1279, 1280 merging with pathogen discovery, 272–278 Gram stain review policy, 23 quality control ranges in dilution testing, microarray-based approaches, 272–273 limitations, sensitivity and specificity, 1292 recent history of, 271–272 16–17 Mites sequencing-based approaches, 273–278 magnification, 17 arthropods as vectors, 2626–2627 Microbial systematics and taxonomy, intro- photomicroscopy, 24–25 endoparasitic arthropods, 2633 duction to, 287–288 properties of light, 17–18 summary of infectious agents and disease, Microbiologists, databases for, 290 provider-performed microscopy (PPM), 24 2621 Microbiology laboratory automation quality assurance, 21 Mobiluncus spp., clinical significance, 944 antimicrobial susceptibility testing, 76 regulatory requirements, 22–24 MOD4, 353 automated inoculation systems, 77 resolution, 18 MOD9, 353 automated specimen processing, 76–77 smart phone cameras, 25 Modified Field’s stain, parasitology, 2413 BD-Kiestra TLA Concept, 78–79, 82 specific applications, 21 Modified Kinyoun stain, parasitology, 2410 criteria for evaluation and selection of, suggested slide retention policy, 24 Modified safranin stain, parasitology, 2413 82–83 utility in molecular era, 16 Modified Ziehl-Neelsen stain, parasitology, digital imaging, 80 Microsporidia 2410 historical perspectives, 76 antimicrobial susceptibilities, 2312 Molds limitations of system, 80, 82 clinical manifestations, 2306 classification and identification of anamor- molecular automation, 76 clinical significance, 2309 phic, 2011–2012 organism identification, 76 collection, transport, and storage of speci- form-class Coelomycetes, 2011–2012 total, 78, 80 mens, 2310 form-class Hyphomycetes, 2012 WASPLab, 80–82 cytological diagnosis, 2311 identification of, 2012 Microbiome description of genera and species, Molecular epidemiology preservation methods, 201 2305–2306, 2308 applications, 180–184 See also Human microbiome detection procedures, 2310–2311 cluster detection and outbreak investiga- Micrococcaceae family Encephalitozoon spp., 2309 tions, 181–182 Arthrobacter genus, 401 Enterocytozoon bieneusi, 2309 data interpretation, 186 Auritibacter genus, 401 epidemiology and transmission, 2308–2309 definitions, 168 clinical significance, 378–379 evaluation, interpretation, and reporting of dynamics of infectious disease, 182–183 description of, 374 results, 2312 forensic microbiology, 184 epidemiology and transmission, 377 examination of biopsy specimens and genotyping for viruses, 181 identification, 385–386, 511–512 corneal scrapings, 2311 libraries for, 186–188 key tests for identification, 375 generalized life cycle of, 2307 method selection, 184–185 Rothia genus, 401 identification, 2312 method validation, 185–186 taxonomy of, 368–369 isolation, 2311–2312 molecular serotyping, 180–181 See also Catalase-positive cocci molecular techniques, 2311 source attribution, 182 Micrococcus spp. phylum of kingdom Fungi, 2011 strain catalogues, 187 susceptibility testing, 1365 serologic tests, 2312 subtyping methods, 167–180 taxonomy of, 367 species pathogenic in humans, 2306 surveillance databases, 187–188 testing conditions, 1352 taxonomy, 2305 vaccination issues, 183–184 Microorganisms Microsporum spp. See also Subtyping methods hierarchy of resistance, 225 characteristics of dermatophytes and der- Molecular methods, drug susceptibility test- resistance profiles of, 226 maphytoids, 2209–2211 ing, 1409 See also Preservation of microorganisms dermatophyte nutritional response, 2221 Molecular microbiology MicroScan, phenotypic identification system, description of, 2222, 2224–2225, 2226 amplified nucleic acid techniques, 87 48–49 grouping of dermatophytes on host and automation and instrumentation, 107–108 MicroScan WalkAway, automated broth habitat, 2216 bacteria and fungi identification by nucleic microdilution, 1302, 1303 growth on BCP-milk solids-glucose medium acid sequencing, 109–110 Microscope (BCPMSG), 2222 branched-DNA (bDNA) assays, 87–88 bright-field including oil immersion, 20 growth on polished rice grains, 2222 cleavage-invader technology, 88–89, 90 components and functions, 18–20 hair invasion, 2219 current applications, 108–111 condenser, 19 preliminary patient examination, 2217 disease prognosis, 110 dark-field illumination, 21 taxonomy, 2208, 2216 future directions for, 116–117 ergonomics, 25–26 See also Dermatophytes hybrid capture assays, 88, 89 example of optical train, 18 Middlebrook 7H9 Broth with Middlebrook initial diagnosis, 108–109 eyepieces, 19 ADC Enrichment, 353 laboratory practice, 111–116 field diaphragm, 18–19 Middlebrook 7H10 Agar with Middlebrook nonamplified nucleic acid probes, 86–87 fluorescent, 20–21 ADC Enrichment, 353 nucleic acid amplification techniques, 86 illuminator, 18 Middlebrook 7H11 Agar with Middlebrook postamplification detection and analysis, Köhler illumination, 19–20, 26 ADC Enrichment, 353 99, 101, 103–106

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quantitative methods, 106–107 MTBC (Mycobacterium tuberculosis complex), Multiple locus variable-number tandem repeat signal amplification techniques, 87–89 1398. See also Drug susceptibility (VNTR), 795 target amplification techniques, 89–99 testing of MTBC; Mycobacterium characteristics and application, 169 therapy duration and response, 110–111 tuberculosis complex (MTBC) international databases for, 187 See also Postamplification detection Mucicarmine stain method, 175–176 and analysis; Target amplification fungi detection, 2036 Multiplex PCR, 6–7, 91–92 techniques mycology, 2028 Mumps virus (MuV) Molecular serotyping, 180–181 Mucor genus antigen detection, 1531, 1536 Molecular taxonomy, 167 culture variability and branching, 2169 clinical significance, 1536 Molecular testing identification, 2169, 2171 collection, transport, and storage of speci- resistance detection, 1281 macroscopic and microscopic features in, 2172 mens, 1536 selecting methods, 1278 micromorphology of, 2171 description, 1528 Mollicutes Mucoraceae family detection and identification methods, 1474 antimicrobial susceptibilities, 1128–1130 genus Actinomucor, 2171–2172 diagnostic methods, 1531 classification and features of mycoplasmas, genus Cokeromyces, 2172 direct examination, 1536–1537 1118 genus Mucor, 2169, 2171 epidemiology and transmission, 1535–1536 clinical significance, 1120–1122 human mucormycosis, 2164 evaluation, interpretation, and reporting of collection, transport, and storage of speci- Mucoraceous molds, morphology by direct results, 1538 mens, 1122–1123 examination, 2039 immunofluorescence staining, 1534 description of, 1117–1119 Mucorales spp. isolation and identification, 1537 direct examination, 1123–1124 culture variability and branching develop- microscopy, 1536 epidemiology and transmission, 1119–1120 ment of, 2169 nucleic acid detection, 1536–1537 evaluation, interpretation, and reporting of flow diagram for identification, 2170 serologic tests, 1537–1538 results, 1130–1131 involvement in mucormycosis, 2164 taxonomy, 1528, 1529 genitourinary infections, 1120–1121 schematic drawing of morphological struc- Münster university Hospital, 187 identification, 1125–1126 tures, 2168 Mupapillomavirus genus, 1848, 1849, 1851 immunosuppressed hosts, 1122 taxonomy, 2163 Mupirocin, 1228 isolation procedures, 1124–1125 See also Mucormycosis resistance, 1264 neonatal infections, 1121–1122 Mucormycosis as resistance target, 1427 respiratory infections, 1120 antifungal susceptibilities, 2177 Murdochiella spp., biochemical features, 930 serologic tests, 1126–1128 antigen detection, 2166 Muscle sites of colonization, metabolism and clinical manifestations, 2165 parasites, 2390 pathogenicity of, 1118 collection, transport, and storage of speci- specimen for parasite detection, 2429, 2432 systemic infections, 1122 mens, 2165–2166 specimen preparation and procedures, 2395 typing systems, 1126 direct examination, 2166 Muscoid flies, arthropods as scalars, 2630 Molluscipoxvirus genus epidemiology and transmission, 2163–2165 Mutation, resistance by, 1243 real-time PCR assays for, 1899 evaluation, interpretation, and reporting of Myceliophthora taxonomy, 1892 results, 2177 clinical significance, 2152 Molluscum contagiosum virus, 1900 family Cunninghamellaceae, 2175 hyphomycetes, 2149 Monkey B virus. See Herpes B virus family Lichtheimiaceae, 2168 Mycobacteria Monkeypox virus (MPxV) family Mucoraceae, 2169, 2171–2172 MALDI-TOF MS identification of, 59–60 electron micrograph of forms, 1896 family Rhizopodaceae, 2173–2175 preservation methods, 201, 202 epidemiology, 1892 family Saksenaeaceae, 2172–2173 reportable organisms for MALDI-TOF Monobactams family Syncephalastraceae, 2175–2176 MS, 56 adverse effects, 1206 histopathology, 2166 as resistance target, 1427 chemical structures of, 1202 identification, 2167–2177 Mycobacterial Growth Indicator Tube mechanism of action, 1206 isolation procedures, 2166 (MGIT), 1400 pharmacology, 1206 microscopy, 2166 Mycobacterial infections, antimicrobial agents spectrum of activity, 1206 molecular identification, 2176–2177 treating, 1398–1399 Mononegavirales order, 1674 nucleic acid detection in clinical materials, Mycobacterium genus Mononucleosis, Epstein-Barr virus (EBV), 2166–2167 acid-fast stain procedures, 563–565 1797, 1798–1799, 1805 PCR-based diagnosis in serum, 2167 agar-based media, 566 Moraxella genus phenotypic identification, 2167–2176 antimicrobial agents treating, 1399 identification, 832, 837–838 prophylaxis, 2165 automated, continuously monitoring taxonomy, 829 screening, 2167 systems, 567 Moraxella catarrhalis, 848 serologic tests, 2177 collection and storage of specimens, clinical significance, 829, 831 treatment of, 2165 561–562 MALDI-TOF mass spectrometry, 833 typing systems, 2177 common digestion-decontamination meth- susceptibility testing, 1366 Mucoromycotina, subphylum of kingdom ods, 570–572 testing conditions, 1352 Fungi, 2009, 2010 CPC method, 571–572 Morganella genus, 726 Mueller-Hinton agar (MHA), 353, 1284 cross-contamination, 568 biochemical characterization, 734 Mueller-Hinton broth, 353 culture, 565–568 epidemiology, transmission, and clinical Mueller-Hinton chocolate agar, 353 description of genus, 558–559 significance, 730–731 Mueller-Hinton II agar, 353 digestion and decontamination methods, nomenclature and source of species, Mueller-Tellurite medium, 353 562–563 726 Mulluscipoxvirus, epidemiology, 1893 egg-based media, 565–566 See also Enterobacterales order Multicentric Castelman disease (MCD), epidemiology and transmission, 559–560 Mosquitoes. See Arboviruses human herpesvirus 8 (HHV-8), 1827 growth indicator tube, 566–567 Moxifloxacin Multidrug resistance (MDR) heme-containing medium, 566 activity against Clostridium spp., 987 laboratory-acquired infection, 216–217 immunodiagnostic tests for tuberculosis, Bacteroides spp., 1384 Pseudomonas, 797 568 MRS agar (DeMan-Rogosa-Sharpe agar, Multilocus sequence typing (MLST), 795 incubation, 567–568 Lactobacillus MRS agar), 353 characteristics and application, 169 isolation and staining procedures, 562–568 MRSA Select Medium, 353 method, 174–175 laboratory safety procedures, 560–561

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Mycobacterium genus (continued) epidemiology and transmission, 576–577 description, 1117–1119 medium selection, 567 evaluation, interpretation, and reporting of detection kit for serum antibodies, 1127 NALC-NaOH method, 570–571 results, 588–590 development of colonies, 1125 nutritional requirements and growth, 559 genes and associated drug-resistance muta- diagnostic tests for, 1113–1114 oxalic acid method, 571 tions in, 587–588 epidemiology and clinical diseases associ- processing of specimens, 562 genotypic strain typing, 582–583 ated with, 1110 quality assurance, 568–570 HPLC, 582 epidemiology and transmission, 1119–1120 quality control of smear, culture, and mo- identification, 580–582 evaluation, interpretation, and reporting of lecular tests, 569–570 immunodiagnostic tests, 583–585 results, 1130–1131 sodium hydroxide method, 571 isolation procedures, 580 fried-egg-type colonies, 1117, 1119 sulfuric acid method, 572 laboratory safety, 579 genitourinary infections, 1120–1121 susceptibility to physical and chemical MALDI-TOF MS, 582 identification, 1125–1126 agents, 559 microscopy, 579 incubation conditions and subcultures, taxonomy, 558–559 molecular line probe assays (LPAs), 582 1125 transportation and transfer of biological molecular methods, 581–582 isolation procedures, 1124–1125 agents, 561 novel proposed species within, 578–579 M. genitalium, 1131 See also Rapidly growing mycobacteria nucleic acid amplification tests, 579–580 M. hominis, 1130 (RGM); Slowly growing nontubercu- PCR-based sequencing, 582 MIC ranges for antimicrobials, 1129 lous mycobacteria (SGM) phenotypic methods, 581 microscopy, 1123 Mycobacterium africanum, clinical significance, safe handling, collection, and storage of M. pneumoniae, 1120, 1130 578 specimens, 579 M. pneumoniae respiratory disease, Mycobacterium avium complex (MAC), 595 schematic of ideal algorithm for mycobacte- 1126–1128 antimicrobial agents for, 1410, 1411 riology testing, 589 neonatal infections, 1121–1122 clinical significance, 598 taxonomy, 576 nucleic acid detection, 1123–1124 indications for susceptibility testing, 1410 typing systems, 582–583 primary sites of colonization, metabolism, properties of, 599 Mycobactosel agar, 353 and pathogenicity, 1118 reporting results, 1411 Mycobactosel L-j medium, 353 respiratory infections, 1120 test methods, 1411 MycoBank database, 2008 serologic tests, 1126–1128 See also Slowly growing nontuberculous Mycobiotic or Mycosel agar, mycology, 2031 spherical colonies of, 1117, 1119 mycobacteria (SGM) Mycological terms, 2013–2015 systemic infections and immunosuppressed Mycobacterium bovis Mycology laboratory hosts, 1122 clinical significance, 578 commercial manufacturers of media, stains, taxonomy, 1117 epidemiology and transmission, 577 and reagents, 2032–2033 term, 1117 IS6110 fingerprinting, 172 laboratory testing, 2025–2026 typing systems, 1126 Mycobacterium bovis BCG media, 2029–2032 See also Mollicutes clinical significance, 578 reagents, 2026–2027 Mycoses. See Dimorphic fungi causing sys- colony morphology, 581 stains, 2027–2029 temic mycoses; Superficial mycoses epidemiology and transmission, 577 Mycology specimens Mycotoxins Mycobacterium canettii abscess, 2018–2019 aflatoxins, 2278–2279, 2281 clinical significance, 578 blood, 2019–2020 bioterrorism and, 2284–2285 colony morphology, 581 bone marrow, 2020 chemical classification and biosynthesis of, epidemiology and transmission, 577 catheter tips (intravascular), 2020–2021 2278–2282 Mycobacterium caprae collection and transport, 2016 citrinin, 2281 clinical significance, 578 collection and transport guidelines, climate change and, 2284 epidemiology and transmission, 577 2017–2018 cyclopiazonic acid, 2281 Mycobacterium kansasii, susceptibility testing, cutaneous, 2021 detection, 2283–2284 1411 eye (corneal scrapings and vitreous humor), ergot alkaloids, 2281 Mycobacterium leprae, PCR, 601 2021 food safety, 2282–2284 Mycobacterium marinum, susceptibility testing, hair, 2021 fumonisins, 2281 1411 handling, pretreatment and safety, 2016, ochratoxins, 2281–2282 Mycobacterium microti 2018 patulin, 2282 acid-fast staining, 581 lower respiratory tract, 2022 prevention and amelioration of contamina- clinical significance, 578 medical devices, 2021 tion, 2284 “Mycobacterium mungi,” clinical significance, nails, 2021 regulation of, 2282–2283 578 pretreatment prior to plating, 2020 sick building syndrome, 2285 “Mycobacterium orygis,” clinical significance, processing and culture guidelines, trichothecenes, 2282 578 2018–2023 zearalenone, 2282 Mycobacterium pinnipedii prostate fluid, 2021–2022 Myelitis, VZV infection, 1758–1759 clinical significance, 578 sites for laboratory recovery of pathogenic Myocarditis, agents of, 896–897 epidemiology and transmission, 577 fungi, 2019 Myonecrosis (gas gangrene), 972–973 “Mycobacterium suricattae,” 578 skin, 2021 Myiasis, endoparasitic arthropods, 2633–2634 Mycobacterium tuberculosis, 269 sterile body fluids, 2022 Myroides odoratimimus clinical significance, 578 stool, 2022 characteristics of, 840 colony morphology, 581 tissue, 2022–2023 identification, 841 CRISPR analysis, 176 upper respiratory tract, 2022 Myroides odoratus epidemiology and transmission, 576–577 urine, 2023 characteristics of, 840 IS6110 fingerprinting, 172 vaginal, 2023 identification, 841 laboratory-acquired infection, 214 Mycoplasma agar base (PPLO agar base), 353 Myriodontium Robert Koch in 1880s, 206 Mycoplasma broth base without crystal violet clinical significance, 2152 Mycobacterium tuberculosis complex (MTBC), and ascitic fluid, 354 hyphomycetes, 2149 576 Mycoplasma spp., 1109 antimicrobial susceptibility testing, 586 antigen detection, 1123 clinical significance, 577–578 antimicrobial susceptibilities, 1128–1130 NAAT. See Nucleic acid amplification testing description, 576 biosafety considerations, 1124 N-Acetyl-l-cysteine (NALC), mycology direct examination, 579–580 clinical significance, 1120–1122 reagent, 2026

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NaCl agar, 354 DNA sequencing, 647 laboratory-acquired infection, 213 Naegleria genus epidemiology and transmission, 640–641 laboratory techniques, 161 classification, 2382 evaluation, interpretation, and reporting of medium, 354 description of, 2487 results, 648–650 molecular typing methods for, 647 detection in humans, 2381 identification, 645–647 nucleic acid detection, 644–645 epidemiology, 2488 immunologic methods for culture confirma- primary pathogen of Neisseria genus, 640, 650 meningoencephalitis, 2488–2489 tion, 646 strategies for testing and reporting of taxonomy, 2486 isolation procedures, 645 results, 1359 See also Free-living amebae laboratory safety for handling meningococ- testing methods, 1349 Nafcillin, 1201 cal cultures, 643 typing systems, 647 Nails MALDI-TOF, 646–647 working with cultures, 206 collection and transport, 2017 microscopic morphology, 646 Neisseria mucosa pathogenic fungi recovery, 2019 microscopy, 643 characteristics of, 645 pretreatment, 2020 multitest identification systems, 646 reporting results, 650 processing and culture guidelines, 2021 nucleic acid detection, 643–645 Neisseria oralis NALC-NaOH (N-acyl-l-cysteine-sodium oxidase test, 646 characteristics of, 645 hydroxide), 335 presumptive identification, 645–646 reporting results, 650 NALC-NaOH method, digestion and decon- serologic tests, 647–648 Neisseria polysaccharea tamination, 562, 570–571 taxonomy, 640 characteristics of, 645 Nannizzia spp. typing systems, 647 reporting results, 650 description of, 2226 Neisseria animaloris Neisseria sicca taxonomy, 2208 characteristics of, 645 characteristics of, 645 Nannizziopsis reporting results, 649 reporting results, 650 clinical significance, 2152 Neisseria bacilliformis Neisseria subflava hyphomycetes, 2149 characteristics of, 645 characteristics of, 645 Nanophyetus salmincola, 2593 reporting results, 649 reporting results, 650 eggs of, 2599 Neisseria cinerea Neisseria weaveri NARMS. See National Antimicrobial characteristics of, 645 characteristics of, 645 Resistance Monitoring System reporting results, 649 reporting results, 650 (NARMS) Neisseria elongata Neisseria zoodegmatis Nasopharyngeal carcinoma characteristics of, 645 characteristics of, 645 Epstein-Barr virus (EBV), 1797, 1805 reporting results, 649 reporting results, 650 methods for prevention, diagnosis, and Neisseria flavescens Nelfinavir monitoring, 1801 characteristics of, 645 drug interactions, 1944 Nasopharynx and sinus cavities, specimen for reporting results, 649–650 HIV therapy, 1939 parasite detection, 2429, 2432 Neisseria gonorrhoeae, 1348 pharmacology, 1944 National Antimicrobial Resistance antimicrobial susceptibilities, 648 Nematoda, classification, 2384–2385, 2386 Monitoring System (NARMS), 1037, ceftriaxone resistance in, 1426 Nematodes, 2551 1362, 1421 characteristics of, 645 Ascaris lumbricoides (roundworm), National Center for Biotechnology collection, transport, and storage of speci- 2555–2558 Information (NCBI), 164, 179, 296 mens, 642–643 collection, transport, and storage of speci- database, 1439, 1444 colonial morphology, 645 mens, 2555 National Credentialing Agency, 116 commercial available nucleic acid amplifi- culture of larval-stage, in stool, 2421, 2423 National Electronic Disease Surveillance cation tests, 644 direct examination, 2555 System, 156 commercial test methods, 1358 eggs and larvae of intestinal, 2554 National Healthcare Safety Network detection of, 322 eggs of various intestinal, 2553 (NHSN), 140, 422, 725 epidemiology and transmission, 640–641 Enterobius vermicularis (pinworm or thread- National Institute for Communicable evaluation, interpretation, and reporting of worm), 2558–2561 Diseases, 1728 results, 648–649 evaluation, interpretation, and reporting of National Institute for Occupational Safety incidence of resistance, 1357–1358 results, 2568 and Health (NIOSH), 560 isolation procedures, 645 helminth recovery and identification, 2423 National Institutes of Health (NIH), 296, 559 nucleic acid detection, 643–644 hookworms, 2561–2563 Human Microbiome Project (HMP), primary pathogen of Neisseria genus, 640, relative sizes of helminth eggs, 2552 254–255 650 Strongyloides fuelleborni, 2566 National Notifiable Diseases Surveillance reference test methods, 1349, 1358 Strongyloides stercoralis, 2563–2566 System, 1713 strategies for testing and reporting of taxonomy of, 2551, 2553 National Survey of Employed Adults and results, 1358 times for completion of life cycles, 2558 Seniors, 1086 subtyping, 175 Trichuris trichuria (whipworm), 2566–2568 Necrotizing enterocolitis (NEC), 971 typing systems, 647 See also Filarial nematodes Necrotizing fasciitis, 325 whole-genome SNP typing, 177 Neobalantidium genus suspected, 976 Neisseria lactamica classification, 2383 Neisseria genus characteristics of, 645 detection in humans, 2381 antigen detection, 643 reporting results, 650 Neobalantidium coli antimicrobial susceptibilities, 648 Neisseria meningitidis clinical significance, 2517 carbohydrate utilization assays, 646 antimicrobial susceptibilities, 648 description of agent, 2517 characteristics of medically relevant spe- characteristics of, 645 direct examination, 2517–2518 cies, 645 collection, transport, and storage of speci- epidemiology, transmission, and preven- chromogenic enzyme substrate tests, 646 mens, 643 tion, 2517 clinical significance, 641–642 colonial morphology, 645 evaluation, interpretation, and reporting of collection, transport, and storage of speci- epidemiology and transmission, 641 results, 2518 mens, 642–643 evaluation, interpretation, and reporting of key features of, 2517 colonial morphology, 645 results, 649 microscopy, 2517–2518 definitive identification, 646–647 gene sequencing, 174 taxonomy, 2516–2517 description of, 640 incidence of resistance, 1358 treatment, 2518 direct examination, 643–645 isolation procedures, 645 trophozoite, 2517

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Neomycin blood agar, 354 Niger seed agar, mycology, 2031 test method, 1409–1410 Neonatal/fetal samples Nigrograna mackinnonii validated species, 596–597 amniotic fluid, 1453 assimilation patterns, 2269 See also Slowly growing nontuberculous virus detection methods, 1448 taxonomy and description, 2263 mycobacteria (SGM) Neonatal herpes, herpes simplex virus (HSV), Nitazoxanide Norovirus 1742 adverse effects, 2652 clinical features, 1659, 1661 Neonatal infections, Mollicutes, 1121–1121 major indications for, 2652 detection and identification methods, 1474 Neorickettsia spp. mechanism of action, 2652 electron micrograph of, 1658 clinical significance, 1168–1169 pharmacokinetics, 2652 molecular assays for detection, 1664 description of, 1163–1164 spectrum of activity, 2652 taxonomy, 1657 epidemiology and transmission, 1164, Nitrate broth, 354 Nosema spp. 1166–1168 Nitrate reduction test, 333–334 description, 2306 features of human and veterinary interest, Nitrofurantoin life cycle of microsporidia, 2307 1165 adverse effects, 1227 Nosocomiicoccus genus, 368, 377 neighbor-joining phylogenetic tree, 1164 mechanism of action, 1226 NS3/4A protease inhibitors, against hepatitis N. sennetsu, 1168, 1169 pharmacology, 1226–1227 C virus (HCV), 1946–1948 sennetsu fever, 1168 resistance, 1259 NS5A inhibitors See also Anaplasmataceae family spectrum of activity, 1227 against hepatitis C virus (HCV), 1947, Neoscytalidium genus, 2238, 2247 Nitroimidazole, 1402 1948–1949 clinical significance, 2151–2152 Nocardia genus hepatitis C virus (HCV), 1971, 1972–1973 hyphomycetes, 2147, 2149 clinical significance, 537–540, 1413 NS5B RNA-dependent RNA polymerase Neoscytalidium dimidiatum, 2238 colonial morphology, 530 inhibitors, against hepatitis C virus Neotestudina rosatii description, 527, 529, 531 (HCV), 1947, 1949–1950 cultures of, 2264, 2265 epidemiology and transmission, 533 Nucleic acid amplification testing (NAAT), microscopy of grains, 2267 human clinical significance, 536 86 morphology by direct examination, 2039 MALDI-TOF MS identification of, non-culture-based methods, 36–37 taxonomy and description, 2263 59–60 BK polyomavirus, 1871 Nessler reagent (acetamide hydrolysis test), microscopic morphology, 532 Campylobacter testing, performance charac- 331 morphologic characteristics, 528 teristics, 1034 Nested PCR, 90–91 N. abscessus, 538 Clostridioides difficile, 978–979 Neuraminidase inhibition assay, antiviral N. asteroides, 538 Ebola virus, 1730, 1731 susceptibility testing, 1988 N. brasiliensis, 538 Epstein-Barr virus, 1802 Neuraminidase inhibitors, against influenza N. brevicatena/N. paucivorans, 538 Escherichia antigen detection from nonstool virus, 1954–1955, 1974–1975 N. cyriacigeorgica, 538–539 specimens, 711 Neurologic specimens, virus detection meth- N. farcinica, 539 Escherichia spp., 707–710 ods, 1448 N. nova, 539 human polyomaviruses, 1870–1871 Neuroretinitis, agents of, 896–897 N. otitidiscaviarum, 539 jC polyomavirus, commercial products, Neurosyphilis N. pseudobrasiliensis, 539–540 1871 clinical and laboratory criteria for diagno- N. transvalensis, 540 laboratory-developed, for rapid identifica- sis, 1087 N. veterana, 540 tion of isolates, 37 tests for, 1101–1102 N. wallacei, 540 Mycobacterium tuberculosis complex Neutropenia, Pseudomonas infection in quality control, 1414 (MTBC), 579–580 patients with, 788 reportable organisms for MALDI-TOF Neisseria gonorrhoeae, commercial available Neutropenic enterocolitis, suspected, with MS, 56 tests, 644 C. septicum, 980 reporting results, 1414 Salmonella spp., 707–710 Nevirapine susceptibility patterns of, 537 Shigella antigen detection from nonstool drug interactions, 1942 testing method, 1413–1414 specimens, 711 HIV therapy, 1938 testing recommendations from CLSI, 1414 Shigella spp., 707–710 mechanism of resistance, 1965, 1967 See also Actinomycetes Zika virus, 271 pharmacology, 1942 Nocardiopsis genus Nuclear magnetic resonance (NMR), 294 Newborn infant, cytomegalovirus (CMV) classification, 526 Nucleic acid probes infection, 1771 clinical significance, 540 fluorescencein situ hybridization (FISH), 87 New Delhi metallo-beta-lactamase (NDM-1), description, 531 hybridization protection assay, 86 1420 recovered from human specimens, 535 in situ hybridization, 86 New World hantavirus species, 1706, 1709 See also Actinomycetes liquid-phase hybridization, 86 identification, 1711–1712 Nomenclature, 291–292 nonamplified, 86–87 See also Hantaviruses Nomenclature Committee for Fungi, 2056 peptide nucleic acid (PNA) probes, 87 New York City medium, 354 Nomenclature and strain tracking, 290 solid-phase hybridization, 86 Next-generation sequencing (NGS), 104 Non-A, non-B (NANB) hepatitis, discovery Nucleic acid sequencing instruments and methodology, 272 of, 271 bacteria and fungi identification, 109–110 method, 176–177 Non-culture-based methods postamplification analysis, 103–104 pathogen discovery and microbial genom- nucleic acid amplification methods, 36–37 Nucleoside/nucleotide reverse transcrip- ics, 17;5–10 surrogate markers for sepsis, 36 tase inhibitors, HIV therapy, 1938, NHANES III (Third National Health and Nonfermenters, Gram-negative, 633, 634 1940–1941, 1965–1967 Nutrition Examination Survey), 1086 Nonnucleoside reverse transcriptase inhibi- Nucleoside reverse transcriptase inhibitors Nicking endonuclease application reaction tors (NNRTIs), HIV therapy, 1938, (NRTIs), resistance of hepatitis B (NEAR) 1941–1942, 1967 virus, 1969–1970 mechanism, 102 Nonsusceptible, breakpoint definition, 1285 Nucleotide and nonnucleoside RdRp process, 99 Nontuberculous mycobacteria (NTM), 558 inhibitor resistance, hepatitis C virus Nifurtimox and benznidazole epidemiology and transmission, 595, 597 (HCV), 1972 adverse effects, 2662 incubation period and temperature for Nupapillomavirus genus, 1848, 1849, 1851 mechanism of action, 2661 testing, 1410 Nutrient agar 1.5%, HiVeg with ascitic fluid, pharmacokinetics, 2661 quality control, 1410 354 spectrum of activity, 2661–2662 slowly growing, 1411–1412 N-Z Amine A glycerol agar, 354

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O157:H7 ID agar, 354 Ophidiomyces Orthopoxvirus genus Occupational health program, 209 clinical significance, 2152 real-time PCR assays for, 1897–1898 Occupational Safety and Health hyphomycetes, 2149 taxonomy, 1892 Administration (OSHA), 226 Ophiostoma genus, 2243–2244, 2250 Orthopoxviruses Ochratoxins Ophiostomatales order cowpox virus (CPxV), 1892 classification and biosynthesis of, Ophiostoma genus, 2243–2244 epidemiology, 1892 2281–2282 overview of genera in, 2236–2237 monkeypox virus (MPxV), 1892 common food substrates, 2282 phaeohyphomycosis, 2247, 2248, 2250 serologic tests, 1899–1900 genetic structure, 2280 Sporothrix genus, 2244 vaccinia virus (VACV), 1892 pathological effects and toxicological refer- taxonomy and description, 2243–2244 variola virus (VARV), 1892 ence values, 2283 typing systems, 2253 Oseltamivir structure of, 2279 Opisthokonta supergroup, eukaryotes, against influenza virus, 1955 See also Mycotoxins 2380–2382 drug interactions, 1955 Ochroconis genus, 2246 Opisthorchiidae family mechanism of resistance, 1974–1975 Ochrobactrum anthropi clinical significance, 2600 pharmacology, 1955 characteristics of, 840 description of agents, 2600 Otitis externa, Pseudomonas, 789 identification, 841 direct examination, 2600 Otitis media, rapidly growing mycobacteria, Ochrobactrum intermedium epidemiology, transmission, and preven- 617 characteristics of, 840 tion, 2600 Ouchterlony, Orjan, 124 identification, 841 geographic distribution, hosts and histories Outbreak Database, 165 Ocular adenovirus infections, 1835 of, 2592 Outbreak investigations, 181–182 Ocular herpes infections, 1742 microscopy, 2599, 2600 Outer membrane porin proteins (OMPs), Odoribacter genus nucleic acid detection, 2600 1243, 1245 characteristics of, 997 serologic testing, 2600 Oxacillin, 1201 phenotypic characteristics of, 1007 treatment, 2600 Oxacillin resistance Oerskovia genus Opisthorchis viverrini, 2600 cefoxitin as surrogate for, 1322 description, 490, 492 eggs of, 2599 detection in staphylococci, 1321–1323 identification, 502, 512 Optical mapping, 173 penicillin resistance in pneumococci, Old World hantavirus species, 1706 Optochin test 1321 identification, 1711–1712 streptococci, 410 staphylococci, 1305 See also Hantaviruses Oral microbiome Oxalic acid, 335, 563, 571 Oligella biogeography and structures of human, Oxazolidinones, 1402 MALDI-TOF mass spectrometry, 833 257 adverse effects, 1222 taxonomy, 829 microbial composition, 255 linezolid as resistance target, 1426–1427 Oligella ureolytica predominant phyla, 256 mechanism of action, 1221 characteristics of, 837 study of, 256–258 pharmacology, 1221 identification, 838 See also Human microbiome spectrum of activity, 1221–1222 Oligella urethralis Oral papillomatosis, human papillomavirus Oxford agar, 354 characteristics of, 837 (HPV), 1852 Oxford university, 187 identification, 838 Oral specimens, collection and processing of Oxidase test, 334 Olsenella spp. virus, 1455 Oxidation-fermentation medium, Hugh- clinical significance, 946 Oral treponemes, 1086 Leifson’s, 354 enzyme reactions, 952 antimicrobial susceptibilities, 1098 Oxidation-fermentation medium, King’s, 354 Ombitasvir collection, transport, and storage of speci- Oxidation-fermentation polymyxin-bacitracin drug interactions, 1948 mens, 1089 lactose, 354 HCV therapy, 1947 Organisms, uncultivated, 291 Oxoid Salmonella chromogenic agar (OSCM), mechanism of resistance, 1971, 1973 Orientia spp. 354 pharmacology, 1948 characteristics of, 1150 Onchocerca volvulus description of genus, 1150–1151 clinical significance, 2575 taxonomy, 1149 P agar, 354 description of, 2575 Orientia tsutsugamushi Paecilomyces diagnosis, 2575 antimicrobial susceptibilities, 1157 clinical significance, 2152 diagrammatic representation of extremities, characteristics of, 1150 hyphomycetes, 2149 2573 clinical significance, 1151 Paenalcaligenes direct examination, 2575–2576 description of, 1150–1151 antimicrobial susceptibilities, 865 epidemiology and transmission, 2575 diagnostic tests for, 1114 clinical significance, 861 lymph nodes, 2575 epidemiology and clinical diseases associ- collection, transport, and storage of microfilariae in humans, 2572 ated with, 1110 specimens, 862 nucleic acid detection, 2576 identification of, 1155 description of, 860 ocular disease, 2575 immunologic detection, 1154 identification, 864 onchocercomata, 2575 isolation procedures, 1155 isolation procedures, 863 parasite of humans, 2571 molecular detection, 1154–1155 taxonomy, 858 serologic tests, 2576 phylogeny of, 1150 Paenibacillus spp. skin, 2575 scrub typhus, 1151, 1152 characters for differentiating species, 468 taxonomy, 2575 serologic tests, 1156 clinical significance, 457 treatment, 2576 taxonomy, 1149 Pantoea genus ONE Broth-Listeria (Oxoid novel enrichment Oritavancin, 1218–1220 epidemiology, transmission, and clinical broth-Listeria), 354 lipoglycopeptide resistance, 1262–1263 significance, 728–729 Önöz Salmonella agar, 354 Oropharyngeal cancer, human papillomavirus identification, 735 ONPG (o-nitrophenyl-b-d-galactopyrano- (HPV) and, 1852–1853 nomenclature and source of species, 726 side), 332 Oroya fever, anthroponotic bartonelloses, See also Enterobacterales order Onychocola 896 Pan American Health Organization (PAHO), clinical significance, 2151–2152 Orthomyxoviridae family, 1510. See also 156 hyphomycetes, 2147, 2149 Influenza viruses Pandemic, influenza viruses, 1511

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Pandoraea, 808 evaluation, interpretation, and reporting of aspirates, 2402 characteristics of, 814 results, 1535 biopsy, 2402 clinical significance, 811 isolation and identification, 1532–1534 blood, 2402–2403 description of, 808 serologic tests, 1534–1535 body sites and, 2390 epidemiology and transmission, 808 See also Human parainfluenza viruses collection and transport, 2389–2400 identification, 817 (HPIVs) collection of blood, 2400 typing systems, 819 Paramphistomidae family, geographic distribu- collection of fresh stool, 2389–2390, 2396 Pannonibacter phragmitetus tion, hosts and egg morphology of, commercially available kits for immunode- characteristics of, 840 2593 tection in serum antibodies, 2392 identification, 841 Paranannizziopsis commercially available kits for immunode- Papanicolaou stain, fungi detection, 2036 clinical significance, 2152 tection in stool samples, 2391 Papillomaviridae family, nucleotide sequence of hyphomycetes, 2149 culture methods, 2403 L1 gene, 1848 Paraphyton spp. direct detection by routine methods, Papillomavirus Episteme (PaVE), 1847 description of, 2226 2400–2404 Papillomaviruses taxonomy, 2208 fecal collection and processing options, description of group of organisms, 1847, Parapoxvirus genus 2397 1849–1850 epidemiology, 1892–1893 formalin as fixative, 2398–2399 detection and identification methods, 1474 real-time PCR assays for, 1898–1899 intestinal tract, 2400–2401 taxonomy, 1847 taxonomy, 1892 nucleic acid detection, 2404 See also Human papillomaviruses (HPVs) Parasites preparation procedures for, 2393–2396 Parabacteroides genus, 995, 996 blood specimens, 2433–2437 preservation of stool, 2396, 2398–2400 antimicrobial activities of potential agents, bone marrow, 2427, 2428 PVA as preservative, 2399, 2400 1013 brain and cerebrospinal fluid, 2427, 2428, respiratory tract, 2401–2402 characteristics of, 997 2429–2430 sodium acetate-acetic acid-formalin (SAF) clinical significance, 1000 egg studies, 2423–2424 as preservative, 2399–2400 phenotypic characteristics of, 1007 eye, 2428, 2430 Schaudinn’s fluid, 2400 Paracoccidioides spp. FDA-approved molecular diagnostic tests, single-vial collection system, 2399, 2400 antigen detection, 2195 2422 test ordering for stool parasitology, 2398 antimicrobial susceptibilities, 2200, 2201 helminth recovery and identification tech- urogenital tract, 2401 biosafety, 2196 niques, 2423 Parasitology stains blastoconidia of, 2191 identification of helminth eggs, 2417 acid-fast trichrome stains, 2411, 2413 clinical significance, 2193 identification of intestinal amebae, 2419 blood film stains, 2410–2411 clinical specimens, 2194 identification of intestinal flagellates, 2419 calcofluor white stain, 2413 culture for yeast phase, 2196 image library and resources, 2404 commercially available, 2410 description of, 2190–2191 immunoassays for detection of intestinal, Delafield’s hematoxylin stain, 2411 epidemiology and transmission, 2192 2420 Giemsa and Wright’s stains, 2410–2411 evaluation, interpretation, and reporting of intestinal tract specimens, 2424–2426 hematoxylin stains, 2411, 2413 results, 2202 kidney and bladder, 2428, 2430 identification, 2408 identification, 2198 liver and spleen, 2428, 2430–2431 iodine, 2409–2410 microscopy, 2194 lungs, 2429, 2431 iron hematoxylin stain, 2411 nucleic acid detection, 2196 lymph node and lymphatics, 2428, modified Field’s stain, 2413 paracoccidioidomycosis, 2192, 2193, 2196, 2431–2432 modified Kinyoun stain, 2410 2200 muscle, 2429, 2432 modified safranin stain, 2413 serologic tests, 2200 nasopharynx and sinus cavities, 2429, 2432 modified Ziehl-Neelsen stain, 2410 taxonomy, 2188 rectal tissue, 2429, 2432 Wheatley trichrome stain, 2411 typing systems, 2199 skin, 2429, 2432–2433 Parasitosis, 2637 Paracoccidioides brasiliensis urogenital specimens, 2426–2427 Parastrongylus (Angiostrongylus) spp. bright-field photomicrograph, 2046 See also Eukaryotes; Stool specimens clinical significance, 2612 morphology by direct examination, 2038 Parasitic worms, classification, 2384–2385 description of agents, 2611 Paracoccidioides brasiliensis var. ceti, 2292 Parasitology information, 2404 direct examination and microscopy, 2612 Paracoccus yeei Parasitology media, 2412, 2413 epidemiology, transmission, and preven- characteristics of, 837 Parasitology reagents tion, 2611–2612 identification, 838 buffered formalin, 2406 P. cantonensis, 2612, 2613 Paraformaldehyde, disinfection with, 238 commercially available vials for parasite serologic tests, 2612 Paragonimus genus, 2590 recovery, 2407 taxonomy, 2611 clinical significance, 2598 Cu-PVA (polyvinyl alcohol), 2408 treatment, 2612 description of agents, 2598 diagnostic parasitology, 2407 Parechovirus (PeV), 1592 direct examination, 2598–2599 formalin preparations, 2406–2407 affecting humans, 1577 epidemiology, transmission, and preven- Hg-PVA, 2408 antiviral susceptibilities, 1585 tion, 2598 merthiolate-iodine-formalion (MIF), clinical significance, 1578–1580 microscopy, 2598–2599 2406–2407 clinical syndromes associated with, 1579 nucleic acid detection, 2599 nonmercury or low-level-mercury, nonfor- collection, transport, and storage of serologic testing, 2599 malin fixatives, 2408 specimens, 1580–1581 taxonomy, 2598 PVA-containing preservatives and fixatives, description, 1577–1578 treatment, 2599 2408 direct examination, 1581–1583 Paragonimus westermani Schaudinn’s fixative/solution, 2408 diseases and specimen selection, 1580 eggs of, 2599 sodium acetate-acetic acid-formalin (SAF), epidemiology and transmission, 1578 life cycles of, 2595 2408 evaluation, interpretation, and reporting of Parainfluenza viruses Zn-PVA, 2408 results, 1585 clinical significance, 1529–1530 Parasitology specimens identification, 1584 detection and identification methods, amniotic fluid, 2401 isolation procedures, 1583–1584 1474 animal inoculation and xenodiagnosis, nucleic acid detection, 1581–1583 direct examination, 1530–1532 2403–2404 serologic test, 1585 epidemiology and transmission, 1529 antigen detection, 2404 susceptibilities of cell lines, 1583

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taxonomy, 1576 biosafety and biosecurity, 206 herpes viruses, 1962–1964 typing systems, 1584–1585 blood-borne, 217 mechanism of resistance, 1963 Parengyodontium Brucella spp., 213 pharmacology, 1954 clinical significance, 2152 Burkholderia mallei and B. pseudomallei, 215 spectrum of activity, 1954 hyphomycetes, 2149 Cladophialophora bantiana, 215 varicella-zoster virus, 1765 Paritaprevir Coccidioides immitis and C. posadasii, 215 Penicillin(s), 1230 drug interactions, 1947 Coxiella, Chlamydia, and rickettsial agents, adverse effects, 1203 HCV therapy, 1947 215–216 Bacteroides spp., 1383–1384 pharmacology, 1946–1947 enteric bacterial pathogens, 216 chemical structures of, 1202 Paromomycin Francisella tularensis, 214 Cutibacterium spp., 1388 adverse effects, 2660 influenza, 217 mechanism of action, 1201 mechanism of action, 2660 multidrug-resistant bacterial, 216–217 pharmacology, 1201 pharmacokinetics, 2660 Mycobacterium tuberculosis, 214 resistance in staphylococci, 1305 spectrum of activity, 2660 Neisseria meningitidis, 213 resistant breakpoint differences, 1378 Patulin potential for laboratory-acquired infections, spectrum of activity, 1201–1203 classification and biosynthesis of, 2282 213–218 syphilis and, 1085 common food substrates, 2282 prions, 217–218 type and name of, 1202 genetic structure, 2280 risk classification of, 206–207 Penicillin/ampicillin, activity against pathological effects and toxicological refer- Streptococcus pyogenes, 216 Clostridium spp., 987 ence values, 2283 viral hemorrhagic fever, 217 Penicillinase-producing N. gonorrhoeae, media structure of, 2279 viral respiratory, 217 for detection of, 338, 54–355 See also Mycotoxins Yersinia pestis, 215 Penicillinases, detection in aerobic and Parvimonas spp. Pathogen Analysis Pipeline, NCBI’s, 179, 187 anaerobic Gram-negative organisms, biochemical features, 930 Pathogen discovery 1328, 1329 change in classification, 926 brief history of, 269–271 Penicillin-binding proteins (PBPs) clinical significance, 928 classical methods, 269 acquisition of foreign, 1249 description, 925 early applications of microbial genomics, modifications of, 1244 epidemiology, 927 271 overexpression, 1248–1249 Parvoviridae family, 1880 merging with microbial genomics, 272–278 PBP-mediated resistance, 1247–1248 Parvovirus B19 molecular strategies, 269, 271 point mutations, 1250 antigen detection, 1883 timeline depicting landmarks of, 270 resistance mutations by recombination with clinical diseases associated with, 1881 See also Microbial genomics foreign DNA, 1249–1250 clinical significance, 1881–1882 Pathogenesis, 290 Penicillium spp., 1201 collection, transport, and storage of speci- Pathogenicity, assessing role of, 278–279 Penicillium marneffei. See Talaromyces (formerly mens, 1882–1883 PCR (polymerase chain reaction) Penicillium) marneffei description of agent, 1880 digital PCR, 95–96 Penile cancer, human papillomavirus (HPV) detection and identification methods, 1474 melting-curve analysis with real-time PCR, and, 1852 diagnosis methods, 1881 95 Pennsylvania State Legionnaires convention, direct examination, 1883 multiplex PCR, 91–92 907 epidemiology and transmission, 1880–1881 nested PCR, 90–91 Pentamidine evaluation, interpretation, and reporting of probes and dyes for real-time PCR, 93, 94 adverse effects, 2660 results, 1884–1885 real-time (homogeneous, kinetic) PCR, mechanism of action, 2659 immune-electron microscopy of, 1881 92–95 mechanism of resistance, 2670 immunosuppressed and immunocompro- reverse transcriptase PCR, 90 pharmacokinetics, 2659 mised patients, 1882 target amplification, 89–90, 91 spectrum of activity, 2659–2660 infection during pregnancy and congenital terms and abbreviations for real-time PCR, Pentatrichomonas genus infection, 1881–1882 92 classification, 2382 isolation procedures, 1884 See also Target amplification techniques detection in humans, 2381 microscopy, 1883 PCR-based typing methods, 795 P. hominis, 2509, 2516 nucleic acid detection, 1883 RT-PCR assays for coronaviruses, 1612, Pentavalent antimonial compounds patients with increased erythropoiesis, 1881 1613–1614 adverse effects, 2659 serological tests, 1884 RT-PCR assays for rhinoviruses, 1595–1597 mechanism of action, 2658 taxonomy, 1880 PCR ribotyping mechanism of resistance, 2670 time course of B19 infections, 1882 characteristics and application, 169 pharmacokinetics, 2658 typing systems, 1884 method, 173 spectrum of activity, 2658–2659 Pasteurella genus PDCA (Plan-Do-Check-Act) cycle, 13 Peptone iron agar, 355 antimicrobial susceptibility, 666 Pediculus humanus humanus (body lice), 1153 Peptoniphilus spp. biochemical reactions of, 665 Pediococcus genus antimicrobial susceptibilities, 933 clinical significance, 659 antimicrobial susceptibilities, 444 biochemical features, 930 direct examination, 661 cellular morphology, 437 changes in classification, 926 epidemiology and transmission, 658 clinical significance, 439 clinical significance, 928 identification of, 663–664 evaluation, interpretation, and reporting of epidemiology, 927 isolation procedures, 661 results, 445 flow scheme for identification of, 932 susceptibility testing, 1366 molecular methods for identification, 444 taxonomy, 925 taxonomy, 657 phenotypic differentiation, 442 Peptoniphilus harei, resistance patterns of, 1390 testing conditions, 1352 susceptibility testing, 1365 Peptostreptococcaceae spp. typing, 665 testing conditions, 1353 clinical significance, 947–948 Pasteurellaceae family See also Catalase-negative, Gram-positive taxonomy and description, 940–941 taxonomy, 656–657 cocci Peptostreptococcus spp. See also Haemophilus spp. Penciclovir antimicrobial susceptibilities, 933 Pasteurella haemolytica selective medium, 354 against herpesviruses, 1952 biochemical features, 930 Pathogen(s) antiviral therapy for herpes simplex virus changes in classification, 926 Bacillus anthracis and B. cereus biovar (HSV), 1742 clinical significance, 928 anthracis, 214 drug interactions, 1954 identification, 929

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Peptostreptococcus spp. (continued) Phenotypic typing methods, 794 Pleistophora spp. resistance patterns of, 1390 Phenylalanine deaminase test, 334 description, 2306 taxonomy, 925 Phialemoniopsis life cycle of microsporidia, 2307 Peracetic acid (PAA), disinfection with, 238 clinical significance, 2151 Pleosporales order, 2262 Peramivir hyphomycetes, 2147 Alternaria genus, 2244 against influenza virus, 1955 microscopy, 2149, 2150 Bipolaris genus, 2244 drug interactions, 1955 Phialemonium Curvularia genus, 2244 mechanism of resistance, 1974–1975 clinical significance, 2151 Emarellia grisea and Emarellia paragrisea, pharmacology, 1955 hyphomycetes, 2147 2263 Perfringens agar, 355 Phialophora genus, 2242, 2249 Exserohilum genus, 2244–2245 Periodic acid-Schiff (PAS) stain Phialophora verrucosa, morphology by direct Falciformispora spp., 2261 fungi detection, 2036 examination, 2039 Hongkongmyces genus, 2245 mycology, 2028–2029 Phillips, G. Briggs, 206 Medicopsis romeroi, 2263 Periodontal disease, 1086 pH indicators, 335 Neotestudina rosatii, 2263 Periodontitis, 257–258 Phleboviruses, commercial diagnostic tests, Nigrograna mackinnonii, 2263 Petragnani medium, 355 1692 overview of genera in, 2237 PFGE. See Pulsed-field gel electrophoresis Phosphate-buffered saline, 335 phaeohyphomycosis, 2247, 2248, 2249, (PFGE) Photobacterium, properties of genus, 776 2250 Pfizer TB medium base with glycerol, egg yolk, Photobacterium damselae, 777, 778–779 taxonomy and description, 2244–2245, glucose, and malachite green, 355 Photobacterium shigelloides, 777 2261, 2263 PGT medium, 355 Photomicroscopy, 24–25 Trematosphaeria grisea, 2261, 2263 Phaeoacremonium genus, 2246, 2250 Photorhabdus genus, nomenclature and source typing systems, 2253–2254 microscopy of grains, 2267 of species, 727 Plesiomonas genus, 724 Phaeohyphomycosis PhyloChip, 273 nomenclature and source of species, 727 antifungal susceptibilities, 2254 Pibrentasvir properties of genus, 776 clinical significance, 2247–2250 drug interactions, 1949 Plesiomonas shigelloides cutaneous and corneal, 2247–2249 HCV therapy, 1947 epidemiology, transmission, and clinical epidemiology and transmission, 2246 mechanism of resistance, 1971, 1973 significance, 731 superficial, 2247 pharmacology, 1949 See also Enterobacterales order systemic, 2249–2250 Picornaviridae family, 1437, 1592, 1625 Pleurostoma genus, 2238–2239, 2248 Pharmaceutical industry, developing antiviral Piedraia hortae, black piedra, 2229 PLET agar, 355 drugs, 1997 Piperaquine, mechanism of resistance, 2670 Pluralibacter genus Pharmacodynamics, 1279–1280 Pike streptococcal broth, 355 differentiation of Pantoea agglomerans, 733 Pharmacokinetics, 1279 Piperacillin-tazobactam epidemiology, transmission, and clinical Phase-contrast microscopy, 21 activity against Clostridium spp., 987 significance, 729 Phenethyl alcohol agar, 355 resistant breakpoint differences, 1378 nomenclature and source of species, 727 Phenol red agar, 355 Placenta, 325 See also Enterobacterales order Phenol red tartrate broth, 355 Placental microbiome, 260. See also Human Pneumococci, penicillin resistance testing Phenotypic identification systems microbiome in, 1321 automated instruments, 47 Plague, biothreat agent, 247–248 Pneumocystis pneumonia (PCP), 2088 automated systems, 48 Plaque reduction assay (PRA) in adults, 2091 BD Phoenix, 49–50 acyclovir resistance in HSV-1, 1987 antimicrobial susceptibilities, 2098–2099 Biolog Microbial Identification System, method, 1986 in children, 2091 50–51 Plasmid profiling clinical significance, 2090–2091 BIOMIC V3 imaging system, 51 characteristics and application, 169 collection, transport, and storage of speci- literature on yeast identification, 49 non-target-specific method, 171–172 mens, 2092 manual kits, assays and nonautomated Plasmodium genus colonization, 2090 platforms, 51 antigen detection, 2444–2447, 2448 high-resolution computerized tomography, MicroScan, 48–49 characteristics of infections, 2439 2091 MIDI, Inc., microbial identification classification, 2383 microscopy for diagnosis, 2094–2095 systems, 51 clinical and laboratory diagnosis, 2441 nucleic acid detection, 2096–2097 nonautomated platforms, 51, 52–53 clinical significance, 2439–2441 serologic tests, 2098 TREK Diagnostic Systems, 50 collection, transport, and storage of speci- trimethoprim-sulfamethoxazole (TMP- Vitek systems, 47–48 mens, 2441 SMx) for, 2098–2099 See also Proteomic identification systems comparison of malaria diagnostic direct Pneumocystis spp., 2087 Phenotypic test methods, 292–293 methods, 2448 antimicrobial susceptibilities, 2098–2099 advantages and disadvantages of, 1320 description of agent, 2438 bronchoalveolar lavage, 2092 classification for resistance detection, 1316 detection in humans, 2381 clinical significance, 2090–2092 detecting antibacterial resistance, direct examination, 2441–2449 collection, transport, and storage of speci- 1317–1319 epidemiology and transmission, 2438–2439 mens, 2092, 2094 detection of non-b-lactam resistance in evaluation, interpretation, and reporting of colonization, 2090 Gram-negative organisms, 1338–1339 results, 2450 comparison of stains for detecting P. Gram-negative bacteria with poor or no Giemsa-stained blood films, 2441–2443, jirovecii, 2093 growth on sheep blood agar (SBA), 2445–2447 description of, 2087–2088 631–633 morphology, 2442, 2444 direct examination, 2094–2098 identification schemes, 631 nucleic acid detection, 2447–2449 electron micrographs of developmental quality control, 1320 serologic tests, 2449 forms of, 2088 reporting considerations, 1320 taxonomy, 2438 epidemiology and transmission, 2088–2090 resistance detection in Gram-negative transmission to humans, 2440 evaluation, interpretation, and reporting of organisms, 1327–1338 treatment and prevention, 2449–2450 results, 2099 resistance detection in Gram-positive Plasmodium falciparum, 272 extrapulmonary pneumocystosis, 2092 organisms, 1320–1327 drug resistance tests in malaria, 2682–2683 high-resolution computerized tomography, specimens versus cultured isolates, 1316, 1320 mechansism of resistance to antimalarials, 2091 terminology, 631 2670–2672 identification, 2094–2098

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immune reconstitution inflammatory Posaconazole microbiome, 201 syndrome, 2091 acquired resistance, 2323 protozoa, 201–203 induced sputum collection, 2092 clinical breakpoints for Candida spp., 2352 short-term methods, 197–198 isolation procedures, 2098 clinical use, 2323 storage in distilled water, 198 microscopy, 2094–2096 spectrum of activity, 2320, 2323 storage on swabs, 198 nasopharyngeal aspirates, 2094 therapeutic drug monitoring, 2323 ultralow-temperature freezing, 199–200 nucleic acid detection, 2096–2098 toxicity and adverse effects, 2323 viruses, 203 open thorax lung biopsy, 2092, 2094 Postamplification detection and analysis yeasts and filamentous fungi, 203 oropharyngeal washes, 2094 allele-specific hybridization, 103 Pretomanid (PA-824), 1402 presentation in adults, 2091 capillary electrophoresis, 101 Prevotella genus presentation in children, 2091 colorimetric microtiter plate (CMP) sys- antimicrobial activities of potential agents, proposed life cycle of, 2088, 2089 tems, 101, 103 1013 putative life cycle, 2088 gel analysis, 99, 101 characteristics of, 997 serologic tests, 2098 high-density arrays, 104–105 clinical importance, 1000–1001 serum (1→3)-b-d-glucan, 2096 hybridization arrays, 104–106 epidemiology and transmission, 998 taxonomy, 2087 low- to moderate-density arrays, 105–106 identification, 1005 transbronchial biopsy, 2094 mass spectrometry, 106 isolation procedures, 1004 typing systems, 2098 nucleic acid sequencing, 103–104 molecular detection, 1004 Pneumocystis jirovecii Posttransplant lymphoproliferative disorders phenotypic characteristics of, 1010 clinical significance, 2090 (PTLD) resistance patterns of, 1385 colonization, 2090 Epstein-Barr virus (EBV), 1797, 1806 Primary effusion lymphoma (PEL), human comparison of stains for detecting, 2093 prevention, diagnosis, and monitoring, herpesvirus 8 (HHV-8), 1827 epidemiology, 2090 1801 Primate T-lymphotropic viruses (PTLVs), b-d-glucan detection, 2049 Potassium hydroxide (KOH) 1477 morphology and tinctorial characteristics fungi detection, 2036 Prion diseases of, 2095 mycology reagent, 2026–2027 acquired, 1925 morphology by direct examination, 2094 Potassium tellurite agar, 355 blood, urine, and nasal brushings, toluidine blue stain, 2045 Potato dextrose agar, mycology, 2031 1929 transmission, 2089 Potato flake agar, mycology, 2031 cerebrospinal fluid, 1929 Pneumonia Poxviridae family, 1891 chemical inactivation, 234 Legionnaires’ disease (LD), 908 Poxviruses classification of, 1927 Mycoplasma pneumoniae, 1120 antigen detection, 1896 clinical significance, 1926 Pseudomonas, 789 antiviral therapy, 1894–1895 collection, transport, and storage of speci- See also Legionella genus clinical significance, 1893–1895 mens, 1926–1927 Polar lipids, 294 clinical utility of laboratory tests for diag- decontamination, 1926–1927 Poliovirus (PV), 269 nosis, 1895 description of agent, 1923–1924 genomic organization of, 1577 collection, handling, and storage of speci- electroencephalography, 1929 taxonomy, 1576 mens, 1895 epidemiology and transmission, 1924–1926 Polyenes description of agents, 1891 evaluation, interpretation, and reporting of amphotericin B, 2320, 2325–2326 detection and identification methods, 1475 results, 1929–1930 clinical and microbiological resistance, diagnostic tests for, 1895 genetic, 1924–1925 2335 direct detection, 1895–1896 genetic testing of PRNP, 1929 epidemiology of resistance, 2342 epidemiology and transmission, 1891–1893 handling reusable instruments, 234, 236 mechanism of action, 2325 evaluation, interpretation, and reporting of histopathology of, 1927–1928 mechanisms of resistance, 2342–2343 results, 1900–1901 identification, 1927–1929 Polymaviridae family, 1863. See also Human isolation and identification, 1899 infection control guidelines, 1927 polyomaviruses (HPyVs) microscopy, 1895–1896 infectivity risk of tissues and body sub- Polymerase chain reaction. See PCR nucleic acid detection, 1896 stances, 235 Polymyxin B resistance, 1257–1259 real-time PCR assays for detection, laboratory-acquired infection, 217–218 Polymyxin E (colistin) resistance, 1257–1259 1897–1899 magnetic resonance imaging (MRI), Polymyxins, 1230 serologic tests, 1899–1900 1928–1929 adverse effects, 1224 taxonomy, 1891, 1892 methods for decontamination and manage- mechanism of action, 1223 PPLO agar, 355 ment of, 235 pharmacology, 1223–1224 Practical use, 225–226 physical inactivation, 234 Pseudomonas resistance to, 797 Praziquantel, 2648–2649 sporadic CjD, 1924 as resistance target, 1427 adverse effects, 2649 taxonomy, 1923 spectrum of activity, 1224 major indications for, 2649 transmission in health care setting, Polyomaviridae family, 1863 mechanism of action, 2649 1925–1926 Polyomavirus-associated nephropathy mechanism of resistance, 2670 types of human, 1924 (PVAN) pharmacokinetics, 2649 Western blot, 1927 antigen detection, 1868 spectrum of activity, 2649 Pritelivir, against herpesviruses, 1954 BKPyV virus, 1865, 1866 See also Anthelmintic agents Progressive multifocal leukoencephalopathy pathology of, 1868 Precancer, human papillomavirus (HPV) and, (PML) Polyomaviruses 1850, 1852 jCPyV virus, 1865–1866 detection and identification methods, Preservation of microorganisms, 197 MR image of brain with, 1866 1474 bacteria, 201 pathology, 1869 See also Human polyomaviruses (HPyVs) direct transfer to subculture, 197–198 ProMED-mail, 164 Polyphasic taxonomy, 292 disaster preparedness, 204 Promicromonosporaceae family Porphyromonas genus, 995–996 drying, 198 description, 492 characteristics of, 997 freeze-drying (lyophilization), 200–201 identification, 513 clinical importance, 1000 freezing at –20°C, 198 Prophylactic vaccines, human papillomavirus identification, 1005 future directions, 204 (HPV) and, 1853 phenotypic characteristics of, 1009 immersion in oil, 198 Propionibacteriaceae, biochemical characteris- resistance patterns of, 1385 long-term methods, 198–201 tics, 952

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Prostate fluid evaluation, interpretation, and reporting of Psychrobacter collection and transport, 2018 results, 800 characteristics of, 837 pathogenic fungi recovery, 2019 identification, 791–794 identification, 836–837, 839 processing and culture guidelines, infections with, 790 taxonomy, 829 2021–2022 intrinsic resistance, 795–796 Public Health Agency of Canada, 207 Prosthetic device infections, rapidly growing isolation procedures, 791 decontamination of instruments for prion mycobacteria, 618 MALDI-TOF MS detection, 794 diseases, 235 Protease inhibitors mechanisms of resistance, 795–796 Special Pathogens Program, 1728 hepatitis C virus (HCV), 1971, 1972 microscopy, 790–791 Public Health England, 725 HIV therapy, 1938, 1942–1945 multidrug resistance (MDR), 797 Public Health Security and Bioterrorism Protein-encoding genes, sequence analysis nucleic acid detection, 791 Preparedness and Response Act of of, 295 serologic tests, 795 2002, 203 Protein families, 290 taxonomy of genus, 787 Pulmonary disease, Mycobacterium kansasii, 1411 Proteobacteria, 289 typing systems, 794–795 Pulsed-field electrophoresis (PFGE), 794–795, predominant phyla in humans, 256 Pseudomonas aeruginosa 1242 Proteomic identification systems characteristics of, 793 characteristics and application, 169 aerobic bacteria, 57–59 colony morphologies of, 789, 790 non-target-specific method, 172 anaerobic bacteria, 59 diversity of biofilms, 791 PulseNet, 164, 181, 187–188 filamentous fungi, 61–63 fluorescent group, 792 Purpureocillium MALDI-TOF MS, 46, 51, 53–63 infections with, 790 clinical significance, 2152 mycobacteria and Nocardia spp., 59–60 normal host defenses against, 788 hyphomycetes, 2149 reportable organisms for FDA-approved nucleic acid detection, 791 microscopy, 2149, 2150 Vitek MS and MALDI system, 55–57 susceptibility of cystic fibrosis isolates, Puumala virus (PuuV), 1707, 1708 yeast, 60–61 799–800 Pyrosequencing, 103, 109, 1990 Proteus genus tolerance to antibiotics of biofilm-grown, Pyrrolidonyl aminopeptidase activity (PYR biochemical characterization, 734 798 test), 334 epidemiology, transmission, and clinical Pseudomonas alcaligenes Pyrantel pamoate significance, 730–731 characteristics of, 793 adverse effects, 2651 identification, 736 nonfluorescent group, 792 mechanism of action, 2651 nomenclature and source of species, 727 Pseudomonas fluorescens pharmacokinetics, 2651 See also Enterobacterales order biotypes of, 787 spectrum of activity, 2651 Proteus mirabilis characteristics of, 793 See also Anthelmintic agents cefazolin as surrogate for oral cephalospo- fluorescent group, 792 Pyrazinamide (PZA), 1400 rins in urinary isolates in, 1337–1338 Pseudomonas isolation agar base with glycerol, MGIT 960 testing of, 1407–1408 detecting resistance, 1316 355 PYR test (l-pyrrolidonyl-b-naphthylamide), Protoparvovirus (human bufavirus), 1880, 1886 Pseudomonas luteola 407–408 Protoparvovirus (tusavirus), 1880, 1886 characteristics of, 793 Pythium insidiosum, 2292 Prototheca wickerhamii nonfluorescent group, 792 antimicrobial susceptibilities, 2298 cultural and biochemical characteristics, Pseudomonas mendocina clinical significance, 2296 2062 characteristics of, 793 collection, transport, and storage of speci- morphological features of, 2063 nonfluorescent group, 792 mens, 2296 Protozoa, preservation methods, 201–203 Pseudomonas monteilii description, 2295 Providencia genus characteristics of, 793 direct examination, 2297–2298 biochemical characterization, 734 fluorescent group, 792 epidemiology and transmission, 2295–2296 epidemiology, transmission, and clinical Pseudomonas mosselii evaluation, interpretation, and reporting of significance, 730–731 characteristics of, 793 results, 2298–2299 nomenclature and source of species, 727 fluorescent group, 792 identification, 2298 See also Enterobacterales order Pseudomonas oryzihabitans isolation procedures, 2298 Provider-performed microscopy (PPM), 6 characteristics of, 793 microscopy, 2297 Prusiner, Stanley, 1923 nonfluorescent group, 792 nucleic acid detection, 2298 Pseudallescheria boydii, morphology by direct Pseudomonas pseudoalcaligenes serologic tests, 2298 examination, 2040 characteristics of, 793 taxonomy, 2295 Pseudochrobactrum nonfluorescent group, 792 typing systems, 2298 characteristics of, 840 Pseudomonas putida identification, 841–842 biovars A and B, 787 Pseudocitrobacter genus characteristics of, 793 Q fever epidemiology, transmission, and clinical fluorescent group, 792 acute, 1185 significance, 730 Pseudomonas stutzeri biothreat agent, 252 See also Enterobacterales order characteristics of, 793 chronic, 1185 Pseudoclavibacter genus, description, 492 genetic diversity of, 787 diagnosis of chronic, 1182 Pseudocowpox virus, 1900 nonfluorescent group, 792 epidemiology and transmission, 1181 Pseudomonas genus Pseudomonas veronii follow-up on, 1185–1186 acquired resistance, 796–797 characteristics of, 793 nucleic acid detection, 1182 adaptive resistance, 797–798 fluorescent group, 792 special considerations, 1186 antimicrobial susceptibilities, 795–800 “Pseudozyma” genus specimen handling, 1182 antimicrobial susceptibility testing, clinical significance, 2066–2067 See also Coxiella burnetii 798–800 description, 2064 Quality assurance (QA), 7, 9–13, 185–186 clinical significance, 788–790 taxonomy and nomenclature, 2058 blood culture detections, 39–40 collection, transport, and storage of speci- Pseudonocardia genus laboratory practice, 113–114 mens, 790 classification, 526 microscopy, 21 commercial identification systems, 794 description, 531 mycobacteria, 568–570 description of agent, 787–788 morphologic characteristics, 529 new test verification and validation, 10–11 direct examination, 790–791 See also Actinomycetes subtyping methods, 185–186 epidemiology and transmission, 788 Psocodea, arthropods as vectors, 2624–2626 training, 11

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Quality control (QC), 5, 8–9 Rabies virus, detection and identification major groups of, 613 agar proportion method, 1406 methods, 1475 MALDI-TOF MS, 622 dilution methods, 1291–1293 Radiation, sterilization, 233 microscopy, 618 disk diffusion testing, 1295–1296 Raillietina spp., human infection, 2616 molecular identification methods, 619 individualized QC plan (IQCP), 8–9 Rainbow Agar O157, 355 multilocus sequence analysis, 621 laboratories, 73 Rainbow Agar Salmonella, 355 nucleic acid detection, 618 laboratory practice, 113–114 RajHans Medium, 355 otitis media, 617 MGIT 960 System, 1407 Ralstonia partial 16S rRNA gene sequence analysis, Nocardia spp., 1414 clinical significance, 811 619–620 nontuberculosis mycobacteria (NTB), 1410 description of, 808 PCR-restriction enzyme analysis (PRA), phenotypic methods, 1320 epidemiology and transmission, 808 621 role of process improvement, 75–76 identification of, 816–817 prosthetic device infections, 618 subtyping methods, 185–186 species, 807–808 pulmonary infections, 616–617 VersaTREK, 1408 typing systems, 819 pulsed-field gel electrophoresis (PFGE), 622 virology laboratory, 1470 Raltegravir pyrosequencing, 621–622 Quality Control for Molecular Diagnostics, drug interactions, 1946 random amplified polymorphic DNA 114, 1743 HIV therapy, 1940 (RAPD) PCR, 622 Quantitative methods, RNA and DNA analy- mechanism of resistance, 1965 repetitive-sequence-based PCR, 622–623 sis, 106–107 pharmacology, 1945–1946 reporting results, 1413 Quest Diagnostics, human herpesvirus 6 RAMBACH agar, 355–356 rpoB sequence analysis, 620–621 (HHV-6) testing, 1818 Raoult, Didier, 291 sequence analysis of other gene targets, 621 Quinoline derivatives Raoultella genus sequencing of hsp65 gene, 620 4-aminoquinolines, 2652–2654 biochemical characterization, 733 serologic tests, 623 8-aminoquinolines, 2656 epidemiology, transmission, and clinical surgical wound infections, 618 antimalarials, 2652–2656 significance, 727–728 taxonomy, 612–613 cinchona alkaloids, 2654 identification, 735 test method, 1412–1413 halofantrine, 2655 nomenclature and source of species, 727 typing systems, 622–623 lumefantrine, 2655 See also Enterobacterales order VNTR analysis, 621, 622 mefloquine, 2654–2655 RAPD/AP-PCR and rep-PCR (random ap- whole-genome sequencing (WGS), 623 synthetic quinoline compounds, 2654–2655 plication of polymeric DNA/arbitrarily See also Slowly growing nontuberculous See also Antimalarial agents primed PCR) mycobacteria (SGM) Quinolones, 1402 characteristics and application, 169 Rapidly growing mycobacteria medium, 356 adverse effects, 1211 method, 173 Rasamsonia alterations in target enzymes, 1255 Rapid fermentation medium, 356 clinical significance, 2152 mechanism of action, 1209 Rapid identification of microbial isolates hyphomycetes, 2149 pharmacology, 1209–1210 antigen detection, 38 Reagents, 2025–2026 plasmid-mediated, resistance, 1255–1256 commercial multiplex PCR and microarray biochemical tests, 331–334 Pseudomonas resistance to, 797 technology, 37–38 buffers, 334–335 resistance by decreased uptake and efflux, direct AST from blood culture bottles, 39 commercial manufacturers of fungal, 1256 laboratory-developed nucleic acid amplifi- 2032–2033 resistance to, 1254–1256 cation tests, 37 decontamination agents, 335 spectrum of activity, 1210–1211 MALDI-TOF mass spectrometry, 38–39 dyes and pH indicators, 335 type, 1209 peptide nucleic acid-fluorescent in situ McFarland standards, 335–336 Quinones, respiratory, 294 hybridization (PNA-FISH), 37 mycology laboratory, 2026–2027 Quintan fever, anthroponotic bartonelloses, Rapidly growing mycobacteria (RGM) preservatives, 335 896 antimicrobial susceptibilities, 623–624 See also Parasitology reagents Quinupristin-dalfopristin, resistance, 1264 antimicrobial susceptibility tests for taxo- Reagents for virology nomic identification, 619 balanced salt solutions, 1462 biochemical testing, 618–619 commercially available, 1464 Rabies bone and joint infections, 616 density gradient media, 1462 antigen detection, 1679–1681 broth microdilution interpretive criteria Dulbecco’s phosphate buffered saline antigenic typing, 1682 for, 1413 (PBS), 1462 antimicrobial susceptibilities, 1682 catheter-associated infections, 617–618 formalin for cell culture preservation, 1463 clinical significance, 1676–1677 central nervous system disease, 617 gentamicin-amphotericin B solution, 1463 collection, transport, and storage of speci- clarithromycin, 1412 HEPES, 1463 mens, 1677, 1679 clinical significance, 613, 615–617 saline, 1463 description of agent, 1674 collection, transport, and storage of speci- sources for, 1470–1471 direct detection methods, 1679–1681 mens, 618 trypsin solutions, 1463 epidemiology and transmission, 1674–1676 community-acquired skin and soft tissue Tween 20-PBS, 1463 evaluation, interpretation, and reporting of infections, 613, 615–616 Real-time PCR, 92–95 results, 1682–1683 corneal infections, 617 dark quencher probes, 93, 94 identification, 1681–1682 currently recognized species of, 614–615 dual hybridization probes, 93, 94 IFA tests, 1682 description of agents, 612–613 melting-curve analysis, 95 isolation procedures, 1681 direct examination, 618 molecular beacons, 93, 94 lyssavirus diversity, 1675 disseminated cutaneous disease, 616 partially double-stranded probes, 93, 94 microscopy, 1679 enterobacterial repetitive intergenic con- probes and dyes for, 93, 94 neutralization tests, 1682 sensus PCR (ERIC PCR), 623 Scorpion probes, 93, 94 nucleic acid detection, 1681 evaluation, interpretation, and reporting of specificity of, 94 nucleotide sequence analysis, 1682 results, 624 terms and abbreviations, 92 routine tests for diagnosis of, 1678 health care-associated infections, 617–618 Recombinant hemagglutinin vaccine, 1512 serologic tests, 1682 HPLC identification, 619 Recombinant viral assays, antiviral suscepti- taxonomy, 1674 identification, 618–622 bility testing, 1988 typing systems, 1682 isolation procedures, 618 Rectal swabs, collection and processing of Rabies lyssavirus (RABV). See Rabies laboratory developed tests, 618 virus, 1456–1457

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Rectal tissue, specimen for parasite detection, Mycoplasma spp., 1120 description, 1592–1593 2429, 2432 parasites in lungs, 2390 detection and identification methods, 1475 Recurrent respiratory papillomatosis (RRP), processing recommendations, 323–324 direct detection, 1595–1597 human papillomavirus (HPV), specimen collection and transport, 307–308 epidemiology and transmission, 1593–1594 1851–1852 specimen preparation and procedures, 2395 evaluation, interpretation, and reporting of Reduviid bug (Triatoma sanguisuga), trematodes of, 2598–2599 results, 1599 2622–2623 Retortamonas genus genome structure, 1593 Regan-Lowe charcoal agar, 356 classification, 2382 genotyping by sequencing, 1598–1599 Regan-Lowe semisolid transport medium, 356 detection in humans, 2381 identification, 1598 Regulatory issues Retortamonas intestinalis isolation procedures, 1597–1598 azole resistance, 2339–2340 flagellate, 2507 multiplexed RT-PCR assays, 1595–1597 laboratory practice, 115–116 key features of trophozoites and cysts of, nucleic acid assays, 1595–1597, 1600 oversight, 225–226 2509 serologic tests, 1599, 1600 Reimbursement issues nonpathogenic flagellate, 2516 taxonomy, 1592 laboratory practice, 115–116 Respiratory tract microbiome temperature sensitivity, 1598 Relapsing fever, 1068 microbial composition, 255 typing systems, 1598–1599 Borrelia species, 1067 predominant phyla, 256 Rhizobium pusense, identification, 842 clinical significance, 1069–1070 study of, 260–261 Rhizobium radiobacter epidemiology and transmission, 1068–1069 See also Human microbiome characteristics of, 840 laboratory diagnosis, 1071 Respirovirus, 1528 identification, 842 Relebactam, 1209 diagram of, 1529 Rhizomucor genus Reproducibility Reston virus culture variability and branching, 2169 molecular epidemiology, 168 animal inoculation, 1730 identification, 2168, 2171 Resistance geography and associated human diseases, Rhizopodaceae family hierarchy of, 225 1723 genus Rhizopus, 2173–2175 molecular detection of, 1281 taxonomy and description, 1720 human mucormycosis, 2164 Resistance-associated substitutions (RASs), See also Filoviridae family identification, 2173–2175 1971 Restriction fragment length polymorphism Rhizopus genus Resistance mechanisms, 1244–1246 (RFLP), 794 calcofluor white stain, 2044 clinical and microbiological, 2334–2335 gel analysis postamplification, 99, 101 characteristics allowing distinction, 2174 efflux pumps, 1245–1246 non-target-specific method, 172 identification, 2173–2175 microbial drivers of, 2343–2344 Result reporting and interpretation, 1281 microscopic features, 2175 modification of antibiotic, 1244 laboratory practice, 114–115 Gomori methenamine silver (GMS), 2044 modification of bacterial target for antimi- Reverse transcriptase (RT), resistance of Rhizopus microsporus, Gram stain, 2042, 2043 crobials, 1244–1245 hepatitis B virus, 1969–1970 Rhodococcus genus restricted access to target, 1245 Reverse transcriptase PCR, 90 classification, 526 Resistant, breakpoint definition, 1285 RFLP. See Restriction fragment length poly- clinical significance, 540–541 Resources, parasitology information, 2404 morphism (RFLP) description, 531 Respiratory pathogens, immunofluorescence RGM. See Rapidly growing mycobacteria microscopic morphology, 532 detection of, 1465, 1466 (RGM) morphologic characteristics, 529 Respiratory quinones, 294 Rhabdoviridae family, 1674 recovered from human specimens, 535 Respiratory specimens Rhinocladiella genus, 2242 See also Actinomycetes collection and processing of virus, Rhinocladiella aquaspersa, morphology by direct Rhodococcus equi, 1413 1455–1456 examination, 2039 Rhodotorula genus virus detection methods, 1448–1449 Rhinosporidium seeberi, 2292 antifungal susceptibilities, 2068 Respiratory syncytial virus (RSV) antimicrobial susceptibilities, 2302 cultural and biochemical characteristics, in adults, 1542, 1544 clinical significance, 2302 2062 antiviral susceptibilities, 1547 collection, transport, and storage of speci- description, 2064 in children, 1542 mens, 2302 morphological features of, 2060 clinical significance, 1542, 1544 description of, 2300–2301 taxonomy and nomenclature, 2058 collection, transport, and storage of speci- direct examination, 2302 RI-67, respiratory illness, 1831 mens, 1544 epidemiology and transmission, 2301 Ribavirin commercially available rapid antigen tests, evaluation, interpretation, and reporting of drug interactions, 1950 1546 results, 2302–2303 HCV therapy, 1947, 1973 description, 1541 identification, 2302 human adenovirus (HAdV), 1840–1841 detection and identification methods, 1475 isolation procedures, 2302 pharmacology, 1949–1950 direct examination, 1544–1545, 1547 microscopy, 2302 Ribotyping, 794 direct fluorescent-antibody tests, 1545, 1548 nucleic acid detection, 2302 Ribosomal Database Project, 635 epidemiology and transmission, 1541–1542 serologic tests, 2302 Rickettsia spp. evaluation, interpretation, and reporting of taxonomy, 2300 antimicrobial susceptibilities, 1157 results, 1547, 1551 typing systems, 2302 characteristics of, 1150 identification, 1547 Rhinoviruses (RVs), 1576 clinical significance, 1151 isolation procedures, 1545, 1547 acid pH stability, 1598 collection, transport, and storage of speci- nucleic acid detection, 1545 affecting humans, 1577 mens, 1151, 1153 replication, 1543 antiviral susceptibilities, 1599 description of genus, 1150–1151 serologic tests, 1547 cell culture, 1597–1598 diagnostic tests for, 1114–1115 taxonomy, 1541 clinical significance, 1594 direct detection, 1153–1155 treatment and prevention, 1544 collection, transport, and storage of speci- direct immunofluorescence staining, 1153 typing systems, 1547 mens, 1594–1595 epidemiology and clinical diseases associ- Respiratory tract commercial multiplex molecular assays, ated with, 1110–1111 direct parasite detection, 2401–2402 1596 epidemiology and transmission, 1151, human adenovirus (HAdV), 1832–1833, comparison of diagnostic methods, 1600 1152 1834 conventional real-time PCR (RT-PCR) identification of isolates, 1155–1156 infectious syndromes, 318 assays, 1595 immunologic detection, 1153–1154

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interpretation and reporting of results, detection and identification methods, 1475 collection, transport, and storage of speci- 1157–1158 direct examination, 1568–1569 mens, 701–702 isolation procedures, 1155 enzyme-linked immunosorbent assays common media for isolation of, 704 molecular detection, 1154–1155 (ELISAs), 1569 description of, 699–700 serologic tests, 1156–1157 epidemiology and transmission, 1567 direct examination, 702 taxonomy, 1149 evaluation, interpretation, and reporting of epidemiology and transmission, 700–701 Rickettsial agents, laboratory-acquired infec- results, 1570–1571 general medium growth requirements, 703 tion, 216 identification, 1568–1569 identification of, 707 Rickettsial diseases, etiology, epidemiology, isolation, 1568–1569 isolation procedures, 703–706 and ecology, 1152 latex agglutination, 1569 next-generation sequencing (NGS)-based Rifabutin, 1400 microbead assays, 1569 typing, 713 Rifampin, 1399–1400 nucleic acid detection, 1568 nucleic acid amplification tests (NAATs) Cutibacterium spp., 1388–1389 prenatal screening, 1570 for, 707–710 resistance, 1260 plaque reduction neutralization (PRN) outbreak, 164 Rifamycins, 1225–1226 assay, 1569–1570 phenotypic traits for differentiating, 700, 707 adverse effects, 1226 serologic tests, 1569–1570 plating media for, 705 mechanism of action, 1226 taxonomy, 1566 role of sequencing to differentiate, 711 pharmacology, 1226 timing of biological markers of infection, specimen enrichment for stool culture, 703 spectrum of activity, 1226 1568 taxonomy, 699 Rifapentine, 1400 utility of sequencing, 1569 typing systems, 711–713 Rilpivirine, 1965 Rubulavirus Salmonella-Shigella agar, 356 drug interactions, 1942 diagram of, 1529 Salmonella enterica serotype Typhimurium, 176 HIV therapy, 1938 taxonomy, 1528 Salmonella enterica, pefloxacin as surrogate for mechanism of resistance, 1965 Ruminococcaceae spp. fluoroquinolone susceptibility, 1338 pharmacology, 1942 clinical significance, 947–948 Salmonellosis, laboratory-acquired infection, Rimantadine, against influenza virus, 1954, taxonomy and description, 940–941 216 1955 Salt meat broth, 356 Risk assessment Salt tolerance medium, 356 matrix, 208 Saaremaa virus (SAAV), 1707, 1708 Sangassou virus (SANGV), 1707, 1708 mitigation of risk and, 207–209 Sabouraud brain heart infusion (SABHI), Sanger, Frederick, 270, 271 occupational health program, 209 mycology, 2031 Sanger sequencing, 1994 Risk classification, pathogens, 206–207 Sabouraud dextrose agar, mycology, general protocol, 1991 Ritonavir 2031–2032 Saprochaete spp. drug interactions, 1944 Saccharomycotina, subphylum of kingdom clinical significance, 2067 HIV therapy, 1939 Fungi, 2010, 2011 description, 2059 mechanism of resistance, 1967 Saccharomonospora genus taxonomy and nomenclature, 2058 pharmacology, 1944 classification, 526 Saquinavir RNA analysis, quantitative methods, 106–107 description, 531 drug interactions, 1944–1945 RNA virus. See Hepatitis A virus (HAV); morphologic characteristics, 529 HIV therapy, 1939 Hepatitis E virus (HEV) See also Actinomycetes pharmacology, 1944 Robert Koch Institute, 187 Saccharomyces spp. Sarcocystis genus Rocky Mountain spotted fever (RMSF), 1151, clinical significance, 2067 classification, 2383 1152, 1158 description, 2059 culture, 2531 Roseburia spp., taxonomy and description, 940 morphological features of, 2060 detection in humans, 2381 Roseolovirus genus, 1814. See also Human her- taxonomy and nomenclature, 2058 direct examination, 2530–2531 pesvirus 6 (HHV-6A and HHV-6B); Saccharomyces cerevisiae epidemiology, transmission, and preven- Human herpesvirus 7 (HHV-7) antifungal susceptibilities, 2068 tion, 2529 Roseomonas spp. cultural and biochemical characteristics, evaluation, interpretation, and reporting of characteristics of, 846 2062 results, 2533 Gram stain of, 848 Saccharopolyspora genus intestinal infections, 2530 identification, 847–848 classification, 526 microscopy, 2530–2531 Ross River virus, commercial diagnostic tests, description, 531 muscle infection by, 2528 1692 morphologic characteristics, 529 muscular infections, 2530 Rotaviruses See also Actinomycetes muscular treatment, 2532 clinical features, 1659 Safety precautions, laboratory-acquired infec- nucleic acid detection, 2531 clinical significance, 1660–1661 tions, 210–213 serologic tests, 2531–2532 description of, 1657 Saksenaea genus structural data for, 2529 detection and identification methods, 1475 identification, 2172–2173 treatment, 2532 electron micrographs, 1658 unbranched sporangiophores, 2174 Sarcocystis hominis epidemiology and transmission, 1659 Saksenaeaceae family life cycle of, 2528 molecular assays for detection, 1664 genus Apophysomyces, 2172 sarcocyst of, 2528 taxonomy of, 1656, 1657 genus Saksenaea, 2172–2173 structural data for, 2529 See also Gastroenteritis viruses human mucormycosis, 2164 Sarcocystis suihominis Rothia genus, 401 identification, 2172–2173 life cycle, 2528 identification, 502, 511–512 St. Louis encephalitis, commercial diagnostic structural data for, 2529 Rothia mucilaginosa test, 1691 Sarcoptes scabiei (scabies), 2632–2633 susceptibility testing, 1366 Salinicoccus genus, 368 Sarocladium testing conditions, 1353 epidemiology and transmission, 377 clinical significance, 2151 Roundworms, Nematoda, 2384–2385, 2386 Salmonella chromogenic agar (OSCM), 356 hyphomycetes, 2147 Rubella virus Salmonella genus SARS-CoV (coronavirus associated with se- clinical significance, 1567 antigenic typing of, 712 vere acute respiratory syndrome), 183 collection, transport, and storage of speci- antimicrobial susceptibilities, 715–716 SAR supergroup mens, 1567–1568 biochemical reactions of species, 690 eukaryotes, 2380–2382 description, 1566–1567 clinical significance, 701 parasitic protists, 2383–2384

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SA Select medium, 356 Scytalidium nucleic acid amplification tests (NAATs) S. aureus ID, 356 clinical significance, 2151–2152 for, 707–710 Scabies, endoparasitic arthropods, 2632–2633 hyphomycetes, 2147, 2149 plating media for, 705 Scedosporium genus, 2243, 2249 Segniliparus genus role of sequencing to differentiate, 711 microscopy of grains, 2267 clinical significance, 541 species, serogroups, and serotypes, 697 morphology by direct examination, 2039 description, 531, 533 specimen enrichment for stool culture, 703 taxonomy and description, 2263 microscopic morphology, 532 taxonomy, 696–697 Scedosporium apiospermum, 2035 morphologic characteristics, 529 typing systems, 711–713 antifungal susceptibilities, 2254 recovered from human specimens, 535 Shigellosis, laboratory-acquired infection, 216 H&E stain, 2045 See also Actinomycetes Sick building syndrome, 2285 Scedosporium boydii, 2238 Select agents Simeprevir in vitro susceptibility, 2272 non-tier 1, 251–252 drug interactions, 1947–1948 Schaedler agar, 356 tier 1, 245–250 HCV therapy, 1947 Schaedler CNA agar with vitamin K and Selenite broth, 356 pharmacology, 1947 sheep blood, 356 Selenite cystine broth, 356 Simian immunodeficiency viruses (SIVs), Schistosoma genus Selenomonas genus, 996 183, 1477 clinical significance, 2590, 2595 characteristics of, 997 SIM medium, 356 description of agents, 2590 clinical importance, 1002 Simmons’ citrate agar, 356–357 direct antigen tests, 2597–2598 phenotypic characteristics of, 1012 Simmons’ citrate agar, modified, 341–342 direct examination, 2597 Sensititre ARIS 2x, automated broth micro- Simonsiella genus eggs of species, 2596 dilution, 1302, 1304 clinical significance, 659 epidemiology, transmission, and preven- Seoul virus (SEOV), 1707 direct examination, 661 tion, 2595–2597 SeqNet, 187 epidemiology and transmission, 658 genitourinary schistosomiasis, 2597 Sequence analysis, protein-encoding genes, identification of, 664 geographical distribution, intermediate 295 isolation procedures, 661 hosts, and egg morphology of schisto- Sequencing approaches, pathogen discovery taxonomy, 657 somes infecting humans, 2591 and microbial genomics, 273–278 Simonsiella muelleri hepatointestinal schistosomiasis, Sequencing studies, 16S rRNA, 294–295 antimicrobial susceptibility, 666 2596–2597 Serotyping, molecular, 180–181 biochemical reactions of, 664 microscopy, 2597 Serratia genus, 724 Single-nucleotide polymorphism (SNP) typ- nucleic acid detection, 2598 biochemical characterization, 734 ing, 795 serologic testing, 2597 epidemiology, transmission, and clinical Single-strand conformation polymorphism species infecting humans, 2594 significance, 730 (SSCP), gel analysis postamplification, taxonomy, 2590 identification, 736 99, 101 treatment, 2598 nomenclature and source of species, 727 Sin Nombre virus (SNV), 1707, 1708 See also Trematodes See also Enterobacterales order Siphonaptera, 2639 Schistosoma haematobium, 2591 Serratia marcescens, outbreak, 162–163 arthropods as vectors, 2623–2624 eggs of, 2596 Serum, approximate antibacterial concentra- summary of, 2621 genitourinary schistosomiasis, 2597 tions in, 1228, 1229–1230 Skim milk, 335 infecting humans, 2594 Serum glucose agar, 356 Skin Schistosoma intercalatum, 2591, 2597 Serum tellurite agar, 356 Clostridium spp., 972–974 Schistosoma japonicum, 2591 Sexual transmission, Chlamydia trachomatis, collection and transport, 2017 eggs of, 2596 1138–1139 disinfection, 31 hepatointestinal schistosomiasis, 2597 SGM. See Slowly growing nontuberculous parasites, 2390 infecting humans, 2594 mycobacteria (SGM) pathogenic fungi recovery, 2019 Schistosoma mansoni, 2591 Shepard’s differential agar, 341 processing and culture guidelines, 2021 eggs of, 2596 Shewanella algae specimen collection and processing of virus, hepatointestinal schistosomiasis, characteristics of, 840 1456 2596–2597 identification, 842 specimens for parasite detection, 2429, infecting humans, 2594 Shewanella putrefaciens 2432–2433 Schistosoma mekongi, 2591 characteristics of, 840 specimen preparation and procedures, 2396 eggs of, 2596 identification, 842 Skin microbiome hepatointestinal schistosomiasis, 2597 Shiga toxin-producing Escherichia coli microbial composition, 255, 262 Schistosomiasis (STEC), processing recommendations, predominant phyla, 256 commercially available kits for diagnosis, 321–322 study of, 261–262 2392 Shigella genus See also Human microbiome mechanisms of resistance, 2675 antigenic typing of, 712 Skirrow Brucella medium, 357 proposed mechanisms of resistance for drugs antimicrobial susceptibilities, 715 Slowly growing nontuberculous mycobacteria against, 2670 biochemical reactions of species, 690 (SGM) selected antiparasitic agents and suscepti- clinical significance, 698–699 AccuProbe culture identification tests, 605 bility testing method, 2683 collection, transport, and storage of speci- antimicrobial susceptibility testing, 607–608 susceptibility test methods, 2686 mens, 701–702 characteristics of recognized species, Schizophyllum common media for isolation of, 704 596–597 basidiomycetes, 2147 description of, 697 clinical significance, 597–598 clinical significance, 2151 differentiation of E. coli and, 697 colony morphology, 602 Schizophyllum commune/radiatum, microscopy, direct examination, 702 direct examination, 598, 601 2145, 2146 epidemiology and transmission, 697–698 direct nucleic acid detection, 601 Schleifer-Kramer agar, 356 general medium growth requirements, 703 epidemiology and transmission, 595, 597 Scopulariopsis genus, 2243, 2247 identification of, 706–707 evaluation, interpretation, and reporting of Scorpions, 2636, 2639 isolation procedures, 703–706 results, 608 Screening, laboratory staff, 212 NAAT and antigen detection from non- genotypic identification, 603–604 Scrub typhus, Orientia tsutsugamushi, 1151, stool specimens, 711 identification, 601–603 1152 next-generation sequencing (NGS)-based important properties of selected species, SCY-078 (MK-3118, Scynexis), 2327 typing, 713 599–600

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IS1245 and IS900 RFLP analysis, 607 general principles of, 302–312 Stability, molecular epidemiology, 168 line probe assays, 605–606 genital discharge, exudates, and lesions, Staff competency, 209 mass spectrometry, 606 306–307, 322–323 Stains, 2025–2026 M. leprae PCR, 601 hardware and prosthetic devices, 310 acid-fast, 337 molecular tests for NTM, 604–606 Legionella (Legionnaires’ disease), 323 acridine orange, 337 multilocus sequence typing, 607 representing infected site, 302, 310–311 auramine-rhodamine, 337 phenotypic methods, 601–602 respiratory tract, 307–308, 323–324 commercial manufacturers of fungal, pigmentation and photoreactivity, 602 selection for bacterial culture, 310 2032–2033 pulsed-field gel electrophoresis (PFGE), sputum, 310 fungi detection, 2036 606–607 stool, 305, 310–311 Gimenez, 337 repetitive-unit sequence-based PCR (rep- swabs, 311 Gram, 336 PCR), 607 tissue biopsy samples, 324–325 immunofluorescent antibody, 337–338 taxonomy, 595 tissues, 308, 311 methylene blue, 336 temperature, 602 transport recommendations, 311–312 M’Fadyean, 336 typing systems, 606–607 urinary tract, 325–326 mycology laboratory, 2027–2029 use of sequence databases, 604 urine, 308–309, 311 parasitology, 2408–2411, 2413 variable-number tandem repeats (VNTRs), volume and size of sample, 311 spore, 336 607 wounds, 303, 326 virology, 1463, 1464, 1470–1471 See also Rapidly growing mycobacteria Specimen handling Wayson, 337 (RGM) documentation of, 312 See also Parasitology stains Small bowel bacterial overgrowth syndrome, initial sample handling, 313–314 Standard fluid medium 10B, 357 322 laboratory safety regarding bacterial patho- Stanford university Medical Center, 584 Small intestinal microbiome, 258. See also gens, 316–317 Staphylococcus agar no. 110, 357 Gastrointestinal microbiome prioritization, 313 Staphylococcaceae family Smallpox, biothreat agent, 248 recommendations for Gram stain and plat- clinical significance, 377–378 Smarticles technology, 1308 ing media, 315–316 description of, 367, 369, 374 Sneath, Peter, 292 rejection criteria, 312–313 differentiation by MALDI-TOF MS, Sneathia genus, 996 remote handling, 313 383–384 clinical importance, 1002 transport for molecular detection of bacte- taxonomy of, 368 phenotypic characteristics of, 1011 ria, 316 See also Catalase-positive cocci Society for Healthcare Epidemiology of Specimen preservative medium, 357 Staphylococcus/Streptococcus selective America, 980, 1386 Spectinomycin, 1212 medium, 357 Sodium hippurate broth, 357 Sphingobacterium Staphylococcal enterotoxins, biothreat, Sodium hydroxide (NaOH), digestion and characteristics of, 840 252–253 decontamination method, 562, 571 identification, 842 Staphylococci Sofosbuvir Sphingobacterium mizutaii coagulase-negative, 376–377 drug interactions, 1949 characteristics of, 843 coagulase-positive, 374–376 HCV therapy, 1947 identification, 845 detection of inducible clindamycin resis- mechanism of resistance, 1970, 1971 Sphingomonas spp. tance, 1326–1327 pharmacology, 1949 characteristics of, 840 high-level mupirocin resistance detection, Soil extract agar, mycology, 2032 identification, 843–844 1327 Solid amplification techniques, 87–89 Spiders, stinging and biting for envenom- inducible clindamycin resistance, 1305 Solid organ transplantation, human mucor- ation, 2636–2637 b-lactamase testing for, 1320 mycosis, 2164 Spirochaetes, 289 linezolid resistance in, 1305 Sorbitol MacConkey agar with BCIG, 357 Spirometra spp. oxacillin resistance in, 1305, 1321–1323 Sordariales order clinical significance, 2617 penicillin resistance in, 1305 Cladorrhinum genus, 2246 description of agents, 2617 reduced glycopeptide susceptibility in, 1305 Madurella spp., 2261 direct examination and microscopy, single-well broth dilution method, 1327 overview of genera in, 2237 2617–2618 tetracycline specific resistance determinant phaeohyphomycosis, 2248 epidemiology, transmission, and preven- in, 1256 taxonomy and description, 2245–2246, tion, 2617 vancomycin resistance detection in, 1324 2261 serologic tests, 2618 Staphylococcus genus Sorensen pH buffers, 335 taxonomy, 2617 antimicrobial susceptibilities, 387–389 Source attribution, 182 treatment, 2618 characteristics of, 371–373 Soyabean medium with 0.1% agar, 357 Spirometra mansonoides, sparganosis, 2582, 2588 clinical significance, 377–378 Sparganosis, Spirometra mansonoides, 2582, Spore stain, 336 differentiation of members of, 370 2588 Sporobolomyces spp. epidemiology and transmission, 374–377 Special infusion broth, with blood, 357 clinical significance, 2067 identification, 380–382, 384–385 Species, 289–291 cultural and biochemical characteristics, See also Catalase-positive cocci Specimen(s) 2062 Staphylococcus aureus laboratory practice for handling, 111–112 description, 2064 detecting resistance, 1316 See also Mycology specimens morphological features of, 2063 epidemiology and transmission, 374–376 Specimen collection and transport taxonomy and nomenclature, 2058 oxacillin-salt agar supplemental test for, aspirates, 302, 310 Sporothrix genus, 2244, 2248 1322 autopsy samples, 317 Sporothrix spp., morphology by direct exami- phenotypic tests for antibacterial resistance, blood cultures, 317, 319 nation, 2038 1317–1319 central venous catheters, 319–320 Sporothrix schenckii, Gomori methenamine phenotypic tests for detecting resistance, cerebrospinal fluid, 320 silver (GMS) stain, 2046 1317–1319 cystic fibrosis, 324 Sporotrichosis State Center for Virology and Biotechnology, ears, 304, 320 antifungal susceptibilities, 2254 1895 etiologies of infectious disease syndromes, clinical significance, 2250 Stavudine 318 epidemiology and transmission, 2247 drug interactions, 1941 eyes, 304, 320 microscopy, 2251 HIV therapy, 1938 gastrointestinal tract, 321–322 Spotted fever group (SFG), 1149 pharmacology, 1941

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Stenotrophomonas genus, 808 connection to Enterococcus genus, 418 Streptogramins, 1264 Stenotrophomonas malophilia description of colonies, 406 adverse effects, 1221 antimicrobial susceptibility, 820 description of genus, 401 mechanism of action, 1220 characteristics of, 818 detecting resistance, 1316 pharmacokinetics, 1220–1221 clinical significance, 810–811 direct examination, 404–405 spectrum of activity, 1221 identification, 817–818 epidemiology and transmission, 401–402 Streptomyces genus, 1413 typing systems, 819 evaluation, interpretation, and reporting of classification, 526 Sterile body fluids results, 413 clinical significance, 541 collection and transport, 2018 identification, 406–411 colonial morphology, 530 pretreatment, 2020 identification of beta-hemolytic strepto- description, 533 processing and culture guidelines, 2022 cocci, 406–408 epidemiology and transmission, 533 Sterilization, 224, 231–234 isolation procedures, 405–406 morphologic characteristics, 529 approach to, 226–227 microscopy, 404 recovered from human specimens, 535 chemical, low-temperature methods, nucleic acid detection techniques, 404–405 See also Actinomycetes 233–234 phenotypic characteristics of, 400, 410, 411 Streptosel agar, 357 dry heat and incineration, 233 phenotypic tests for testing resistance, 1317 Strict aerobes, 633, 634 laboratory, 236–239 physiologic tests, 410–411 Strongyloides fuelleborni, 2566 principles and definitions, 224 resistance, 1305–1306 Strongyloides stercoralis radiation, 233 screening for group B, 322–323 agar plate culture for, 2421 steam, 231–233 serologic tests, 412 Baermann technique, 2423 typical steam process, 232 taxonomy, 399–401 clinical significance, 2564–2565 Stool specimens testing methods, 1349 culture, 2565 approaches to parasitology in, 2398 tetracycline specific resistance determinant description, 2563 collection and processing options, 2397 in, 1256 direct examination, 2565 collection and processing of virus, typing systems, 411–412 eggs, 2554, 2563 1456–1457, 2022 Streptococcus agalactiae (group B streptococci) epidemiology and prevention, 2563–2564 collection and transport, 305, 2018 antigen detection in cerebrospinal fluid, filter paper/slant culture technique, 2423 collection of fresh, 2389–2390, 2396 404 Harada-Mori filter paper strip culture, 2423 commercially available kits for parasitic clinical significance, 402 larvae, 2563 organism detection, 2391 identification of, 409 life cycle completion time, 2558 concentration wet mount, 2414–2415 nucleic acid detection, 405 life cycle of, 2564 culture of larval-stage nematodes, 2421, special procedures for screening, 406 microscopy, 2565 2423 Streptococcus anginosus group nucleic acid detection, 2565 direct wet mount in saline, 2414, 2417 clinical significance, 403 serologic tests, 2565–2566 egg studies, 2423–2424 identification of, 409 summary of, 2559 identification of helminth eggs, 2417 Streptococcus bovis group taxonomy, 2563 identification of intestinal amebae, 2419 clinical significance, 403 transmission and life cycle, 2563 identification of intestinal flagellates, 2419 identification of, 410 treatment, 2566 immunoassay methods, 2420 Streptococcus dysgalactiae subsp. equisimilis worms, 2563 modified acid-fast staining, 2418 (human group C and G streptococci), See also Nematodes modified trichrome stains, 2418, 2420 clinical significance, 402 Strongyloidiasis, commercially available kits molecular methods, 2420, 2422 Streptococcus mitis group for diagnosis, 2392 permanent stained smears, 2415, 2418, clinical significance, 403 Stuart transport medium, modified, 357 2420 identification of, 409 Study of the Efficacy of Nosocomial Infection preservation of, 2396, 2398–2400 Streptococcus mutans group Control (SENIC), 141 processing for ovum and parasite (O&P) clinical significance, 403 Subtyping methods examination, 2415, 2416 identification of, 409–410 application of, 169 pros and cons of fecal fixatives, 2399 Streptococcus pneumoniae, 1348 characteristics, 167–171 See also Parasites antigen detection in cerebrospinal fluid, convenience parameters, 170–171 Strain catalogues, 187 404 CRISPR analysis, 176 Strand displacement amplification, 97–99 antigen detection in urine samples, 404 discriminatory power, 170 StrepB Carrot Broth, 357 antimicrobial susceptibility, 412–413 DNA heteroduplex mobility assay, 173 Streptobacillus genus beta-lactam resistance in, 1426 DNA microassays, 179–180 biochemical reactions of, 663 clinical significance, 402–403 gene sequencing, 174–175 clinical significance, 659 colony morphology of, 407 IS6110 fingerprinting, 172–173 taxonomy, 657 commercial methods for testing, 1354 MALDI-TOF MS, 180 Streptobacillus moniliformis identification of, 409–411 non-target-specific methods, 171–173 antimicrobial susceptibility, 666 incidence of resistance, 1349–1350, 1354 PCR-based, 173 direct examination, 661 nucleic acid detection, 405 PCR-RFLP, 174 epidemiology and transmission, 658 resistance test methods, 1349, 1354 PCR ribotyping, 173 identification of, 664–665 strategies for testing and reporting of PFGE (pulsed-field gel electrophoresis), 172 isolation procedures, 661 results, 1354–1355 plasmid profiling, 171–172 Streptococci Streptococcus pyogenes (group A streptococci) procedural principles, 171, 174 antimicrobial susceptibility, 412–413 clinical significance, 402 RAPD/AP-PCR and Rep-PCR, 173 classical differentiation of, 399–401 colony morphology of, 407 reproducibility and stability, 168 detection of inducible clindamycin resis- direct antigen detection from throat speci- RFLP (restriction fragment length polymor- tance, 1326–1327 mens, 404 phism), 172 preservation methods, 201, 202 laboratory-acquired infection, 216 target-specific methods, 173–180 single-well broth dilution method, 1327 nucleic acid detection, 404–405 typeability, 167–168 Streptococcus genus, 399, 400, 1348 special procedures for throat cultures, variable-number tandem-repeat (VNTR) antigen detection, 404 405–406 analysis, 175–176 antimicrobial susceptibilities, 412–413 Streptococcus salivarius group WGM (whole-genome mapping), 173 clinical significance, 402–404 clinical significance, 403 WGS (whole-genome sequencing), collection, transport, and storage of speci- identification of, 410 176–177, 179 mens, 404 Streptococcus selective medium, 357 Sucrose-Teepol-tellurite agar, 357

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Sudan virus phenotypic assays, 1986–1988 taxonomy and description, 1720 animal inoculation, 1730 plaque reduction assay (PRA), 1986, 1987 See also Filoviridae family geography and associated human diseases, recombinant viral assays, 1988 Talaromyces (formerly Penicillium) marneffei 1723 Susceptible, breakpoint definitions, 1285 antigen detection, 2045 taxonomy and description, 1720 Susceptible dose-dependent (SDD), break- antimicrobial susceptibilities, 2123 See also Filoviridae family point definition, 1285 clinical significance, 2121 Sulbactam, 1208 Sutterella genus, 997, 998 collection, transport, and storage of speci- Sulfadoxine, mechanism of resistance, 2670 Suttonella genus, taxonomy, 657 mens, 2121 Sulfolobales, 294 Suttonella indologenes direct examination, 2121 Sulfonamides antimicrobial susceptibility, 666 epidemiology and transmission, 2121 adverse effects, 1223 biochemical reactions of, 664 evaluation, interpretation, and reporting of mechanism of action, 1222 clinical significance, 659 results, 2124 pharmacology, 1222 direct examination, 661 identification, 2122 spectrum of activity, 1222–1223 isolation procedures, 661 isolation procedures, 2122 Superficial mycoses Swimming pool granuloma, 1411 microscopy, 2121 black piedra, 2229 Syncephalastraceae family morphology by direct examination, 2038 tinea nigra, 2228–2229 genus Syncephalastrum, 2175–2176 neighbor-joining tree of pathogenic, 2123 tinea versicolor, 2227–2228 human mucormycosis, 2164 nucleic acid detection, 2121–2122 white piedra, 2229–2230 Syncephalastrum genus serologic tests, 2122–2123 See also Dermatophytes identification, 2175–2176 taxonomy, 2120–2121 SuperPolymyxin medium, 357 sporangiosphores, 2176 typing systems, 2122 Supplementary tests, 1281 Syphilis white colonies of, 2122 Suramin clinical and laboratory criteria for diagnosis, Wright-Giemsa stain, 2046 adverse effects, 2660–2661 1087–1088 Tanapox virus, 1900 mechanism of action, 2660 collection, transport, and storage of speci- Tannerella genus, characteristics of, 997 mechanism of resistance, 2670 mens, 1089 Tapeworms pharmacokinetics, 2660 epidemiology and transmission, 1085 Cestoda, 2384, 2385 spectrum of activity, 2660 natural course of untreated, 1086 scolex search, 2424 Surface disinfection, 227–230 tests in HIV infection, 1102 Taphrinomycotina, subphylum of kingdom chemical, 228–230 venereal, 1085 Fungi, 2010–2011 heat, 230 See also Treponema pallidum Target amplification techniques uV germicidal irradiation, 230 Systemic infections, Mycoplasma and digital PCR, 95–96 Surgical wound infections, rapidly growing Ureaplasma spp., 1122 helicase-dependent amplification, 99 mycobacteria, 618 loop-mediated amplification, 99 Surveillance databases, 187–188 melting-curve analysis, 95 Susceptibility testing Taenia spp., human infection, 2616 multiplex PCR, 91–92 clinical and bacteriological response rates, Taenia crassiceps, cysticercosis, 2582, 2588 nested PCR, 90–91 1280 Taenia multiceps, coenurosis, 2582, 2588 nicking endonuclease amplification, 99 common sources of error in antibacterial, Taenia saginata PCR, 89–90, 91 1296 characteristics of, 2583 real-time (homogeneous, kinetic) PCR, drugs used for, 1402–1403 clinical significance, 2584 92–95 establishing breakpoints, 1279–1281 collection, transport, and storage of speci- reverse transcriptase PCR, 90 future directions and needs in, 1281–1282 mens, 2584 strand displacement amplification (SDA), inhibition zone diameter distributions for description of agent, 2584 97–99 disk diffusion methods, 1280–1281 direct examination, 2584–2585 transcription-based amplification methods, methods, 1277–1278 epidemiology, transmission, and preven- 96, 97 MIC distributions, 1279 tion, 2584 Tatumella genus, nomenclature and source of molecular detection of resistance, 1281 evaluation, interpretation, and reporting of species, 727 objective of, 1277 results, 2585 Taxonomic ranks, 289 pharmacokinetics and pharmacodynamics, microscopy, 2584–2585 Taxonomy, 1435 1279–1280 nucleic acid detection, 2585 changing face of, 296 reporting results, 1281 serologic tests, 2585 character-based descriptors for, 1436–1437 selecting agents for routine testing, taxonomy, 2584 chemotaxonomy, 293–294 1278–1279 treatment, 2585 criteria for classification, 1437 selecting method, 1278 Taenia serialis, coenurosis, 2582, 2588 databases, 1439, 1444 use of confirmatory and supplementary Taenia solium definition, 167 tests, 1281 characteristics of, 2583 demarcation via sequence similarity, zone diameter comparisons, 1280 clinical significance, 2585 1438 See also Antimicrobial susceptibility testing collection, transport, and storage of speci- future challenges for viruses, 1444 systems; Antimicrobial susceptibility mens, 2585 future perspectives, 296–297 tests (ASTs) cysticercosis, 2587–2588 human pathogens, 1439 Susceptibility test methods description of agent, 2585 microbial systematics and, 287–288 African trypanosomiasis, 2686 direct examination, 2585–2586 nomenclature, 291–292 future perspectives, 2686–2687 epidemiology, transmission, and preven- polyphasic approach to, 292 leishmaniasis, 2685–2686 tion, 2585 sequence-based characters, 1437–1439 malaria, 2682–2685 evaluation, interpretation, and reporting of viral, 1435–1436 schistosomiasis, 2686 results, 2586 Tazobactam, 1208 trichomoniasis, 2685 microscopy, 2585–2586 Telavancin, 1218–1220 Susceptibility test methods: viruses nucleic acid detection, 2586 lipoglycopeptide resistance, 1262–1263 dye uptake (Du) assay, 1988 serologic tests, 2586 Telbivudine enzyme immunoassays, 1988 taxonomy, 2585 drug interactions, 1951 genotypic assays, 1988–1993 treatment, 2586 HBV therapy, 1950 genotypic platforms, 1989–1991 Taï Forest virus mechanism of resistance, 1969 genotyping applications, 1991–1993 geography and associated human diseases, pharmacology, 1951 neuraminidase inhibition assay, 1988 1723 Telithromycin, 1214–1215

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Tenofovir, mechanism of resistance, 1965, glanders and melioidosis, 250–251 diagnosis in newborns, 2480–2481 1966, 1969, 1970 hemorrhagic fever viruses (HFVs), 249 diagnosis of acute acquired infections, Tenofovir alafenamide (TSF) plague, 247–248 2479–2480 drug interactions, 1941, 1951 smallpox, 248 diagnosis of ocular infection, 2481 HBV therapy, 1950 tularemia, 248–249 direct examination, 2476 HIV therapy, 1938 Tigecycline, 1217–1218 epidemiology and transmission, 2473–2475 pharmacology, 1941, 1951 Tinea nigra, 2228–2229 guide to interpretation of serology results, Tenofovir disoproxil fumarate (TDF) direct examination, 2229 2478 drug interactions, 1941, 1951 isolation, 2229 isolation procedures, 2476 HBV therapy, 1950 Tinea versicolor, 2227–2228 life cycle, 2473, 2474 HIV therapy, 1938 direct examination, 2228 microscopy, 2476 pharmacology, 1941, 1951 isolation and culture, 2228 nucleic acid detection, 2476 Terbinafine Malassezia furfur, 2227, 2228 prevention, 2475 acquired resistance, 2319 Tinidazole, mechanism of resistance, 2670 serologic tests, 2476–2479 allylamine, 2319–2320 Tinsdale agar, 358 taxonomy, 2473 clinical use, 2319 Tipranavir treatment, 2482 drug interactions, 2319–2320 drug interactions, 1945 Toxoplasma gondii, 2473 pharmacokinetics, 2319 HIV therapy, 1939 life cycle of, 2473–2474 spectrum of activity, 2319 pharmacology, 1945 risk factors for, 2475 toxicity and adverse effects, 2320 Tissue three life stages of, 2474 Terms, common mycological, 2013–2015 biopsy samples, 324–325 Toxoplasmosis, commercially available kits for Tetanus, 975–976, 980–981 collection and processing of virus, 1457 diagnosis, 2392 Tetanus neurotoxin (TeNT), 970, 975, 981 collection and transport, 2018 Trachipleistophora hominis Tetracyclines curved Gram-negative rods and infections, description, 2306 adverse effects, 1218 1027 life cycle of microsporidia, 2307 efflux proteins, 1256–1257 pathogenic fungi recovery, 2019 Transplant-Associated Infection Surveillance enzymatic inactivation, 1257 pretreatment, 2020 Network (TRANSNET), 2106 mechanism of action, 1216 processing and culture guidelines, Training, 209 pharmacology, 1216–1217 2022–2023 Transcription-based amplification methods, resistance, 1256–1257 specimen collection and transport, 308 96, 97 resistance determinants, 1256 Todd-Hewitt broth, 358 Transmissible spongiform encephalopathies, ribosomal protection, 1257 Togaviridae family, 1685, 1687 234–236 Rickettsia spp., 1157 Togniniales order Transmissible spongiform encephalopathy spectrum of activity, 1217–1218 overview of genera in, 2237 agents, detection and identification target-based resistance, 1257 Phaeoacremonium genus, 2246 methods, 1475 third-generation, evading resistance, 1257 phaeohyphomycosis, 2249, 2250 Transplantation Tetraparvovirus (human parvovirus 4, taxonomy and description, 2246 Epstein-Barr virus (EBV) DNA load, 1797, PARV4), 1880, 1886 Toluidine blue 1806 Tetrathionate broth, Hajna, 357 fungi detection, 2036 human adenovirus (HAdV) infection, Tetrazolium tolerance agar, 357–358 mycology, 2029 1833, 1835 Thallic conidiogenesis, 2012 Torovirinae subfamily, 1606 human herpesviruses in patients, 1816 Thaumarchaeota, 294 Total laboratory automation (TLA) Transport and metabolic functions, 290 Thayer-Martin medium, 358 advantages and disadvantages of, 82 Transport medium Stuart, 358 Thermoactinomyces genus BD-Kiestra TLA Concept, 78–80, 82 TREK Diagnostic Systems, phenotypic identi- description, 533 WASPLab, 80–82 fication system, 50 morphologic characteristics, 529 See also Microbiology laboratory TREK Sensitive MYCOTB MIC plate See also Actinomycetes automation method, 1408 Thermothelomyces Toxocara spp. Trematoda, classification, 2384, 2385 clinical significance, 2152 clinical significance, 2609 Trematodes hyphomycetes, 2149 description of agents, 2609 collection, transport, and storage, 2590 Thiabendazole. See Benzimidazoles direct examination and microscopy, 2609 digeneans of circulatory system: schisto- Thioglycolate bile broth, 358 epidemiology, transmission, and preven- somes, 2590, 2595–2598 Thioglycolate medium, enriched, 358 tion, 2609 digeneans of human gastrointestinal tract, Thiosulfate citrate bile salt sucrose (TCBS) microscopy of, 2607 2593 agar, 357 serologic tests, 2609 eggs of parasites, 2599 Third National Health and Nutrition taxonomy, 2609 foodborne digeneans, 2598–2603 Examination Survey (NHANES III), treatment, 2609 helminth recovery and identification, 1086 Toxocariasis, commercially available kits for 2423 Thorny-headed worms, Acanthocephala, 2384 diagnosis, 2392 lung and hepatic digeneans of humans, Ticarcillin, 1203 Toxoplasma genus 2592 Tick-borne encephalitis, commercial diagnos- algorithms for diagnoses, 2479, 2480 See also Foodborne digeneans; Schistosoma tic tests, 1691 antigen detection, 2476 genus Ticks cell-mediated immune responses, 2476 Trematosphaeria grisea, 2035 arthropods as vectors, 2626–2628, classification, 2383 assimilation patterns, 2269 2631–2632 clinical significance, 2475 cultures of, 2264, 2265 human-biting, and infections, 2630 clinical use of diagnostic tests, 2479–2482 in vitro susceptibility, 2272 hypostome of, 2628 collection, transport, and storage of speci- morphological identification, 2268 life cycles, 2628 mens, 2475 morphology by direct examination, 2040 medically important, of united States, 2627 commercially available IgG kits, 2477, taxonomy and description, 2261, 2263 pictorial key to major genera in u.S., 2629 2478 Trench fever, anthroponotic bartonelloses, summary of infectious agents and disease, detection in humans, 2381 896 2621 determination of immune status, 2479 Treponema spp. Tier 1 select agents, 245–250 diagnosis during pregnancy, 2480 direct detection, 1090 anthrax, 246–247 diagnosis in immunocompromised hosts, taxonomy, 1083 botulism, 247 2481–2482 tissue infections, 1027

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Treponema denticola epidemiology, transmission, and preven- microscopy, 2567 antimicrobial susceptibilities, 1098 tion, 2513–2514 relative sizes of eggs, 2552 collection, transport, and storage of speci- evaluation, interpretation, and reporting of summary of, 2559 mens, 1089 results, 2516 taxonomy, 2566 description of, 1084 flagellate, 2507 transmission and life cycle, 2566, 2567 oral treponemes, 1084, 1086 key features of trophozoites and cysts of, treatment, 2568 taxonomy, 1083 2509 See also Nematodes Treponema pallidum microscopy, 2514 Triclabendazole. See Benzimidazoles antimicrobial susceptibilities, 1096, 1098 nucleic acid detection technique, Trifluridine chemiluminescence immunoassays, 1096, 2515–2516 against herpesviruses, 1952 1099 susceptibility testing, 2685 drug interactions, 1954 collection, transport, and storage of speci- taxonomy, 2513 pharmacology, 1954 mens, 1089 treatment, 2516 Trimethoprim direct detection, 1090, 1098, 1100 Trichomoniasis adverse effects, 1223 direct fluorescent antibody test for, 1090 mechanisms of resistance, 2672–2673 mechanism of action, 1222 enzyme immunoassays, 1093, 1094, 1095, proposed mechanisms of resistance for drugs pharmacology, 1222 1096 against, 2670 as resistance target, 1427 evaluation and interpretation of results, selected antiparasitic agents and suscepti- spectrum of activity, 1222–1223 1098, 1100–1102 bility testing method, 2683 Trimethoprim-sulfamethoxazole, resistance, immunoblot assays, 1096, 1098 susceptibility test methods, 2685 1260 isolation procedures, 1091 Trichophyton agars, mycology, 2032 Troglotrematidae MHA-TP test, 1093 Trichophyton spp. clinical significance, 2602 microscopy and immunofluorescent stain- anatomic specificity, 2217 description of agents, 2602 ing, 1098 characteristics of dermatophytes and der- diagnosis, 2602 multiplex flow immunoassays, 1096, 1099 maphytoids, 2211–2215 epidemiology, transmission, and preven- nontreponemal tests, 1092–1093, 1100 dermatophyte nutritional response, 2221 tion, 2602 oligonucleotide primers/probes for genital description of, 2222–2223, 2225, 2226 treatment, 2602 ulcer disease, 1090 epidemiology and transmission, 2216 Troglotrematidae family PCR detection of, 1098, 1100 evaluation, interpretation, and reporting of geographic distribution, hosts and egg PCR for detection, 1090, 1092 results, 2227 morphology of, 2593 rapid syphilis tests, 1096, 1097, 1101 grouping of dermatophytes on host and geographic distribution, hosts and histories reverse screening algorithm, 1101 habitat, 2216 of, 2592 serologic tests, 1092–1093, 1096, growth on BCP-milk solids-glucose medium Tropheryma whipplei, 271 1100–1101 (BCPMSG), 2222 antimicrobial susceptibilities, 1194–1195 syphilis tests in HIV infection, 1102 hair invasion, 2219–2220 classical Whipple disease, 1190 tests for congenital syphilis, 1102 in vitro hair perforation test, 2221 clinical significance, 1190–1192 tests for neurosyphilis, 1101–1102 nucleic acid detection, 2220 collection, transport, and storage of speci- treponemal tests, 1093, 1096, 1100–1101 nutritional requirements, 2221 mens, 1192–1193 typing systems, 1091, 1092 physiological tests, 2221–2222 culture, 1189 visualization in tissues, 1098 sample preparation and practice, 2218 description of, 1189 Treponema pallidum subspecies taxonomy, 2208, 2216 diagnostic tests for, 1116 description of, 1083 temperature tolerance and enhancement, direct examination, 1193–1194 host-associated spirochetes, 1083–1085 2222 epidemiology and clinical diseases associ- morphology of, 1084 typing systems, 2227 ated with, 1111 Triadelphia genus, 2243, 2247, 2250 urea hydrolysis, 2222 epidemiology and transmission, 1189–1190 Triatoma sanguisuga (reduviid bug), 2622–2623 See also Dermatophytes evaluation, 1195 Trichinella spp. Trichophyton rubrum, calcofluor white stain, genome, 1189 clinical significance, 2608 2045 healthy carriers, 1192 description of agents, 2608 Trichosporon genus identification, 1194 direct examination and microscopy, 2608 antifungal susceptibilities, 2068 interpretation, 1195 epidemiology, transmission, and preven- clinical significance, 2067 isolated organ manifestations, 1190–1192 tion, 2608 cultural and biochemical characteristics isolation procedures, 1194 microscopy of T. spiralis, 2607 of, 2062 morphology, 1189 nucleic acid detection, 2608 description, 2064 pathogenesis and immunology, 1190 serology, 2608 morphological features of, 2063 reporting results, 1195 taxonomy, 2608 taxonomy and nomenclature, 2058 serologic tests, 1194 treatment, 2608–2609 white piedra, 2230 symptoms and signs of infection, 1191 Trichoderma spp. Trichothecenes taxonomy, 1189 clinical significance, 2152 classification and biosynthesis of, 2282 typing systems, 1194 hyphomycetes, 2149 common food substrates, 2282 See also Whipple disease microscopy, 2149, 2150 genetic structure, 2280 Trueperella genus Trichodysplasia spinulosa polyomavirus pathological effects and toxicological refer- description, 493 (TSPyV), 1863, 1865, 1867 ence values, 2283 identification, 513–514 Trichomonas genus structure of, 2279 Trypanosoma genus classification, 2382 See also Mycotoxins classification, 2382 detection in humans, 2381 Trichrome stain detection in humans, 2381 Trichomonas hominis parasitology, 2411 life cycle stages of, 2460 flagellate, 2507 stool specimens, 2418, 2420 Trypanosoma brucei gambiense key features of trophozoites and cysts of, 2509 Trichuris trichiura (whipworm) clinical significance, 2468 Trichomonas vaginalis clinical significance, 2566–2567 collection of specimens, 2468 antigen detection, 2514–2515 description, 2566 culture and animal inoculation, 2469 clinical significance, 2514 direct examination, 2567 diagnosis, 2468 culture, 2514 epidemiology and prevention, 2566 direct examination, 2468–2469 description of agent, 2513 life cycle completion time, 2558 epidemiology and transmission, 2467–2468 direct detection, 2514–2516 macroscopic examination, 2567 life cycle and morphology, 2467

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Trypanosoma brucei gambiense (continued) Typhus group (TG), 1149 parasites, 2390 microscopic detection, 2468 Typing systems specimen preparation and procedures, 2396 nucleic acid detection, 2469 genotypic methods, 794–795 specimens, 2426–2427 serologic tests, 2469 PFGE (pulsed-field gel electrophoresis), urticating caterpillars, stinging and biting for treatment and prevention, 2469 794–795 envenomation, 2635–2636 Trypanosoma brucei rhodesiense phenotypic methods, 794 u.S. Army Medical Research Institute of clinical significance, 2468 Pseudomonas, 794–795 Infectious Diseases, 245, 1728 collection of specimens, 2468 restriction fragment length polymorphism u.S. Department of Agriculture (uSDA), culture and animal inoculation, 2469 (RFLP), 794 156, 479 diagnosis, 2468 ribotyping, 794 u.S. Department of Health and Human direct examination, 2468–2469 Services, 460 epidemiology and transmission, 2467–2468 Coxiella burnetii, 1183 life cycle and morphology, 2467 u9B broth, 358 u.S. Department of Transportation (DOT), microscopic detection, 2468 ultralow-temperature freezing, preservation, specimen transportation regulations, nucleic acid detection, 2469 199–200 1457 serologic tests, 2469 uncultivated organisms, 291 u.S. Food and Drug Administration (FDA), treatment and prevention, 2469 united Kingdom Department of Health, 5, 187, 479, 1701, 1709–1710 Trypanosoma congolense, 2469 decontamination of instruments for antiviral agents, 1937 Trypanosoma cruzi prion diseases, 235 cytomegalovirus (CMV) infection, 1772 American trypanosomiasis, 2463–2467 university of Washington, human herpesvirus disease surveillance, 156 Chagas’ disease, 2463, 2622 6 (HHV-6) testing, 1818 gradient diffusion method, 1348 clinical significance, 2465 upper respiratory tract specimens Mycobacterium tuberculosis, 580 collection of specimens, 2465 collection and transport, 2018 nucleic acid-based tests, 115–116 culture and animal inoculation, 2466 pathogenic fungi recovery, 2019 oversight, 13–14 diagnosis, 2465 pretreatment, 2020 quality testing of reagents and stains, 1463 direct examination, 2465–2466 processing and culture guidelines, 2022 u.S. Naval Medical Research Center, 464 epidemiology and transmission, 2464–2465 urea agar, 358 uTI chromogenic agar, 358 life cycle, 2464 urea hydrolysis, streptococci, 411 uV germicidal irradiation surface microscopic detection, 2465–2466 Ureaplasma spp., 1109 disinfection, 230 morphology, 2464 antigen detection, 1123 uVM modified Listeria enrichment broth, 358 nucleic acid detection, 2466 antimicrobial susceptibilities, 1128–1130 serologic tests, 2466 biosafety considerations, 1124 treatment and prevention, 2466–2467 clinical significance, 1120–1122 V8 agar, mycology, 2032 xenodiagnosis, 2466 description, 1117–1119 Vaborbactam, 1208–1209 Trypanosoma evansi, 2469 development of colonies, 1125 VACC agar, 359 Trypanosoma lewisi, 2469–2470 diagnostic tests for, 1116 Vaccination Trypanosoma rangeli, 2467 epidemiology and clinical diseases associ- human immunodeficiency virus (HIV), 1481 Trypanosomes, techniques for parasite recov- ated with, 1111 influenza viruses, 1512 ery and identification, 2436 epidemiology and transmission, 1119–1120 issues, 183–184 Trypanosomiasis evaluation, interpretation, and reporting of Vaccines African, 2467–2469 results, 1130–1131 brucellosis, 889 American, 2463–2467 genitourinary infections, 1120–1121 cytomegalovirus (CMV) disease, 1772 Trypsin solutions, 1463 granular, brown, urease-positive colonies, hantaviruses, 1710 Trypticase soy agars, 358 1117, 1119 human adenovirus (HAdV), 1841 Trypticase tellurite agar base, 358 identification, 1126 human papillomavirus (HPV) and, 1853 Tryptic soy blood agar, 358 incubation conditions and subcultures, 1125 invasive meningococcal disease (IMD), 641 Tsukamurella genus, 1413, 1414 isolation procedures, 1124–1125 Vaccinia virus (VACV), 1462, 1892 classification, 526 MIC ranges for antimicrobials, 1129 V agar, 358 clinical significance, 541 neonatal infections, 1121–1122 Vaginal cancer, human papillomavirus (HPV) colonial morphology, 530 nucleic acid detection, 1124 and, 1852 description, 533 primary sites of colonization, metabolism, Vaginal microbiome, 260 epidemiology and transmission, 533 and pathogenicity, 1118 microbial composition, 255 microscopic morphology, 532 serologic tests, 1128 predominant phyla, 256 morphologic characteristics, 529 typing systems, 1126 See also Human microbiome recovered from human specimens, 535 See also Mollicutes Vaginal specimens See also Actinomycetes urease test, 334 collection and transport, 2018 Tuberculosis (TB) ureidopenicillins, 1203 processing and culture guidelines, 2023 database, 187 urinary tract, infectious syndromes, 318 Vagococcus genus latent infection, 577 urine antimicrobial susceptibilities, 444 public health, 558 collection and processing of virus, 1457 clinical significance, 439 See also Mycobacterium tuberculosis collection and transport, 2018 identification, 440 Tubulinosema spp., description, 2306, 2308 pathogenic fungi recovery, 2019 molecular methods for identification, 444 Tularemia pretreatment, 2020 phenotypic differentiation, 442 biothreat agent, 248–249 processing and culture guidelines, 2023 See also Catalase-negative, Gram-positive cocci Francisella tularensis as causative agent, 871 specimen collection and transport, 308–309 Valacyclovir in united States, 879 virus detection methods, 1449 against herpes B virus, 1750 See also Francisella tularensis urogenital amebae, 2498 against herpesviruses, 1952 Tumors, Epstein-Barr virus (EBV)-associated, urogenital Mycoplasma broth base, 358 antiviral therapy for herpes simplex virus 1799–1800 urogenital system (HSV), 1742 Turicella genus, 401, 510–511 antigen detection, 2427 drug interactions, 1953 Tusavirus, 1880, 1886 culture, 2426–2427 herpes viruses, 1962–1964 Tween 20-PBS, 1463 direct parasite detection, 2401 mechanism of resistance, 1963 Type species, 289–291 direct wet mount, 2426 pharmacology, 1953 Type strains, 289–291 parasite detection, 2426 spectrum of activity, 1953

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Valganciclovir quantitative VZV DNA in patients with molecular typing of vibrios, 782–783 against herpesviruses, 1952 VZV-associated diseases, 1761 phenotypic test results of species, 777 cytomegalovirus (CMV) resistance to, 1788 schematic of linear double-stranded DNA serologic tests, 783 drug interactions, 1953 genome, 1758 serotyping, 782 pharmacology, 1953 serologic tests, 1764–1765 specimen collection, transport, and storage, spectrum of activity, 1953 taxonomy, 1757 779 Vancomycin, 1218–1220, 1230 Variola major (smallpox), biothreat agent, typing systems, 782–783 glycopeptide antibiotics, 1261–1262 248 Vibrio parahaemolyticus, 777, 778, 782 resistance in enterococci, 1304 Variola virus (VARV), epidemiology, 1892 Vibrio vulnificus, 777, 778 Vancomycin-intermediate Staphylococcus Vectors. See Arthropods as vectors Viracor, human herpesvirus 6 (HHV-6) test- aureus (VISA) Veillonella spp. ing, 1818 detection, 1324 antimicrobial susceptibilities, 933 Viral hemorrhagic fever (VHF) viruses, 1719 detection of heteroresistant (hVISA), clinical significance, 928 laboratory-acquired infection, 217 1324–1325 description, 926 Viral meningitis, VZV infection, 1758–1759, Vancomycin-resistant Enterococcus (VRE) epidemiology, 927 1761 commercially available agar-based media molecular methods, 929, 932 Viral particle, schematic of, 1478 for, 424 resistance patterns of, 1390 Viral respiratory pathogens, laboratory- detection, 1323–1324 taxonomy, 925 acquired infection, 217 emergence of acquired vancomycin resis- Velpatasvir ViroChip, 180, 273 tance, 429, 430 drug interactions, 1949 Virology, 1472–1476 FDA-cleared molecular assays for detection, HCV therapy, 1947 advances in diagnostics, 1472, 1475 1423 mechanism of resistance, 1971, 1973 cell culture media, 1469–1470 health concerns of, 420–421 pharmacology, 1948–1949 cell cultures, 1463, 1465–1469 incidence of, 423 Venereal Research Disease Laboratory direct fluorescent-antibody (DFA) reagents, media for detection of, 338 (VDRL), 128 1463, 1464 molecular detection of, 1422, 1424 Venereal syphilis indirect fluorescent-antibody (IFA) Vancomycin-resistant Staphylococcus aureus clinical significance, 1086, 1088 reagents, 1463, 1464 (VRSA), detection, 1324 epidemiology and transmission, 1085 quality control in diagnostic laboratory, Vancomycin-variable Enterococcus faecium Ventilator-associated pneumonia, 1470 (VVE), 1424 Pseudomonas, 789 reagents, 1462–1463, 1464 Van Leeuwenhoek, Anton, 16, 269, 270, 1083 Venturiales order sources of reagents, stains, media, and cell Vapor-phase hydrogen peroxide/peracetic acid Ochroconis genus, 2246 lines, 1470–1471 disinfection with, 238 overview of genera in, 2237 stains, 1463 Variable-number tandem-repeat (VNTR) phaeohyphomycosis, 2249, 2250 ViroSeq, HIV susceptibility, 1994 analysis, method, 175–176 taxonomy and description, 2246 Viruses, 1435 Variably protease-sensitive prionopathy Verruconis genus, 2246 advances in diagnostics, 1472, 1475 (VPSPR), 1923 Veronaea genus, 2242 challenges and future perspectives, Varibaculum spp. Verruconis genus, 2246, 2249, 2250 1475–1476 biochemical characteristics, 951 Verruga peruana, anthroponotic bartonelloses, characteristics differentiating families of, clinical significance, 944 896 infecting humans, 1442 Varicella-zoster virus (VZV), 1962, 1985 VersaTREK, 1408 collection and processing of specimens, antigen detection, 1760 inoculum and incubation, 1408 1453–1457 antiviral drug resistance, 1964 quality control, 1408 commercially available reagents for, 1464 antiviral susceptibility, 1765 reading and interpreting results, 1408 criteria for taxonomic classification, antiviral therapy, 1765 Vibrio spp. 1436–1439 cell culture methods, 1763 algorithm for identification of, 1025 genotyping for, 181 cellular immunity, 1765 bacteremia, 1027 ICTV classification of, 1435–1436 clinical significance, 1757–1759 gastrointestinal-tract infections, 1024, 1026 methods for detection and identification, collection, transport, and storage of speci- properties of genus, 776 1473–1475 mens, 1759–1760 susceptibility testing, 1366–1367 morphology, 1443 description of agent, 1757 testing conditions, 1353 preservation methods, 202, 203 detection and identification methods, 1475 tissue infections, 1027 processing and storage conditions, 1452 diagnostic tests for VZV-induced disease, Vibrio alginolyticus, 777, 778 specimen collection, 1446, 1449–1450 1759 Vibrio cholerae, 4, 775–776 specimens and methods for detection, direct examination, 1760–1763 laboratory techniques, 161 1447–1449 electron micrograph of, in skin vesicle fluid, phenotypic test results, 777 specimen selection, 1446 1758 toxin detection, 782 specimen storage and processing, epidemiology and transmission, 1757 V. cholerae non-O1, non-O139, 776, 778 1451–1453 evaluation, interpretation, and reporting of V. cholerae O1, 776, 779–780 susceptibility profiles, 1468, 1469 results, 1765 V. cholerae O139, 776 taxonomical classification of, infecting gene targets for antiviral resistance testing, Vibrio cincinnatiensis, 777, 779 humans, 1440–1441 1989 Vibrio fluvialis, 777, 779 taxonomic challenges, 1444 genetic VZV strain characterization, Vibrio furnissii, 777, 779 transportation regulations, 1457 1763–1764 Vibrio metschnikovii, 775, 777 transport conditions, 1450–1451 genotyping application, 1992 Vibrio mimicus, 777, 778 transport medium, 1450, 1451 identification from cell culture, 1763 Vibrionaceae See also Susceptibility test methods: viruses isolation and identification, 1763–1764 antimicrobial susceptibilities, 783 Virus Identification Pipeline (VIP), 277 mechanisms and mutations of antiviral drug description of, 775 Vitek system, phenotypic identification resistance, 1963 direct examination, 779–780 system, 47–48 microscopy, 1760 evaluation, interpretation, and reporting of VITEK Systems, automated broth microdilu- nucleic acid detection, 1760–1763 results, 783 tion, 1302–1303 PCR analysis, 1759–1763, 1765 identification, 781–782 Vittaforma spp. proposed guidelines for phenotypic antiviral isolation procedures, 780–781 description, 2306, 2308 susceptibility, 1987 molecular methods, 782 life cycle of microsporidia, 2307

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Vogel and johnson agar, 359 systemic, 1190 parasite of humans, 2571 Voges-Proskauer test, 334, 408 See also Tropheryma whipplei taxonomy, 2570 Voriconazole White piedra, 2229–2230 acquired resistance, 2323 Whitman, William, 292 clinical breakpoints for Candida spp., 2352 WHO Collaborating Centers, 758, 1062 Xenopsylla cheopis (Oriental rat flea), 2624 clinical use, 2323–2324 Whole-genome mapping (WGM) xLD (xylose lysine deoxycholate) agar, 359 spectrum of activity, 2320, 2323 characteristics and application, 169 xylose lactose Tergitol 4 (xLT-4), 359 therapeutic drug monitoring, 2324 optical mapping, 173 xylose sodium deoxycholate citrate agar, 359 toxicity and adverse effects, 2324 Whole-genome sequencing (WGS), 295, 630, Voxilaprevir 795, 1421 drug interactions, 1948 characteristics and application, 169 Yalow, Rosalyn S., 124 HCV therapy, 1947 development of new discriminative PCRs, Yatapoxvirus genus pharmacology, 1948 637–638 epidemiology, 1892 V. parahaemolyticus agar (VP agar), 359 disease detection, 161–162 real-time PCR assays for, 1898 V. parahaemolyticus sucrose agar, 359 homologous gene cluster, 637 taxonomy, 1892 VP test, streptococci, 411 identification and typing, 636–637 Yeast carbon agar, mycology, 2032 VRE agar, 359 k-mer-based analyses, 179 Yeast extract phosphate agar with ammonia VRE Select medium, 359 methods, 176–177, 179, 295 (Smith’s medium), mycology, 2032 VT-1598 and VT-1161 (Viamet multilocus sequence typing (MLST), 179 Yeasts Pharmaceuticals), 2328 proposed workflow for, 277 agar-based alternative approaches for, Vulvar cancer, human papillomavirus (HPV) SNP typing, 177–179 2362–2363 and, 1852 Wilkins-Chalgren anaerobe broth, 359 alternative susceptibility approaches for, Williamsia genus 2360–2363 clinical significance, 541 antigen detection, 2070–2071 Walker, David H., 1153 colonial morphology, 530 antimicrobial susceptibilities, 2077 Wallenstein medium, 359 description, 533 ascomycetous, 2056–2058 Warts, human papillomavirus (HPV), 1851 microscopic morphology, 532 basidiomycetous, 2058 Water agar, mycology, 2032 morphologic characteristics, 529 chromogenic agars, 2073–2074 Wautersia eutropha, 807 recovered from human specimens, 535 clinical significance, 2065–2067 Wautersiella falsenii See also Actinomycetes collection, transport, and storage of speci- characteristics of, 843 Woese, Carl, 288, 630 mens, 2067 identification, 845 Wolbachia spp. colorimetric methods, 2361 Wayson stain, 337 contributions to human disease, 1169 description of agents, 2058–2064 Weeksella virosa description of, 1163 direct examination, 2069–2072 characteristics of, 843 epidemiology and transmission, 1164 direct susceptibility testing, 2363 identification, 845–846 neighbor-joining phylogenetic tree, 1164 epidemiology and transmission, 2064–2065 Weissella genus Wohlfahrtiimonas chitiniclastica evaluation, interpretation, and reporting of cellular morphology, 437 characteristics of, 837 results, 2077–2078 clinical significance, 439 identification, 839 flow cytometry, 2361–2362 evaluation, interpretation, and reporting of Workflow historical approaches to identification, results, 445 batch versus immediate testing, 74–75 2072–2073 phenotypic differentiation, 442 role of process improvement, 75–76 identification, 2011, 2072–2076 taxonomy, 436 World Federation of Culture Collections, 291 India ink, 2070 See also Catalase-negative, Gram-positive World Health Organization (WHO), 226, isolation procedures, 2072 cocci 1693, 1926, 2261 KOH and microscopy, 2069–2070 Westerdijk Fungal Biodiversity Institute, 2252 collaborating centers (WHOCC), 1895, MALDI-TOF MS identification of, 60–61 Western encephalitis virus, commercial diag- 1901 microscopy, 2069–2070 nostic tests, 1692 decontamination of instruments for prion molecular methods, 2074–2075, 2363 West Nile virus, commercial diagnostic tests, diseases, 235 morphology studies, 2074 1690–1691 disease surveillance, 156 nonautomated identification system, 53 Wheatley trichrome stain, parasitology, 2411 Global Tuberculosis Report, 558 nucleic acid detection, 2071–2072 Whipple, George Hoyt, 1189 health care infections, 139 organisms resembling, 2076 Whipple disease, 271 hepatitis C virus, 1646 preservation methods, 202, 203 acute gastroenteritis, 1192 human herpesvirus 6 (HHV-6), 1817 proteomics, 2363 antigen detection, 1193–1194 influenza pandemic, 1511 purity of cultures, 2073 central nervous system (CNS), 1191 malaria eradication, 2669–2670 reportable organisms for MALDI-TOF classical, 1190, 1193 measles, 1560 MS, 57 endocarditis, 1191 microorganism classifications, 206 scheme for identification of, 2069 epidemiology and transmission, 1189–1190 tuberculosis (TB), drug-resistant, 1398 serologic tests, 2077 estimated annual incidence of, 1189 venereal syphilis, 1085 standardized broth dilution methods for, evaluation, interpretation, and reporting, World War II, 751 2354–2358 1195 Wounds standardized disk diffusion method for, eyes, 1191 botulism, 975 2362 healthy carriers, 1192 processing recommendations, 326 taxonomy and nomenclature, 2056–2058 hierarchical scheme for diagnosis of, 1193 specimen collection and transport, 303 in tissue sections, 2070 immune reconstitution inflammatory Wright’s stain typing systems, 2076–2077 syndrome (IRIS), 1191–1192 blood, 2434 Vitek 2 yeast susceptibility testing, 2361 isolated, 1193 parasitology, 2410–2411 Yellow fever virus, 269 joints, 1190–1191 Wuchereria bancrofti commercial diagnostic test, 1691 lungs, 1192 description, 2570 Yersinia selective agar base, 359 microscopy, 1193 diagrammatic representation of extremities, Yersinia species nucleic acid detection, 1194 2573 antigen detection, 756 organ manifestations, 1190–1192 epidemiology and transmission, 2570–2571 antimicrobial susceptibilities, 760 skin, 1192 microfilariae in humans, 2572 characteristics of, 752

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clinical significance, 754–755 Yersinia pestis, 184 structure of, 2279 Crohn’s disease, 754–755 bioterrorism potential, 1359 See also Mycotoxins description of the agents, 751, 753 biothreat agent, 247–248 Zidovudine direct examination, 755–757 laboratory-acquired infection, 215 drug interactions, 1941 enteropathogenic, 754 testing conditions, 1350 HIV therapy, 1938 epidemiology and transmission, 753–754 Yersinia ruckeri, biochemical reactions of, 690 mechanism of resistance, 1965, 1966 evaluation, interpretation, and reporting of pharmacology, 1941 results, 760–761 Zika virus, 183 identification, 758–759 Zaki, Sherif, 1153 commercial diagnostic tests, 1691 isolation procedures, 757–758 Zanamivir laboratory techniques, 161 microscopy, 755 against influenza virus, 1955 next-generation sequencing (NGS), 274 nucleic acid detection, 756–757 drug interactions, 1955 nucleic acid amplification, 271 serologic tests, 760 mechanism of resistance, 1974–1975 outbreak, 155, 1694 specimen collection, transport, and storage, pharmacology, 1955 transmission, 276 755 Zearalenone Zone diameter distributions, disk diffusion taxonomy, 751 classification and biosynthesis of, 2282 methods, 1280–1281, 1284 typing systems, 759–760 common food substrates, 2282 Zoonosis investigation, 183 Y. enterocolitica, 754 genetic structure, 2280 Zoonotic bartonellosis, 896–897 Y. pestis, 753–754 pathological effects and toxicological refer- Zygomycota, phylum of kingdom Fungi, Y. pseudotuberculosis, 754, 755 ence values, 2283 2009

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