Volume 1 Manual of Clinical Microbiology 12th Edition Downloaded from www.asmscience.org by IP: 94.66.220.5 MCM12_FM.indd 1 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM Volume 1 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 Downloaded from www.asmscience.org by IP: 94.66.220.5 MCM12_FM.indd 2 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM Volume 1 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 Downloaded from www.asmscience.org by IP: 94.66.220.5 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 Printed in Canada 10 9 8 7 6 5 4 3 2 1 Address editorial correspondence to: ASM Press, 1752 N St., N.W., Washington, DC 20036-2904, USA. Send orders to: ASM Press, P.O. Box 605, Herndon, VA 20172, USA. Phone: 800-546-2416; 703-661-1593. Fax: 703-661-1501. E-mail: [email protected] Online: http://estore.asm.org Downloaded from www.asmscience.org by IP: 94.66.220.5 MCM12_FM.indd 4 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM Contents 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 Downloaded from www.asmscience.org by IP: 94.66.220.5 MCM12_FM.indd 5 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM vi n CONTENTS 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