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For the Laboratory Sciences

For the Laboratory Sciences

Introduction to for the Laboratory Sciences

Maria Dannessa Delost, PhD, MT(ASC-P) Professor and Director of Medical Laboratory Programs Department of Health Professions The Bitonte College of Health & Human Services Youngstown State University Youngstown, OH

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Library of Congress Cataloging-in-Publication Data Delost, Maria Dannessa, author. Introduction to diagnostic microbiology for the laboratory sciences / Maria Dannessa Delost. p. ; cm. Includes bibliographical references and index. ISBN 978-1-284-03231-4 (pbk.) I. Title. [DNLM: 1. Clinical Laboratory Techniques—Problems and Exercises. 2. Microbiological Techniques—Problems and Exercises. QY 18.2] RB38.25 616.07'5076—dc23 2013034746 6048 Printed in the United States of America 18 17 16 15 14 10 9 8 7 6 5 4 3 2 1

9781284032314_FMxx_00i_0xx.indd 2 14/02/14 12:42 PM Dedication

To the memory of my Dads, Amil M. Dannessa and George Delost, Jr., who served their country in World War II as members of our Greatest Generation and who taught me the values of hard work, loyalty, and honesty

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Preface ...... xv Acknowledgments ...... xvii Reviewers ...... xix

Chapter 1 Introduction to Clinical Microbiology 1 Classification and Taxonomy ...... 2 Characteristics of Eukaryotes and Prokaryotes ...... 3 Bacterial Components ...... 4 Cellular Metabolism ...... 5 Exotoxins and Endotoxins ...... 6. The Role of Clinical Microbiology ...... 6 . The Infectious Process ...... 7 Normal Flora ...... 7 Modes of Transmission—Routes of Infection ...... 8 True versus Opportunistic Pathogens ...... 9. Host Defense Mechanisms ...... 10 Signs of Infection ...... 13 Nosocomial and Health Care–Associated Infections ...... 14 Review Questions ...... 14 Bibliography ...... 16

Chapter 2 Safety in the Clinical Microbiology Laboratory 17 Laboratory Safety ...... 18 Exposure Control ...... 18 Safety Education ...... 18 Universal Precautions and Standard Precautions ...... 19 Personal Protective Equipment ...... 20 Engineering Controls ...... 21 Postexposure Plan ...... 22 Fire Safety ...... 24 Chemical Safety ...... 26 Review Questions ...... 27 Bibliography ...... 27

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Chapter 3 Specimen Collection, Transport, and Processing: Preliminary Identification Methods 29 General Specimen Guidelines ...... 31 Specimen Collection Requirements for Specific Sites ...... 33 Respiratory Tract ...... 33 Gastrointestinal Tract ...... 34 Urine ...... 35 Blood ...... 36 Cerebrospinal Fluid ...... 36 Genital Tract ...... 37 Wound and Abscesses ...... 37 Specimen Transport and Processing ...... 37 Initial Specimen Plating and Identification Methods ...... 38 Microscopic Examination of Clinical Specimens ...... 38 Selection and Inoculation of Primary Media ...... 39 Preliminary Biochemical Tests ...... 43 Carbohydrate Utilization ...... 43 ...... 44 Oxidase ...... 44 ...... 44 Spot ...... 44 PYR Hydrolysis ...... 44 Quality Control ...... 45 Laboratory Procedures ...... 45 Quality Control ...... 48 Quality Control ...... 48 Review Questions ...... 48 Bibliography ...... 49

Chapter 4 Microscopy, , and Traditional Methods of Examination 51 Microscopy ...... 52 Brightfield Microscopy ...... 52 Direct Examination Methods ...... 53 Staining Methods ...... 53 Methylene Blue ...... 54 ...... 54 Acid-Fast Stains ...... 54 Fluorescent Stains ...... 55 Fungal Stains ...... 56 -Conjugated Stains ...... 56 Laboratory Procedures ...... 56 Quality Control ...... 57 Laboratory Exercises ...... 57 Review Questions ...... 57 Bibliography ...... 58

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Chapter 5 Automation, Immunodiagnostics, and Molecular Methods 59 Multitest Systems ...... 60 Automated Identification Systems ...... 62 Principles ...... 62 Automated Systems for Identification ...... 62 Immunochemical Methods ...... 64 Antigens and ...... 64 Immunochemical Methods to Detect Microorganisms ...... 65 ...... 69 Immunoserological Techniques ...... 70 Acute and Convalescent Phase Specimens ...... 70 Immunoserological Applications ...... 71 Introduction to Molecular Techniques ...... 72 Nucleic Acid Probes ...... 72 Amplification Methods ...... 74 Nucleic Acid Sequencing ...... 76 Review Questions ...... 80 Bibliography ...... 81

Chapter 6 Antimicrobial Susceptibility Testing 83 Overview of Antibiotic Susceptibility Testing ...... 84 Selection of Antibiotics ...... 85 Categories and Types of Antibiotics ...... 86 Antimycobacterial Agents ...... 92 Antifungal Agents ...... 93 Antiviral Agents ...... 93 Resistance to Antimicrobial Agents ...... 95 Intrinsic Resistance ...... 95 Acquired Resistance ...... 95 Laboratory Methods for Susceptibility Testing ...... 97 Disk Diffusion Susceptibility Testing ...... 98 Quantitative Dilution Susceptibility Testing ...... 100 Specific Methods to Determine Bacterial Resistance ...... 115 Laboratory Procedures ...... 119 Laboratory Exercises ...... 124 Review Questions ...... 127 Bibliography ...... 128

Chapter 7 Staphylococci and Other Catalase-Positive Gram-Positive Cocci 131 Gram-Positive Cocci ...... 132 ...... 133 Staphylococcus aureus ...... 135 Specimen Collection ...... 137 Infectious Processes ...... 137 Detection of Antibiotic-Resistant Staphylococcus aureus ...... 139

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Coagulase-Negative Staphylococci ...... 140 Staphylococcus epidermidis ...... 140 Staphylococcus saprophyticus ...... 141 Laboratory Procedures ...... 141 Laboratory Exercises ...... 145 Review Questions ...... 147 Bibliography ...... 148

Chapter 8 , , and Related Organisms 149 Streptococcus ...... 150 Classification ...... 151 β-Hemolytic Streptococcus ...... 152 Streptococcus pyogenes (Group A Streptococcus) ...... 152 (Group B Streptococcus) ...... 155 Miscellaneous β-Hemolytic Streptococcus ...... 156 Viridans Streptococci ...... 157 Streptococcus pneumoniae ...... 158 Streptococcus bovis Group ...... 159 Enterococcus ...... 160 Nutritionally Variant Streptococci (NVS): Abiotrophia and Granulicatella ...... 161 Other Catalase-Negative Streptococcal-Like Organisms ...... 161 Laboratory Procedures ...... 162 Laboratory Exercises ...... 166 Review Questions ...... 167 Bibliography ...... 168

Chapter 9 Neisseria 171 Characteristics of Neisseria ...... 172 Identification of Neisseria Species ...... 172 Infectious Process ...... 174 ...... 174 ...... 178 ...... 180 Miscellaneous Neisseria ...... 180 Laboratory Procedures ...... 180 Laboratory Exercises ...... 183 Review Questions ...... 183 Bibliography ...... 185

Chapter 10 Enterobacteriaceae 187 Characteristics of Enterobacteriaceae ...... 188 Serological Characteristics ...... 189 ...... 189 Identification ...... 190

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Identification and Significance of Selected Enterobacteriaceae ...... 194 ...... 194 Shigella ...... 195 Klebsiella-Enterobacter-Serratia-Hafnia Group (Tribe Klebsielleae) . . . . 198 Proteeae ...... 205 Antibiotic Susceptibility and Treatment ...... 209 Laboratory Procedures ...... 210 Laboratory Exercises ...... 218 Review Questions ...... 221 Bibliography ...... 223

Chapter 11 Nonfermentative Gram-Negative Bacilli 227 Characteristics of Nonfermenters ...... 228 Identification of Nonfermenters ...... 229 Family Pseudomonadaceae ...... 231 ...... 231 Pseudomonas fluorescens and P. putida ...... 233 P. stutzeri and P. mendocina ...... 234 Burkholderia ...... 234 Ralstonia ...... 235 Acinetobacter ...... 236 Stenotrophomonas ...... 236 Alcaligenes ...... 237 Achromobacter ...... 237 Moraxella ...... 238 Oligella ...... 238 Chryseobacterium ...... 238 Kingella ...... 239 Laboratory Procedures ...... 239 Laboratory Exercises ...... 241 Review Questions ...... 242 Bibliography ...... 242

Chapter 12 Miscellaneous Gram-Negative Bacilli: Part 1 245 Vibrio ...... 246 Vibrio cholerae ...... 246 Other Vibrio ...... 247 Campylobacter ...... 248 Helicobacter ...... 250 Aeromonas ...... 250 Plesiomonas ...... 251 Laboratory Procedures ...... 251 Review Questions ...... 252 Bibliography ...... 252

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Chapter 13 Miscellaneous Gram-Negative Bacilli: Part 2 255 Haemophilus ...... 256 Isolation ...... 256 Identification ...... 257 Haemophilus influenzae ...... 258 Miscellaneous Haemophilus Species ...... 260 Legionella ...... 260 Bordetella ...... 262 Brucella ...... 264 Pasteurella ...... 265 Francisella ...... 266 Streptobacillus ...... 267 HACEK Group ...... 267 Chromobacterium ...... 268 Laboratory Procedures ...... 268 Laboratory Exercises ...... 270 Review Questions ...... 271 Bibliography ...... 272

Chapter 14 Gram-Positive Bacilli 275 Spore Formers ...... 276 Bacillus ...... 276 Nonspore Formers ...... 278 Catalase Positive and Nonbranching ...... 278 Catalase Negative and Simple Branching ...... 281 Branching or Partially Acid Fast Gram-Positive Bacilli ...... 282 Miscellaneous Gram-Positive Bacilli ...... 283 Review Questions ...... 284 Bibliography ...... 285

Chapter 15 Spirochetes 287 Borrelia ...... 288 Relapsing Fever ...... 288 Borrelia burgdorferi ...... 289 Treponema ...... 291 Treponema pallidum ...... 292 Other Treponemes ...... 293 Miscellaneous Spirochetes ...... 293 Leptospira ...... 294 Review Questions ...... 295 Bibliography ...... 296

Chapter 16 Anaerobes 299 Overview of Anaerobes ...... 300 Oxygen Tolerance ...... 301

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Specimen Collection and Transport ...... 301 Identification ...... 302 Anaerobic Culture Media and Incubation ...... 303 Culture Media ...... 303 Incubation ...... 304 Biochemical and Other Identification Methods ...... 305 Clinically Relevant Anaerobes ...... 307 Anaerobic Gram-Negative Bacilli ...... 307 Anaerobic Gram-Positive Spore-Forming Bacilli: Clostridium ...... 310 Clostridium tetani ...... 310 Clostridium botulinum ...... 310 ...... 311 Clostridium difficile ...... 312 Miscellaneous Clostridia ...... 313 Anaerobic Gram-Positive Non–Spore-Forming Bacilli ...... 313 Anaerobic Gram-Positive Cocci ...... 314 Anaerobic Gram-Negative Cocci ...... 315 Antimicrobial Susceptibility Testing for Anaerobes ...... 316 Laboratory Procedures ...... 317 Laboratory Exercises ...... 319 Review Questions ...... 320 Bibliography ...... 322

Chapter 17 325 Classification ...... 326 Specimen Collection ...... 327 Specimen Processing ...... 327 Staining ...... 328 Culture Media ...... 329 Identification ...... 329 Mycobacterium Complex ...... 332 Mycobacterium tuberculosis and Tuberculosis ...... 332 Photochromogens ...... 337 Scotochromogens ...... 338 Nonphotochromogens ...... 339 Rapid Growers: Mycobacterium Fortuitum Chelonei Complex . . . . . 340 Laboratory Procedures ...... 340 Laboratory Exercises ...... 345 Review Questions ...... 346 Bibliography ...... 348

Chapter 18 Chlamydia, Mycoplasma, and Rickettsia 351 Chlamydiaceae ...... 352 Chlamydia trachomatis ...... 352 Chlamydophila psittaci ...... 354 Chlamydophila pneumoniae ...... 354

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Mycoplasma ...... 354 Rickettsiaceae ...... 356 Rickettsia rickettsii ...... 357 Rickettsia akari ...... 357 Rickettsia prowazekii ...... 357 Rickettsia typhi ...... 357 Orientia tsutsugamushi ...... 358 Anaplasmataceae ...... 358 Ehrlichia ...... 358 Coxiella ...... 358 Review Questions ...... 359 Bibliography ...... 360 Chapter 19 Introduction to Virology 363 Viral Structure and Characteristics ...... 364 Viral Replication ...... 365 Specimen Selection, Collection, and Processing ...... 367 Laboratory Methods in Virology ...... 369 Serological Detection of Viral Antibodies ...... 371 Selected Medically Important Viruses ...... 372 Adenovirus ...... 372 Hepatitis Viruses ...... 372 Herpes Viruses ...... 375 Papillomaviridae ...... 378 Papovaviruses ...... 379 Poxviruses ...... 380 Arboviruses ...... 380 Filoviridae ...... 383 Picornaviridae ...... 383 Orthomyxoviridae ...... 384 Paramyxoviridae ...... 385 Rhabdoviridae ...... 387 Reoviridae ...... 387 Caliciviruses ...... 387 Retroviridae ...... 388 Review Questions ...... 389 Bibliography ...... 391 Chapter 20 Introduction to Medical Mycology 395 Introduction to Mycology ...... 396 Specimen Collection ...... 398 Identification Methods ...... 398 Culture Media ...... 402 Microscopic Examination of Growth ...... 403 Incubation and Macroscopic Morphology ...... 403 Fungal Infections ...... 405 Superficial Mycoses ...... 405 Subcutaneous Mycoses ...... 412

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Systemic Mycoses: Dimorphic Fungi ...... 414 Yeast and Yeast-Like Fungi ...... 418 Candida ...... 420 Opportunistic Saprobic Fungi ...... 423 Serological Testing ...... 425 Laboratory Procedures ...... 426 Laboratory Exercises ...... 429 Review Questions ...... 431 Bibliography ...... 432

Chapter 21 Introduction to Medical Parasitology 435 Introduction and Definitions ...... 437 Specimen Collecting, Processing, and Examining of Stool Specimens . . . . 438 Collection and Processing of Stool Specimens ...... 438 Microscopic Examination ...... 439 Direct Smears ...... 439 Concentration Methods for Stool Specimens ...... 439 Permanently Stained Mounts ...... 440 Blood Specimens ...... 440 Protozoa ...... 440 Intestinal Amoebas ...... 441 Free-Living Amoebas ...... 441 Intestinal Flagellates ...... 445 Intestinal Ciliate ...... 446 Intestinal Coccidia ...... 446 Miscellaneous Protozoa ...... 449 Sporozoa from Blood and Tissue ...... 450 Hemoflagellates ...... 456 Trypanosomes ...... 456 Nematodes ...... 458 Strongyloides stercoralis ...... 459 Hookworms: Necator americanus and Ancylostoma duodenale . . . . 459 Enterobius vermicularis ...... 462 Ascaris lumbricoides ...... 463 Trichuris trichiura ...... 465 Trichinella spiralis ...... 465 Blood and Tissue Nematodes: Filarial Worms ...... 468 Cestodes ...... 470 Diphyllobothrium latum ...... 471 Hymenolepsis nana ...... 473 Hymenolepsis diminuta ...... 473 Dipylidium canium ...... 474 Taenia saginata, T. solium, and T. asiatica ...... 476 Echinococcus granulosus ...... 476 Trematodes ...... 478 Intestinal Flukes ...... 479 Schisotosomes: Blood Flukes ...... 483

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Laboratory Procedures ...... 485 Laboratory Exercises ...... 489 Review Questions ...... 490 Bibliography ...... 493

Chapter 22 Clinical Specimens 495 Introduction ...... 496 Primary Plating of Specimens ...... 496 Blood Cultures and Bacteremia ...... 496 Types and Causes of Bacteremia ...... 497 Specimen Collection ...... 497 Manual Blood Cultures ...... 501 Automated Blood Culture Systems ...... 503 Microorganisms Associated with Blood Infections ...... 503 Cerebrospinal Fluid—Meningitis and Central Nervous System Infections . . . 504 Collection and Analysis of CSF ...... 507 Respiratory Tract Specimens and Infections ...... 509 Upper Respiratory Tract ...... 509 Throat Specimens ...... 509 Lower Respiratory Tract ...... 510 Diagnosis of Lower Respiratory Tract Infections—Sputum Specimens . . . 512 Eye and Ear Specimens and Infections ...... 514 Urinary Tract Specimens and Infections ...... 514 Urine Collection and Processing ...... 516 Colony Count ...... 517 Automated Urine Screening Methods ...... 518 Gastrointestinal Tract Specimens and Infections ...... 518 Specimen Collection and Processing ...... 520 Genital Tract Specimens and Infections ...... 522 Specimen Collection for Urogenital Infections ...... 523 Direct Examination ...... 523 Skin and Wound Specimens and Infections ...... 525 Specimen Collection for Wound and Skin Infections ...... 526 Pleural, Peritoneal, Pericardial, and Synovial Fluids ...... 526 Pleural Fluid ...... 528 Peritoneal Fluid ...... 528 Pericardial Fluid ...... 528 Synovial Fluid ...... 528 Laboratory Procedures ...... 529 Case Studies and Review Questions ...... 538 Bibliography ...... 542

Glossary ...... 545 Index ...... 559

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Introduction to Diagnostic Microbiology for the Labora- which introduce the student to the increased attention tory Sciences provides a concise study of clinically signif- required in antibiotic testing, as well as the identifica- icant microorganisms for the medical laboratory science tion of resistance patterns. The expanded information student and the laboratory professional. This text is on on molecular diagnostics provides the student with the recommended reading list to prepare for the ASCP the essential framework and examples of the expand- MLT (American Society for Clinical Pathology, Medical ing use of molecular technologies in the microbiol- Laboratory Technician) exam. Although comprehensive ogy laboratory. The text also introduces the student textbooks for diagnostic microbiology abound, this text to current automation in the microbiology laboratory, is unique in its focus on what is most essential for the be- including contemporary instrumentation used in mi- ginning student. The concept of this text was originally crobial identification, antibiotic susceptibility testing, suggested by my medical laboratory technology students and blood culture technologies. who were frustrated by the length and depth of other Chapters 7 through 18 address medically impor- microbiology textbooks. Students became discouraged tant bacteria, including their isolation, identifica- with the vast amount of information included in these tion, and treatment. Each chapter focuses on major texts, which serve as excellent learning resources but divisions of bacteria, including gram-positive cocci, were inappropriate for the beginning student. gram-negative cocci, gram-negative bacilli, gram- This text provides an overview of diagnostic mi- positive bacilli, mycobacterium, anaerobes, spiro- crobiology that is relevant and essential to medical chetes, chlamydia, and rickettsia. Each chapter includes laboratory students and entry level medical laboratory concise information on the isolation, identification, technicians. Chapters 1 through 6 begin by providing and clinical relevance of those microorganisms that a an overview of the infectious process, including dis- microbiologist may encounter in the clinical setting. ease transmission and host immunity. The importance These chapters also include news pieces that describe of specimen collection is emphasized with both gen- a timely concern related to a specific microorganism eral and specific requirements, instilling in the student and its associated public health concern. Examples the importance of pre-analytical factors in specimen include antibiotic resistance in Staphylococcus aureus, management and quality laboratory testing. The goal meningococcoal disease, listeriosis, Lyme Disease, and is to provide a thorough yet succinct discussion of iso- legionellosis. These items attempt to instill in the stu- lation media, as well as the basics of preliminary test- dent the relevance of clinical microbiology in their ing in the microbiology laboratory. everyday life by relating contemporary events to the Essential manual methods are addressed both in lessons presented in the chapter. theory and method so the student can understand, Chapters 19 through 21 provide an orderly presen- practice, and apply each laboratory procedure. The tation of clinical virology, mycology, and parasitology chapters mesh didactic theory with laboratory test- that can be realistically covered in an introductory ing and interpretation, creating an orderly and com- course. These topics are often overwhelming in both plete presentation. Additional testing methods, such quantity and depth of information in most micro- as serology, immunoassay, antibiotic susceptibility biology texts, leading to frustration in many stu- testing, and molecular diagnostics are also presented dents. These important topics are summarized in with pertinent applications. Current modes of antibi- a format that encourages the student to review and otic resistance and the required testing are included apply central concepts in each discipline. Chapter 19,

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Introduction to Virology summarizes viral replica- charts, figures, and laboratory exercises. This format tion, classification of DNA and RNA viruses, and the also provides a quick reference to the most frequently isolation and identification of medically important utilized manual procedures and most commonly viruses. This chapter also summarizes and describes referred topics in clinical microbiology. significant viral infections and the role of the labora- tory in the diagnosis of viral infections. Chapter 20, Key Features Introduction to Medical Mycology discusses the clas- Introduction to Diagnostic Microbiology for the Labora- sification of mycoses, specimen collection, and fungal tory Sciences includes learning objectives, laboratory culture media. Clear identification schemes utilizing exercises, news features, and review questions. Both both macroscopic colonial appearance and micro- didactic and psychomotor skills are presented and re- scopic characteristics as well as biochemical methods inforced in each chapter. for medically important fungi are included. Super- 77 Learning Objectives–Clearly outlines for the reader ficial, subcutaneous, systemic, and opportunistic the desired outcomes of the chapter, focuses read- mycoses are addressed. This chapter includes im- ing, and provides a basis to gauge learning. ages that are vital in the correct identification of the 77 Laboratory Exercises–Engages the reader by hav- fungi. Chapter 21, Introduction to Medical Parasi- ing them apply what they learned in a lab activity, tology provides an organized classification outline record their results, and push their analysis fur- of medically relevant parasites and infections. Speci- ther with critical thinking questions. men collection requirements unique to parasitology 77 News Feature–Highlights current issues that face are described as well as concentration methods and the contemporary medical laboratory technician, stains. The chapter is divided into units which discuss grounding the information in a real-word context. protozoans such as the amebae, sporozoans and he- 77 Review Questions–Provides a way to apply what moflagellates, nematodes, cestodes, and trematodes. has been learned in the chapter and also provides Extensive, clearly drawn life cycles with images of the practice for preparation for the Medical Lab Tech- infectious stage and diagnostic stage are included for nician (MLT) certification examination. clinically relevant parasites. The final chapter, Chapter 22, Clinical Speci- Many reference texts in clinical microbiology are mens, ties the components of the text together by available with complex descriptions and highly de- summarizing the medically important pathogens typi- tailed methods which can intimidate the beginning cally found in clinical specimens with identification student. The purpose of Introduction to Diagnostic schemes. Complete work-ups of microorganisms from Microbiology for the Laboratory Sciences is to provide major clinical sites are included with flowcharts and a condensed and practical approach for students and suggested laboratory protocols. Students are able to novice microbiologists. A mastery of the material and apply the didactic and laboratory concepts presented procedures in this text will provide students with a throughout the text to evaluate clinical specimens and strong background for pursuing higher levels in clini- develop appropriate testing schemes to correctly iden- cal microbiology. Additionally, the text is an excel- tify pathogens and differentiate these from normal lent resource to prepare for the ASCP certification flora. examination. It further serves as a valuable review for The goal of the text is to provide the medical labo- laboratory professionals who are returning to the mi- ratory student with the information and skills neces- crobiology field after an absence. The concise format sary for entry into the medical laboratory profession. provides a quick and thorough review mechanism for The information is organized into a format that fa- students and laboratory professionals who may need a cilitates learning through the use of integrated text, refresher course in diagnostic microbiology.

9781284032314_FMxx_00i_0xx.indd 16 14/02/14 12:42 PM Acknowledgments

Special thanks to my husband, Raymond, and my sons, Gregory and Michael, and my entire family for their encouragement and support during this project. Also, thank you to all of my medical laboratory students at Youngstown State University from whom I have learned so much during my thirty years of teaching.

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Angela R. Bell, MS, MLS(ASCP)SM, DLM Michelle M. Hill, MS, MT(ASCP) Tidewater Community College Instructor, MLT Program Virginia Beach, VA Southwest Tennessee Community College Memphis, TN Janet E. Cooper, MSNS, BSMT(ASCP)H Instructor in Medical Laboratory Technology Benjamin F. Newsome Jr., MA/MS, MT(AMT), CM Mississippi Delta Community College Director Moorhead, MS San Jacinto College Pasadena, TX Katrina P. Ghazanfar, PhD, MT(ASCP) University of Hawaii-Kapiolani Dale Telgenhoff, PhD, HTL(ASCP) Community College Associate Professor Honolulu, HI Tarleton State University Fort Worth, TX

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