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Textbook of

Diagnostic Microbiology

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Textbook of

Diagnostic Microbiology

F I F T H E D I T I O N

Connie R. Mahon, MSDirector, Staff and Organization DevelopmentHealth Resources and Services AdministrationHIV/AIDS BureauRockville, MarylandAdjunct FacultyDepartment of Clinical Research and LeadershipSchool of Medicine and Health SciencesGeorge Washington UniversityWashington, DC

Donald C. Lehman, EdD, MT(ASCP), SM(NRM)

Associate ProfessorDepartment of Medical Laboratory SciencesUniversity of DelawareNewark, Delaware

George Manuselis, MA, MT(ASCP)EmeritusMedical Technology DivisionOhio State UniversityColumbus, OhioAdjunct FacultyDepartment of Natural Sciences and Forensic ScienceCentral Ohio Technical CollegeNewark, Ohio

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3251 Riverport LaneMaryland Heights, Missouri 63043

TEXTBOOK OF DIAGNOSTIC MICROBIOLOGY, ISBN: 978-0-323-08989-0FIFTH EDITION

Copyright © 2015 Saunders, an imprint of Elsevier, Inc.

All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without written permission of the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions.

This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein).

Notices

Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary.

Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility.

With respect to any drug or pharmaceutical products identified, readers are advised to check the most current information provided (i) on procedures featured or (ii) by the manufacturer of each product to be administered, to verify the recommended dose or formula, the method and duration of administration, and contraindications. It is the responsibility of practitioners, relying on their own experience and knowledge of their patients, to make diagnoses, to determine dosages and the best treatment for each individual patient, and to take all appropriate safety precautions.

To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein.

The views and opinions of contributors to the Work who are employees of the National Institutes of Health, Department of Defense, or other Departments of the U.S. Government do not necessarily state or reflect those of the U.S. Government, nor does the NIH, Department of Defense, or the U.S. Government endorse, warrant, or guarantee the information contained therein.

Previous editions copyrighted 2011, 2007, 2000, 1995Library of Congress Cataloging-in-Publication Data

Textbook of diagnostic microbiology / [edited by] Connie R. Mahon, Donald C. Lehman, George Manuselis.—Fifth edition. p. ; cm. Includes bibliographical references and index. ISBN 978-0-323-08989-0 (hardcover) I. Mahon, Connie R., editor of compilation. II. Lehman, Donald C., editor of compilation. III. Manuselis, George, editor of compilation. [DNLM: 1. Microbiological Techniques. 2. Bacterial Infections--diagnosis. 3. Communicable Diseases—diagnosis. 4. Mycoses—diagnosis. 5. Virus Diseases—diagnosis. QW 25] QR67 616.9′041—dc23

2013045846

Vice President and Publisher: Andrew AllenManaging Editor: Ellen Wurm-CutterContent Development Specialist: Amy WhittierPublishing Services Manager: Julie EddyProject Managers: Celeste Clingan/Nisha Selvaraj/Devendran KannanDesign Direction: Karen Pauls

Printed in China

Last digit is the print number: 9 8 7 6 5 4 3 2 1

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To my husband, Dan, for his love and continued support

and understanding, my son, Sean, who inspires me, my daughter, Kathleen, for showing me courage, and my granddaughters, Kelly Amelia and Natalie Page,

who have given us so much pleasure.CRM

To my wife, Terri, who has given me constant support and encouragement, and whose love makes anything I do possible,

and my parents, Gerald and Sherrie, who have always been proud of me—even though they have passed away, I know they still look over me.

DCL

To my daughters, Kristina and Shellie, my sisters, Libby and Helen, and my brother, Demetrious and, in memory of my parents, Katherine and George, for their love and encouragement.

GM

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viivii

Reviewers

Daniel deRegnier, MS, MT(ASCP)Associate ProfessorProgram Director of Clinical Laboratory ScienceFerris State UniversityBig Rapids, Michigan

Delfina Dominguez, MT(ASCP), MS, PhDProfessorUniversity of Texas at El PasoEl Paso, Texas

Frances Pouch Downes, HCLD(ABB), PhDProfessorBiomedical Laboratory Diagnostics ProgramMichigan State UniversityEast Lansing, Michigan

Shawn Froelich, MLS(ASCP)Adjunct Instructor of Medical Laboratory SciencesAllen CollegeWaterloo, Iowa

Amy Kapanka, MS, MT(ASCP)SCDirector, Medical Laboratory Technology ProgramHawkeye Community CollegeWaterloo, Iowa

Michael Majors, BS, MLS(ASCP)Microbiology Technical SpecialistProvidence Sacred Heart Medical Center and Children’s HospitalSpokane, Washington

Nicholas Moore, MS, MLS(ASCP)Laboratory DirectorKindred Healthcare, Inc.Kindred Hospital ChicagoNorth Chicago, Illinois

Dawn Nelson, MA, MT(ASCP)Director of Medical Laboratory Technology ProgramFlorence Darlington Technical CollegeFlorence, South Carolina

Jennifer Sanderson, MS, MLS(ASCP)Curriculum ConsultantSiemans Healthcare DiagnosticsWilmington, Delaware

Lynne Steele, MS, MLS(ASCP)Chair and ProfessorMedical Laboratory Technology and PhlebotomyOakton Community CollegeDes Plaines, Illinois

Ron Walker, MBA, CNMT, PETProfessorThe University of FindlayFindlay, Ohio

Karen Golemboski, Ph.D., MLS(ASCP)Associate ProfessorMedical Laboratory ScienceBellarmine UniversityLouisville, Kentucky

Mildred K. Fuller, PhD, MT(ASCP)Former Department Chair, Allied HealthMedical Technology ProgramNorfolk State UniversityNorfolk, Virginia

Lori A. Woeste, EdDAssistant Dean and Associate ProfessorCollege of Applied Science and TechnologyIllinois State UniversityNormal, Illinois

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ixix

Contributors

Wade K. Aldous, PhD(ABMM)Chief, MicrobiologyDepartment of Clinical Support ServicesU.S. Army Medical Department Center and SchoolFort Sam Houston, Texas

Carl Brinkley, PhDDepartment of Chemistry and Life ScienceColonel United States Military AcademyWest Point, New York

Maximo O. Brito, MD, FACPAssistant Professor of MedicineVice Chair for Urban Global Health, Department of MedicineDirector, Infectious Diseases Fellowship Training ProgramChief of Infectious Diseases Fellowship, Jesse Brown VA

Medical CenterDivision of Infectious DiseasesUniversity of Illinois at ChicagoChicago, Illinois

Nina M. Clark, MDAssociate Professor of Infections DiseaseDepartment of MedicineDivision of Infectious DiseasesMedical Director, Transplant Infectious DiseasesLoyola University Medical CenterMaywood, Illinois

James L. Cook, MDProfessor of Infectious DiseaseCo-Director, Infectious Disease and Immunology InstituteLoyola UniversityMaywood, IllinoisDirector, Division of Infectious DiseasesDepartment of MedicineLoyola University Medical CenterMaywood, IllinoisChief, Infectious DiseasesEdward Hines Jr. VA HospitalChicago, Illinois

Robert C. Fader, PhD, D(ABMM)Section Chief, Microbiology/Virology LaboratoryScott and White Memorial HospitalBaylor Scott & White HealthAssistant ProfessorDepartment of PathologyTexas A&M University College of MedicineTemple, Texas

Annette W. Fothergill, MA, MBA, MT(ASCP), CLS(NCA)Assistant ProfessorDepartment of PathologyTechnical Director, Fungus Testing LabUniversity of Texas Health Science Center at San AntonioSan Antonio, Texas

Gerri S. Hall, PhD, D(ABMM), F(AAM)Retired as Medical Director in Clinical MicrobiologyForestville, New York

Amanda T. Harrington, PhD, D(ABMM)Director, Microbiology ServiceAssistant Professor, PathologyUniversity of Illinois at ChicagoChicago, Illinois

Christopher Hatcher, MS, M(ASCP)Major, United States ArmyArmy Medical Department Student DetachmentFort Sam Houston, Texas

Michelle M. Jackson, PhDSenior MicrobiologistU.S. Food and Drug AdministrationCenter for Drug Evaluation and ResearchSilver Spring, Maryland

Deborah Ann Josko, PhDAssociate ProfessorDirector, Medical Laboratory Science Program Rutgers, The State

University of New JerseySchool of Health Related ProfessionsNewark, New Jersey

Edward F. Keen III, PhD, SM(ASCP)Major, Medical Service Corps, United States ArmyChief, MicrobiologyDepartment of Pathology and Area Laboratory ServicesWilliam Beaumont Army Medical CenterEl Paso, Texas

Arun Kumar, PhDAssistant Professor of Medical Laboratory SciencesUniversity of DelawareNewark, Delaware

Donald C. Lehman, EdD, MT(ASCP), SM(NRM)Associate ProfessorDepartment of Medical Laboratory SciencesUniversity of DelawareNewark, Delaware

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x CONTRIBUTORS

Steven D. Mahlen, PhD, D(ABMM)Director, Clinical and Molecular MicrobiologyAffiliated Laboratory, Inc.Eastern Maine Medical CenterBangor, Maine

Connie R. Mahon, MS, MT(ASCP), CLSMicrobiologist and Senior Education Program SpecialistStaff College, Center for Veterinary MedicineU.S. Food and Drug AdministrationRockville, MarylandAdjunct FacultyDepartment of Clinical Laboratory SciencesSchool of Medicine and Health SciencesGeorge Washington UniversityWashington, DC

George Manuselis, MA, MT(ASCP)EmeritusMedical Technology DivisionOhio State UniversityColumbus, OhioAdjunct FacultyDepartment of Natural Sciences and Forensic ScienceCentral Ohio Technical CollegeNewark, Ohio

Kevin McNabb, PhD, MT(ASCP)Director, Microbiology and ImmunologyNew Hanover Regional Medical CenterWilmington, North Carolina

Frederic J. Marsik, PhD, ABMMMicrobiology ConsultantNew Freedom, Pennsylvania

Sarojini R. Misra, MS, SM(NRM), SM(ASCP)Manager, Microbiology, Immunology, & VirologyUniversity of DelawareChristiana Care Health ServicesNewark, Delaware

Paula C. Mister, MS, MT(ASCP)SMEducational Coordinator, Medical MicrobiologyJohns Hopkins HospitalBaltimore, Maryland

Linda S. Monson, MS, MT(ASCP)Microbiologist–Biosafety OfficerDPALS Department of Pathology and Area Lab ServicesBrooke Army Medical CenterFort Sam Houston, Texas

Sumathi Nambiar, MD, MPHDivision of Anti-infective ProductsCenter for Drug Evaluation and ResearchU.S. Food and Drug AdministrationSilver Spring, Maryland

Susan M. Pacheco, MDStaff PhysicianEdward Hines, Jr. VA HospitalAssistant Professor of Infectious DiseaseDepartment of MedicineLoyola UniversityChicago, Illinois

Lester Pretlow, PhD, C(ASCP), NRCC(CC)Associate Professor and ChairDepartment of Medical Laboratory, Imaging, and Radiologic SciencesGeorgia Regents UniversityAugusta, Georgia

Gail E. Reid, MDAssistant Professor, MedicineDivision of Infectious DiseasesDepartment of MedicineLoyola University Medical CenterMaywood, Illinois

Lauren Roberts, MS, MT(ASCP)Microbiology SupervisorSt. Joseph’s Hospital & Medical CenterPhoenix, Arizona

Prerana Roth, MD, FACPAssistant Professor of MedicineDivision of Infectious DiseasesUniversity of Illinois at ChicagoChicago, Illinois

Barbara L. Russell, EdD, MLS(ASCP)SHAssociate Professor and Program DirectorProgram of Clinical Laboratory ScienceDepartment of Biomedical and Radiological TechnologiesMedical College of GeorgiaAugusta, Georgia

Linda A. Smith, PhD, MLS(ASCP)Professor and ChairDepartment of Clinical Laboratory SciencesThe University of Texas Health Science CenterSan Antonio, Texas

Kalavati Suvarna, PhDMicrobiologistBiotech Manufacturing Assessment BranchOffice of Manufacturing and Product QualityOffice of ComplianceCenter for Drug Evaluation and ResearchU.S. Food and Drug AdministrationRockville, Maryland

Daniel A. Tadesse, DVM, PhDResearch MicrobiologistDivision of Animal and Food MicrobiologyFDA-CVMLaurel, Maryland

Kimberly E. Walker, PhD, MT(ASCP)Manager, Public AffairsAmerican Society for MicrobiologyWashington, DC

A. Christian Whelen, PhD, (D)ABMMState Laboratories DirectorHawaii Department of HealthPearl City, Hawaii

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CONTRIBUTORS xi

Shaohua Zhao, DVM, MPVM, PhDSenior Research MicrobiologistDivision of Animal and Food MicrobiologyFDA-CVMLaurel, Maryland

PowerPoint WriterPerry Scanlan, PhD, MT(ASCP)Associate Professor and Program Director Medical Laboratory

Science ProgramDepartment of Allied Health SciencesAustin Peay State UniversityClarksville, Tennessee

Test Bank WriterJanice M. Conway-Klaassen, PhD, MT(ASCP)SMDirector, Clinical Laboratory Science ProgramUniversity of MinnesotaMinneapolis, Minnesota

Laboratory Manual WriterStephen D. Dallas, PhD, D(ABMM), MT(ASCP)SMAssistant Director and Assistant Professor of MicrobiologyDepartment of Clinical Laboratory SciencesSan Antonio, Texas

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xiiixiii

Preface

We welcome you to the fifth edition of the Textbook of Diagnostic Microbiology.

This edition embodies our commitment to convey information on the ever-evolving, complex, and challenging field of diagnostic microbiology. Similar to previous editions, we remain committed to preserving the tradition of providing a well-designed and organized textbook. This edition maintains the building block approach to learning, critical thinking, and problem solving, features that clinical laboratory science and clinical laboratory technician students, entry-level clinical labo-ratory practitioners, and others have found valuable and effec-tive. In response to our readers’ needs, we continue to enhance these features that have made this textbook user-friendly.

Because the goal of the Textbook of Diagnostic Microbiology is to provide a strong foundation for clinical laboratory science students, entry-level practitioners, and other health care profes-sionals, discussions of organisms are limited to those that are medically important and commonly encountered, as well as new and re-emerging pathogens. Students and other readers are pro-vided with valuable learning tools to help them sort through the vast amount of information—background theoretic concepts, disease mechanisms, identification schemas, diagnostic charac-teristics, biochemical reactions, and isolation techniques—to produce clinically relevant results.

In this edition, considerable changes have been made to show the vital nature of the field of diagnostic microbiology. A discus-sion on forensic microbiology has been included in Chapter 30, Agents of Bioterror. The text has been updated to reflect patho-gens newly recognized in the past decade, present new applica-tions of immunologic and/or molecular approaches to diagnose infections and identify infectious agents, and determine antimi-crobial resistance in microorganisms. Despite the progress made and significant advances that have occurred in their control, pre-vention, and treatment, infectious diseases remain a major threat to human health. The combined affects of rapid demographic, environmental, societal, technologic, and climatic changes, as well as changes in the way we live our lives, have affected the occurrence of infectious disease. This fifth edition discusses the continuing spread of infectious diseases and the emerging public health issues associated with them.

Whereas the recovery of etiologic agents in cultures has remained the gold standard in microbiology in determining the probable cause of an infectious disease, the increase in our capa-bilities for microbial detection and identification can be attributed to the advances in molecular diagnostic techniques and how they are applied in clinical laboratories. Extensive biomedical research has focused on the potential applications of nanotechnology to medicine—nanomedicine. Chapter 12 has been updated by

incorporating discussions on the use of nanotechnology in drug delivery systems, and Chapter 39 includes a discussion of bio-markers in the diagnosis of septicemia. The application of matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry in microbial identification has been added to Chapter 11.

OrganizationPart I has remained the backbone of the textbook, providing important background information, Part II emphasizes the labo-ratory identification of etiologic agents, and Part III focuses on the clinical and laboratory diagnoses of infectious diseases at various body sites—the organ system approach.

Part I presents basic principles and concepts of diagnostic microbiology, including quality assurance, which provide stu-dents with a firm theoretic foundation. Chapters 7 (Microscopic Examination of Infected Materials) and 8 (Use of Colony Mor-phology for the Presumptive Identification of Microorganisms) still play vital roles in this text. These two chapters help students and practitioners who may have difficulty recognizing bacterial morphology on direct smear preparations, as well as colony mor-phology on primary culture plates, develop these skills through the use of color photomicrographs of stained direct smears and cultures from clinical samples. These two chapters also illustrate how microscopic and colony morphology of organisms can aid in the initial identification of the bacterial isolate. A summary of the principles of the various biochemical identification methods for gram-negative bacteria is described in Chapter 9. This chapter contains several color photographs to help students understand the principles and interpretations of these important tests.

Part II highlights methods for the identification of clinically significant isolates. Bacterial isolates are presented based on a taxonomic approach. Although diseases caused by the organisms are discussed, the emphasis is on the characteristics and methods used to recover and identify each group of organisms. Numerous tables summarize the major features of organisms, and schematic networks are used to show the relationships and differences among similar or closely related species. Chapters devoted to anaerobic bacterial species, medically important fungi, parasites, and viruses affirm the significance of these agents. Chapter 29 describes viral pathogens, including severe acute respiratory syn-drome and the highly pathogenic avian influenza virus. Chapter 31 describes an increasingly complex entity—biofilms. Recently, it has become evident that microbial biofilms are involved in the pathogenesis of several human diseases.

The organ system approach in Part III has been the foundation of the Textbook of Diagnostic Microbiology and provides an

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xiv PREFACE

opportunity for students and other readers to “pull things together.” Chapters begin with the anatomic considerations of the organ system to be discussed and the role of the usual microbiota found at the particular site in the pathogenesis of a disease. Before students can recognize the significance of the opportunis-tic infectious agents they are most likely to encounter, it is impor-tant for them to know the usual inhabitants at a body site. The case studies included in the chapters in Part III enhance problem solving and critical-thinking skills, and help students apply knowledge acquired in Parts I and II. The case studies describe the clinical and laboratory findings associated with the patients, allowing students opportunities to correlate these observations with possible etiologic agents. In most cases, the cause of the illness is not disclosed in the case study; rather, it is presented elsewhere in the chapter to give students the opportunity to think the case through.

Pedagogic FeaturesAs with the previous editions, each chapter is introduced by a Case in Point. These introductory case studies represent an important pathogen, infectious disease, concept, or principle that is discussed in the chapter text and is used to introduce the learner to the main context discussed in the chapter. The Case in Point is followed by “Issues to Consider.” These are points in a bulleted format that the learners are asked to think about as they read the chapter.

New to this edition are the Case Checks, a feature that aims to reinforce understanding of the content or concept within the context of the Case in Point at the beginning of the chapter or case study at the beginning of a section within the chapter. The Case Check highlights a particular point in the text that intends to help the learner connect the dots between the content under discussion, as illustrated by the case study.

To further reinforce learning, identification tables, flow charts, and featured illustrations have been updated, and new ones have been added. Learning objectives and a list of key terms are also found at the beginning of each chapter. The key terms include abbreviations used in the text; this places abbreviations where students can easily find them. At the end of each chapter, readers will find Points to Remember and Learning Assessment Ques-tions to reinforce comprehension and understanding of important concepts. Points to Remember includes a bulleted list of impor-tant concepts that the reader should have learned from reading the chapter.

This edition of the Textbook of Diagnostic Microbiology, as in the previous editions, incorporates the expertise of contribu-tors along with elements such as full-color photographs and pho-tomicrographs, an engaging and easy-to-follow design, learning assessment questions and answers, opening case scenarios, hands-on procedures, and lists of key terms to strengthen the learning strategy.

Ancillaries for Instructors and StudentsFor this edition, we continue offering a variety of instructor ancil-laries specifically geared for this book. For instructors, the Evolve website includes a test bank in ExamView containing more than 1200 questions. It also includes an electronic image collection and PowerPoint slides. For students, the Evolve website includes a laboratory manual.

Connie R. MahonDonald C. LehmanGeorge Manuselis

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Acknowledgments

We are grateful to all contributing authors, students, and instructors and many other individuals who have made significant suggestions and invaluable comments on ways to improve this edition.

Connie R. MahonDonald C. LehmanGeorge Manuselis

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Contents

PART I INTRODUCTIONTOCLINICALMICROBIOLOGY

1 BacterialCellStructure,Physiology,Metabolism,andGenetics,2

2 Host-ParasiteInteraction,23 3 TheLaboratoryRoleinInfectionControl,47 4 ControlofMicroorganisms,59 5 PerformanceImprovementintheMicrobiology

Laboratory,93 6 SpecimenCollectionandProcessing,111 7 MicroscopicExaminationofMaterialsfrom

InfectedSites,126 8 UseofColonyMorphologyforthePresumptive

IdentificationofMicroorganisms,169 9 BiochemicalIdentificationofGram-Negative

Bacteria,18110 ImmunodiagnosisofInfectiousDiseases,19811 ApplicationsofMolecularDiagnostics,22612 AntimicrobialAgentMechanismsofActionand

Resistance,25413 AntimicrobialSusceptibilityTesting,274

PART II LABORATORYIDENTIFICATIONOFSIGNIFICANTISOLATES

14 Staphylococci,31415 Streptococcus,Enterococcus,andOther

Catalase-Negative,Gram-PositiveCocci,32816 AerobicGram-PositiveBacilli,34917 NeisseriaSpeciesandMoraxella catarrhalis,37218 HaemophilusandOtherFastidiousGram-Negative

Bacilli,39019 Enterobacteriaceae,42020 Vibrio,Aeromonas,Plesiomonas,andCampylobacter

Species,45521 NonfermentingandMiscellaneousGram-Negative

Bacilli,47422 AnaerobesofClinicalImportance,49523 TheSpirochetes,52924 Chlamydia,Rickettsia,andSimilarOrganisms,537

25 MycoplasmaandUreaplasma,55226 Mycobacterium tuberculosisandNontuberculous

Mycobacteria,56327 MedicallySignificantFungi,58928 DiagnosticParasitology,62529 ClinicalVirology,68830 AgentsofBioterrorandForensicMicrobiology,72731 Biofilms:ArchitectsofDisease,752

PART III LABORATORYDIAGNOSISOFINFECTIOUSDISEASES:ANORGANSYSTEMAPPROACHTODIAGNOSTICMICROBIOLOGY

32 UpperandLowerRespiratoryTractInfections,76533 SkinandSoftTissueInfections,80434 GastrointestinalInfectionsandFoodPoisoning,83535 InfectionsoftheCentralNervousSystem,85436 BacteremiaandSepsis,86837 UrinaryTractInfections,88438 GenitalInfectionsandSexuallyTransmitted

Infections,90139 InfectionsinSpecialPopulations,93340 ZoonoticDiseases,94241 OcularInfections,955

Appendices

A SelectedBacteriologicCultureMedia,977B SelectedMycologyMedia,Fluids,andStains,994C AnswerstoLearningAssessmentQuestions,997D SelectedProcedures,1019

Glossary,1026Index,1048

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