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Kone111an's co o s · _·x oo o Diagnostic M. crob ·o logy i Koneman’s Color Atlas and Textbook of Diagnostic Microbiology ii iii Koneman's Color Atlas and Textbook of Diagnostic Microbiology Gary W. Proeop, MD, MS ,\_k ol_it.t l .b,.r .«..t.~.. .f..,.l. ft~ T03 .u.:.;., ~.r.z.;.m,...,., ".u"w"/"1*\J","tl·.~. .CJ"M 'n'1"1"1t0"1I"M " ~'('a ~ ,...,.,.. "'I'Dlbol.yy Ond.nJOut~e l.n"htr c.Nltrtttrf~'tkJtt:JN.,('~ \\OINII' ~tot'!~£ llllh:tMfy 1M c::JtwVM Qllk Otw¥,.;1. OfiNt Deirdre L Church. MD. PhD. FRCPC, D(ABMMI Pwt{m41f of Anllology Cl-U.botwory Mb/;tjtWt~•td Mffllwtt l'nMf)IIJ o{CiA~ry CJilliaJJS<rtiQrl Clritf, Mio~ OtlJ.""'1' LaiHtwtor}' Srn·iuJ!Ali•l'rlo.~ Ht>all1• ,'i«Vitn l'Algtlry. AfL~t:rtD, C'.anllt'l.a Geraldine S. Hall, PhD, D(ABMMI Rnira! Clinir.rJ Mi170b•M:1gi$r 'lht Clm-lnlfd Cl111k Cill'l'tl.llltd, ()hil) William M. Janda, PhD. D(ABMMI Prrl/mN &t•mrus. P.rliloll>,t)'"''d Mkrobwt<Jgy Umm.. · inS~-tJf,/,'i1l Cy lrlu(r lrll. i.nu fl:ir$roDb1I 1C1lll•tigcy: a4t~ ~Cd A\ ''ikmg<lo (gify M r.liritlt' Dtp4tr.ltl<flll tJfP~thology }.lim H .Srt(}J.'tr. Jr. Ho.spii.J/c.oo! Cmnll')' Htuhh mtfl llaspilotf) $ys(l'ltl Chkflge\1/JI'IOis ElmerW. Koneman. MD l'nJfd.UN EmmluJ L'mwrsiry fi/C~J" School of o\WJtlnrt "'"""~~· r oioow.~ct Paul C. Schreckenberger. PhD, D(ABMM) ,of,;., of~ D'IM."'tM. ('hiUI'IIIo\~ A,s.M.w,t_( Ou,tc_tar. M~f4, Pr.t~· IAy(JU t •~mitT \kt:&Ml Cnw Gail L Woods. MD ""''t--'Oo<f<f-""""""' l~. ...·...., .<,Adf. ... ~ -JM '""""'""""" 1.11/J.t bd:. NLbtwJ Cil ~~te<S ~I Uppncott Wolliams & Wilons .-.-..-..·.*..." &. .. ... ,. -..."""'"-·-- ~ iv Acquisitions Editor: Jonathan Joyce Product Development Editor: John Larkin Editorial Assistant: Tish Rogers Marketing Manager: Leah Thomson Production Project Manager: David Orzechowski Design Coordinator: Steven Druding Manufacturing Coordinator: Margie Orzech Prepress Vendor: S4Carlisle Publishing Services Seventh edition Copyright © 2017 Wolters Kluwer. Copyright © 2005 Lippincott Williams & Wilkins. All rights reserved. This book is protected by copyright. No part of this book may be reproduced or transmitted in any form or by any means, including as photocopies or scanned-in or other electronic copies, or utilized by any information storage and retrieval system without written permission from the copyright owner, except for brief quotations embodied in critical articles and reviews. Materials appearing in this book prepared by individuals as part of their official duties as U.S. government employees are not covered by the above-mentioned copyright. To request permission, please contact Wolters Kluwer at Two Commerce Square, 2001 Market Street, Philadelphia, PA 19103, via email at [email protected], or via our website at lww.com (products and services). 9 8 7 6 5 4 3 2 1 Printed in China Library of Congress Cataloging-in-Publication Data Names: Procop, Gary W., author. Title: Koneman’s color atlas and textbook of diagnostic microbiology / Gary W. Procop, Deirdre L. Church, Geraldine S. Hall, William M. Janda, Elmer W. Koneman, Paul C. Schreckenberger, Gail L. Woods. Other titles: Color atlas and textbook of diagnostic microbiology Description: Seventh edition. | Philadelphia : Wolters Kluwer Health, [2017] | Preceded by Koneman’s color atlas and textbook of diagnostic microbiology / Washington C. Winn Jr. … [et al.]. 6th ed. c2006. | Includes bibliographical references and index. Identifiers: LCCN 2016002803 | ISBN 9781451116595 (hardback) | eISBN 9781469829401 | VST 9781469836164 Subjects: | MESH: Microbiological Phenomena | Microbiological Techniques | Laboratory Manuals Classification: LCC QR67 | NLM QW 25 | DDC 616.9/041—dc23 LC record available at http://lccn.loc.gov/2016002803 This work is provided “as is,” and the publisher disclaims any and all warranties, express or implied, including any warranties as to accuracy, comprehensiveness, or currency of the content of this work. This work is no substitute for individual patient assessment based on healthcare professionals’ examination of each patient and consideration of, among other things, age, weight, gender, current or prior medical conditions, medication history, laboratory data, and other factors unique to the patient. The publisher does not provide medical advice or guidance, and this work is merely a reference tool. Healthcare professionals, and not the publisher, are solely responsible for the use of this work, including all medical judgments, and for any resulting diagnosis and treatments. Given continuous, rapid advances in medical science and health information, independent professional verification of medical diagnoses, indications, appropriate pharmaceutical selections and dosages, and treatment options should be made, and healthcare professionals should consult a variety of sources. When prescribing medication, healthcare professionals are advised to consult the product information sheet (the manufacturer’s package insert) accompanying each drug to verify, among other things, conditions of use, warnings, and side effects and to identify any changes in dosage schedule or contraindications, particularly if the medication to be administered is new, infrequently used, or has a narrow therapeutic range. To the maximum extent permitted under applicable law, no responsibility is assumed by the publisher for any injury and/or damage to persons or property, as a matter of products liability, negligence law or otherwise, or from any reference to or use by any person of this work. LWW.com DEDICATION v In Remembrance of Our Former Colleagues and Co-Authors Wash —We particularly remember your leadership in the College of American Pathology and as the editor-in-chief of the sixth edition of this text. You are sorely missed. Steve —We particularly remember your leadership on the American Board of Pathology and in Infectious Disease Pathology. You are sorely missed. Gerri —We particularly remember you as the consummate educator, whom all the students loved, and for your leadership in the American Society for Microbiology and other national organizations. You, too, are sorely missed, and this edition of this text would not have been possible without you - thanks. Washington C. Winn Jr, MD, MBA Director, Clinical Microbiology Laboratory Fletcher Allen Health Care Professor of Pathology University of Vermont College of Medicine Burlington, Vermont Stephen D. Allen, MD Professor of Pathology and Laboratory Medicine, Indiana University School of Medicine Director, Division of Clinical Microbiology, Clarian Health—Methodist, Indiana University, and Riley Hospitals Chief, Clinical Microbiology Laboratory, Roudebush Veterans Affairs Hospital Pathologist, Wishard Memorial Hospital Indianapolis, Indiana Geraldine S. Hall, PhD, D(ABMM) Section Head, Clinical Microbiology Cleveland Clinic Professor of Pathology Cleveland Clinic Lerner College of Medicine of Case Western Reserve University Cleveland, Ohio AUTHOR DEDICATIONS vi vii To Tamera and London—the best wife and son a guy could have. The Best of the Best! Gary W. Procop, MD To my husband Gord and family for all their support Deirdre L. Church, MD, PhD Thanks for the support of my husband Geraldine S. Hall, PhD To my parents, Robert and Geraldine, my brothers, Robert and Martin, and to Matthew, my life partner. William M. Janda, PhD In recognition of the ongoing hard work and dedication of microbiology technologists Elmer W. Koneman, MD I thank my wife Ann for her immense support and patience during the prolonged writing phase of this work and for her 45-plus years of steadfast love and encouragement. I also thank my son Adam for his creation of the Web ID Program used for identification of bacteria, which is described in detail in Chapters 6 and 7 of this text. Paul C. Schreckenberger, PhD In loving memory of my father Gail L. Woods, MD Foreword viii ix T he diagnostic process for infectious diseases is complex. An astute clinician may be able to make a clinical diagnosis based on the history, presenting features, physical examination, and epidemiologic exposures, including relevant travel. For example, pneumonia is a clinical diagnosis albeit with radiographic confirmation. Establishing an etiologic diagnosis may be much more difficult and is dependent on obtaining a relevant specimen of interpretable quality, swift reliable transport, and the testing repertoire of the supporting clinical microbiology laboratory. Moreover, presenting features of different causative agents often overlap and an infectious process may involve multiple organ systems, thereby adding further complexity to the task of establishing an etiologic diagnosis on which specific antimicrobial therapy depends. Indeed without an accurate and timely etiologic diagnosis, empirical treatment ensues or is prolonged, which may consist of multiple antimicrobial agents, those with unnecessarily broad activity, or both. This increases the risk of adverse drug reactions, alters the patient’s microbiome, and promotes selection of resistant mutants that indirectly put other patients at risk. Such collateral damage emphasizes only the need for rapid and accurate tests wisely deployed for the optimal outcome of patient care. Thus, the founding objective of Koneman’s Color Atlas and Textbook of Diagnostic Microbiology was to provide a clear exposition of procedures routinely employed in the laboratory identification of microbial agents causing infectious diseases. Since its first edition in 1979, the recognition and emergence of new infectious agents; better tools for their microbiologic diagnosis; more immunocompromised patients due to organ and stem cell transplantation, chemotherapy of malignancies, and immune-modulating agents; and a changing environment both of care and exposures have vastly complicated the quest for an etiologic diagnosis. These transformative developments have only accelerated since the sixth edition in 2006. Fortunately, the tools available for the challenges at hand have also expanded and improved. Quantitative viral load determinations have become essential for care of patients with HIV and hepatitis C virus infections. Many other molecular test procedures are now commonplace in diagnostic microbiology laboratories large and small. The identification of microorganisms has been transformed by the introduction of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Increasing advanced next-generation sequencing strategies are being deployed for microbial agents that have eluded diagnosis in the past or remain difficult to identify. Concurrently, traditional growth and isolation techniques remain important for many, if not most, bacterial, fungal, and mycobacterial agents and are required for reliable antimicrobial susceptibility testing given the growing threat of multidrug- resistant microorganisms. Recovery and testing is also crucial for infection control measures and for public health surveillance. As a result, now more than ever, the invaluable contribution of medical microbiology lies in providing, fostering, and promoting a proper balance between the science of the possible with the art of the appropriate. This is a professional team endeavor incumbent upon all entrusted with the stewardship of finite resources. Therefore, it is fortuitous that Dr. Gary W. Procop now assumes the role of editor-in-chief for the seventh edition of Koneman’s Color Atlas and Textbook of Diagnostic Microbiology, owing to his many contributions to the field in molecular microbiology, medical mycology, the histopathology of infectious diseases, and his leadership in advancing appropriate testing strategies for improved patient outcomes wherein true value lies. He and his fellow cadre of contributors are admirably positioned by virtue of knowledge, training, and experience in the field to not only maintain but also to augment the usefulness of this edition for all those who might benefit from its content: medical microbiologists, infectious disease specialists, pathologists, and clinical laboratory scientists. L. Barth Reller, MD, DTM&H Professor of Medicine and Pathology Duke University School of Medicine Durham, North Carolina and Glenn D. Roberts, PhD Professor Emeritus of Laboratory Medicine, Microbiology and Pathology Mayo Clinic College of Medicine Rochester, Minnesota Preface x xi T he seventh edition of this text represents a comprehensive update to our audience of the increasingly complex and challenging realm of diagnostic microbiology. Koneman’s Color Atlas and Textbook of Diagnostic Microbiology is in recognition of Elmer W. Koneman as one of the founding authors of this classic text and a driving force behind publication of the first six editions. Dr. Koneman has continued to provide guidance and editorial support, so his expertise remains an important part of this seventh edition. The seventh edition welcomes back long-time authors Drs. Paul C. Schreckenberger and William (Bill) M. Janda, who share their in-depth expertise of bacteriology. Dr. Gail Woods also returns to share her world-renowned expertise in mycobacteriology. This edition welcomes Dr. Deirdre Church, a premiere clinical microbiologist and infectious diseases clinician, and Dr. Gerri Hall, who shares her in-depth expertise in anaerobic bacteriology, mycoplasmas, and aerobic actinomycetes. It is a pleasure to join this august company in the production of this next edition of Koneman’s Color Atlas and Textbook of Diagnostic Microbiology. There have been substantial advances in clinical microbiology since the last edition of this textbook, with which the authors were challenged to incorporate in clinically meaningful ways. Mass spectrometry, commercially available highly multiplexed syndrome-based PCR assays, and next-generation sequencing were research tools at best when the last edition was published. Some of these, such as MALDI-TOF mass spectrometry and user-friendly nucleic acid amplification tests, are becoming commonplace in even smaller clinical laboratories. It is clear, however, that all laboratories have not adopted these technologies, and even if they desire to do so, the implementation rate is not uniform. Therefore, we were also challenged to retain traditional methods of organisms’ detection and identification that are still used in many laboratories, while also including new and advanced methods. This edition attempts to bridge the divide between the traditional and the newer advanced methods that are being employed. It is for this reason that some traditional tests, which will likely become entirely replaced by newer methods, are in part retained. We have recommended previous editions for those assays and methods that are more universally considered antiquated. The general organization of the text remains similar to the previous edition, but all sections have been significantly updated. The first two chapters are an introduction to clinical microbiology. Associated image plates for these chapters include artifacts in Gram-stained smears, emphasizing the importance of knowing what is not real, as well as the morphology of microorganisms. The expanded discussion of management, quality, compliance, and regulatory issues in the diagnostic microbiology laboratory confers necessary knowledge for those in the modern medical practice. Additionally, we have attempted to provide guidance to questions that clinical microbiologists face daily, such as: What do we work up, when do we work it up, and how extensively do we work it up? These challenges have become as important as the more traditional scientific issues confronted in the clinical laboratory, given the ever- dwindling financial and personnel resources. The traditional techniques that are still important for clinical laboratories receive appropriate attention