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Koneman’s Color Atlas and Textbook of
Diagnostic Microbiology
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Koneman's Color Atlas and
Textbook of Diagnostic Microbiology
Gary W. Proeop, MD, MS
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Seventh edition
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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
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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
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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
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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
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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
