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POCKET GUIDE TO Clinical Microbiology
4th Edition
Christopher D. Doern
Assistant Professor, Pathology Director of Clinical Microbiology Virginia Commonwealth University Health System Medical College of Virginia Campus
Copyright 2017 American Society for Microbiology. All rights reserved. No part of this publication may be reproduced or transmitted in whole or in part or reused 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: Doern, Christopher D., author.
Title: Pocket guide to clinical microbiology / Christopher D. Doern.
Description: Fourth edition. | Washington, DC : ASM Press, 2018.
Identifiers: LCCN 2018008388 | ISBN 9781683670063 (pbk. : alk. paper)
Subjects: LCSH: Medical microbiology–Handbooks, manuals, etc.
Classification: LCC QR46 .M92 2018 | DDC 616.9/041–dc23 LC record available at https://lccn.loc.gov/2018008388
doi:10.1128/9781683670070
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Cover: “La peste en Mandchourie” Le Petit Journal n° 1057 du 19 Fev. 1911
Design: Lou Moriconi (http://lmoriconi.com/)
Online: http://www.asmscience.org
To Drs. Carey-Ann Burnham, Mike Dunne, and Betz Forbes: invaluable mentors and dear friends.
Preface
The Pocket Guide to Clinical Microbiology is unique among reference texts in that its primary purpose is to present usable information in a concise and accessible manner. Now in its fourth edition, this iconic text has remained popular over the years because it has successfully condensed most of the information needed by the practicing clinical microbiologist into a pocket-sized guide. As Dr. Patrick Murray articulated in the preface of the third edition, with each iteration of this text the format has been honed to enhance its usability. Although the overall format of the fourth edition remains true to the template of previous editions, this edition reflects the tremendous evolution that has occurred in clinical microbiology over the past decade. In particular, three key advances have reshaped the practice of clinical microbiology, and have therefore, reshaped this edition.
First, the widespread adoption of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for organism identification has altered the way many laboratories practice clinical microbiology. Despite the fact that those using MALDI-TOF MS are less dependent on biochemical reactions to identify organisms, understanding biochemical profiles is still required for the troubleshooting of failed or ambiguous MALDI-TOF MS identifications. As such, this text has updated, but maintained, much of the biochemical reactions required to identify organisms the “old school” way. It is my belief that understanding and using these reactions to confirm organism identifications, remains one of the foundations of good clinical microbiology. This pocket guide should provide quick reference to everything the microbiologist needs to confidently identify most organisms encountered in the clinical laboratory. In addition, new information has been added in Section 8 that outlines the specifics of MALDI-TOF MS performance for individual bacteria, mycobacteria, and fungi.
Second, the development of molecular techniques has revolutionized the diagnosis of infectious diseases. Most notably, nucleic acid amplification
