Tai Lieu Chat Luong Molecular Microbiology DIAGNOSTIC PRINCIPLES AND PRACTICE THIRD EDITION Molecular Microbiology DIAGNOSTIC PRINCIPLES AND PRACTICE THIRD EDITION EDITORS IN CHIEF David H. Persing Cepheid, Sunnyvale, California Fred C. Tenover Cepheid, Sunnyvale, California EDITORS Randall T. Jude Children’s Research Hospital, Memphis, Tennessee Margareta Ieven Vaccine and Infectious Disease Institute (VIDI), University of Antwerp, Antwerp, Belgium Melissa B.
Miller University of North Carolina School of Medicine, Chapel Hill, North Carolina Frederick S. Nolte Medical University of South Carolina, Charleston, South Carolina Yi-Wei Tang Memorial Sloan Kettering Hospital, New York, New York Alex van Belkum bioMérieux, La Balme Les Grottes, France Washington, DC Cover: courtesy of Jared Tipton, Cepheid, Sunnyvale, California Copyright Ó 2016 by ASM Press. ASM Press is a registered trademark of the American Society for Microbiology. All rights reserved.
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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: Persing, David H. Title: Molecular microbiology : diagnostic principles and practice / editors: David H. Description: 3rd ed.
| Washington, DC : ASM Press, [2016] | ?2016 Identifiers: LCCN 2016012321 (print) | LCCN 2016014483 (ebook) | ISBN 9781555819088 | ISBN 9781555819071 () Subjects: LCSH: Diagnostic microbiology. Classification: LCC QR67 .9/041—dc23 LC record available at http://lccn.1128/9781555819071 Printed in the United States of America 10 9 8 7 6 5 4 3 2 1 Address editorial correspondence to: ASM Press, 1752 N St., Washington, DC 20036-2904, USA. Send orders to: ASM Press, P. Box 605, Herndon, VA 20172, USA.
E-mail: books@asmusa.org Online: http://estore.org Contents Contributors ix Preface xv section II I Metagenomics: section Implications for Diagnostics Novel and Emerging 10 The Skin Microbiome: Insights into Potential Technologies Impact on Diagnostic Practice / 117 1 Nucleic Acid Amplification Methods ELIZABETH A. GRICE Overview / 3 11 The Gastrointestinal Microbiome / 126 FREDERICK S. NOLTE AND CARL T. WITTWER ABRIA MAGEE, JAMES VERSALOVIC, AND RUTH ANN LUNA 2 Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology 12 The Vaginal Microbiome / 138 Laboratory / 19 DAVID N.
SIMMON, AND 13 Microbial Communities of the Male CATHY A. PETTI Urethra / 146 3 Microbial Whole-Genome Sequencing: BARBARA VAN DER POL AND DAVID E. NELSON Applications in Clinical Microbiology and Public 14 The Human Virome in Health and Disease / 156 Health / 32 KRISTINE M. WYLIE AND GREGORY A.
PEACOCK 4 Digital PCR and Its Potential Application to III Microbiology / 49 JIM F. GARSON, AND ALEXANDRA S. WHALE 5 Massively Parallel DNA Sequencing and section Microbiology / 58 Health Care-Associated ULF GYLLENSTEN, RUSSELL HIGUCHI, AND DAVID PERSING Infections 6 Next-Generation Sequencing / 68 15 Molecular Detection of Staphylococcus aureus CHARLES CHIU AND STEVE MILLER Colonization and Infection / 169 7 Pathogen Discovery / 80 KATHY A. MANGOLD AND LANCE R.
LIM AND DAVID WANG 16 Molecular Diagnostics for Clostridium 8 Matrix-Assisted Laser Desorption Ionization- difficile / 185 Time of Flight Mass Spectrometry for Microbial FRÉDÉRIC BARBUT AND CURTIS J. DONSKEY Identification in Clinical Microbiology / 92 17 Overview of Molecular Diagnostics in Multiple- ALEX VAN BELKUM, VICTORIA GIRARD, Drug-Resistant Organism Prevention: Focus on MAUD ARSAC, AND ROBIN PATEL Multiple-Drug-Resistant Gram-Negative 9 Multiplex Technologies / 102 Bacterial Organisms / 197 KEVIN ALBY AND MELISSA B. SULLIVAN AND DANIEL J. DIEKEMA v vi - CONTENTS 18 Detection of Vancomycin-Resistant 29 Syndromic Diagnostic Approaches to Bone and Enterococci / 212 Joint Infections / 401 ALLISON J.
MCGEER AND BARBARA M. MCADAM section IV Molecular Diagnostics section VI and Public Health Virology 19 The Impact of Molecular Diagnostics on 30 Molecular Detection and Characterization of Surveillance of Foodborne Infections / 235 Human Immunodeficiency Virus Type 1 / 417 JOHN BESSER, HEATHER CARLETON, ANGELA M. CALIENDO AND COLLEEN S. KRAFT RICHARD GOERING, AND PETER GERNER-SMIDT 31 Molecular Detection and Characterization of 20 Role of Molecular Methods in Improving Public Hepatitis C Virus / 430 Health Surveillance of Infections Caused by MICHAEL S.
FORMAN AND Antimicrobial-Resistant Bacteria in Health Care ALEXANDRA VALSAMAKIS and Community Settings / 245 32 Molecular Detection and Characterization of FRED C. TENOVER Hepatitis B Virus / 449 21 Molecular Diagnostics: Huge Impact on the JEFFREY J. GERMER AND JOSEPH D. YAO Improvement of Public Health in China / 256 33 Molecular Detection of Human HUI WANG, BIN CAO, YAWEI ZHANG, AND Papillomaviruses / 465 SHUGUANG LI DENISE I.
QUIGLEY AND ELIZABETH R. UNGER 22 Surveillance and Epidemiology of Norovirus 34 Molecular Diagnostics for Viral Infections in Infections / 266 Transplant Recipients / 476 JOHN P. BINNICKER AND 23 Molecular Diagnostic Assays for the Detection RAYMUND R. RAZONABLE and Control of Zoonotic Diseases / 275 J.
SCOTT WEESE section V section VII Fungi and Protozoa Syndromic Diagnostics 35 Molecular Detection and Identification of Fungal 24 Molecular Approaches to the Diagnosis of Pathogens / 489 Meningitis and Encephalitis / 287 KATRIEN LAGROU, JOHAN MAERTENS, AND KAREN C. BLOCH AND YI-WEI TANG MARIE PIERRE HAYETTE 25 Using Nucleic Acid Amplification Techniques in 36 Molecular Approaches for Diagnosis of a Syndrome-Oriented Approach: Detection of Chagas’ Disease and Genotyping of Respiratory Agents / 306 Trypanosoma cruzi / 501 KATHERINE LOENS AND MARGARETA IEVEN PATRICIO DIOSQUE, NICOLAS TOMASINI, AND 26 Molecular and Mass Spectrometry Detection MICHEL TIBAYRENC and Identification of Causative Agents of 37 Molecular Approaches for Diagnosis of Malaria Bloodstream Infections / 336 and the Characterization of Genetic Markers for ONYA OPOTA, KATIA JATON, GUY PROD’HOM, Drug Resistance / 516 AND GILBERT GREUB LISA C. RANFORD-CARTWRIGHT AND 27 Molecular Diagnosis of Gastrointestinal LAURA CIUFFREDA Infections / 362 38 Molecular Detection of Gastrointestinal BENJAMIN A. PINSKY AND NIAZ BANAEI Parasites / 530 28 Diagnostic Approaches to Genitourinary Tract JACO J.
VERWEIJ, ALEX VAN BELKUM, AND Infections / 386 C. RUNE STENSVOLD CLAIRE C. BRISTOW AND JEFFREY D. KLAUSNER CONTENTS - vii section VIII Point-of-Care/Near-Care 48 WHONET: Software for Surveillance of Infecting Microbes and Their Resistance to Antimicrobial Agents / 692 JOHN STELLING AND THOMAS F.
O’BRIEN 49 Cloud-Based Surveillance, Connectivity, and Diagnostics Distribution of the GeneXpert Analyzers for Diagnosis of Tuberculosis (TB) and Multiple- 39 Molecular Diagnostics and the Changing Face of Drug-Resistant TB in South Africa / 707 Point-of-Care / 545 WENDY S. STEVENS, BRAD CUNNINGHAM, DAVID L. DOLINGER AND ANNE M. WHALEN NASEEM CASSIM, NATASHA GOUS, AND 40 Point-of-Care Technologies for the Diagnosis of LESLEY E.
SCOTT Active Tuberculosis / 556 GRANT THERON 41 Molecular Diagnostics for Use in HIV/AIDS Care and Treatment in Resource-Limited Settings / 580 MAURINE M. MURTAGH section XI Quality Assurance 42 Rapid Point-of-Care Diagnosis of Malaria and Dengue Infection / 589 50 Molecular Method Verification / 721 LIESELOTTE CNOPS, MARJAN VAN ESBROECK, DONNA M. WOLK AND ELIZABETH M. MARLOWE AND JAN JACOBS 51 Molecular Microbiology Test Quality Assurance and Monitoring / 745 IX MATTHEW J.
BANKOWSKI 52 Proficiency Testing and External Quality section Assessment for Molecular Microbiology / 754 ROBERTA M. MADEJ The Host and Host 53 Practices of Sequencing Quality Response Assurance / 766 KARA L. NORMAN AND DAVID M. DINAUER 43 Implications of Pharmacogenetics for 54 Verification and Validation of Matrix-Assisted Antimicrobial Prescribing / 613 Laser Desorption Ionization Time of Flight Mass AR KAR AUNG, ELIZABETH J.
PHILLIPS, TODD Spectrometry-Based Protocols / 784 HULGAN, AND DAVID W. BUCHAN, AND 44 Exploiting MicroRNA (miRNA) Profiles for NATHAN A. LEDEBOER Diagnostics / 634 XII ABHIJEET BAKRE AND RALPH A. TRIPP 45 Host Response in Human Immunodeficiency Virus Infection / 655 PAUL J.
MCLAREN AND AMALIO TELENTI section 46 Biomarkers of Gastrointestinal Host Responses The Business of to Microbial Infections / 663 Diagnostics RANA E. EL FEGHALY, HANSRAJ BANGAR, AND DAVID B. HASLAM 55 Improved Diagnostics in Microbiology: Developing a Business Case for Hospital Administration / 799 X ELIZABETH M. NOVAK- WEEKLEY, AND MARK LAROCCO section 56 Molecular Diagnostics and the Changing Legal Information Technology Landscape / 803 MARK L.
HAYMAN, JING WANG, AND 47 Point-of-Care Medical Device Connectivity: JEFFREY M. LIBBY Developing World Landscape / 685 JEFF BAKER Index 811 Contributors KEVIN ALBY JOHN BESSER Department of Pathology and Laboratory Medicine, Perelman Enteric Disease Laboratory Branch, Centers for Disease School of Medicine, University of Pennsylvania, Philadelphia, Control & Prevention, 1600 Clifton Rd, Atlanta, GA 30333 PA 19104 MATTHEW J. BINNICKER MAUD ARSAC Mayo Clinic, Clinical Microbiology, 200 First Street SW - bioMérieux SA, R&D Microbiology, 3 Route de Port Hilton 454, Rochester, MN 55905 Michaud, 38390 La Balme Les Grottes, France KAREN C. BLOCH AR KAR AUNG Vanderbilt University Medical Center, A-2200 MCN, Department of General Medicine and Infectious Diseases, The Nashville, TN 37232 Alfred Hospital, Melbourne, Victoria, Australia CLAIRE C.
BRISTOW JEFF BAKER Division of Global Public Health, Department of Medicine, JESA Consulting, 63 Putnam Street, Suite 203, Saratoga University of California San Diego, La Jolla, CA 92093 Springs, NY 12866 BLAKE W. BUCHAN ABHIJEET BAKRE Department of Pathology, Medical College of Wisconsin, University of Georgia, Dept. of Infectious Diseases, Athens, 9200 West Wisconsin Ave., Milwaukee, WI 53226 GA 30602 NIAZ BANAEI ANGELA M. CALIENDO Stanford University School of Medicine, Stanford, CA 94305, Department of Medicine, Alpert Medical School of Brown and Clinical Microbiology Laboratory, Stanford Hospital & University, 593 Eddy Street, Providence, RI 02903 Clinics and Lucile Packard Children’s Hospital, Palo Alto, CA 94304 BIN CAO China-Japan Friendship Hospital, Beijing, China 100029 HANSRAJ BANGAR Division of Infectious Disease, Cincinnati Children Hospital HEATHER CARLETON Medical Center, Cincinnati, OH 45229 Enteric Disease Laboratory Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd., Atlanta, GA MATTHEW J.
BANKOWSKI 30333 Diagnostic Laboratory Services, Inc. (The Queen’s Medical Center), Microbiology Department, Aiea, HI 96701, and John NASEEM CASSIM A. Burns School of Medicine and the University of Hawaii at Faculty of Health Sciences, University of the Witwatersrand, Manoa, Department of Pathology, Honolulu, HI 96813 7 York Road, Third Floor, Room 3B22, Parktown, Johannesburg, South Africa FRÉDÉRIC BARBUT UHLIN (Unité d’Hygiène et de Lutte contre les Infections CHARLES CHIU Nosocomiales), National Reference Laboratory for University of California, San Francisco, Laboratory Medicine, Clostridium difficile, Groupe Hospitalier de l’Est Parisien 185 Berry Street, Suite 290, Box #0134, San Francisco, CA (HUEP), Site Saint-Antoine, 75012 Paris, France 94107 ix x - CONTRIBUTORS LAURA CIUFFREDA PETER GERNER-SMIDT University of Glasgow, College of Medical, Veterinary and Enteric Disease Laboratory Branch, Centers for Disease Control Life Sciences, Sir Graeme Davies Building, 120 University and Prevention, 1600 Clifton Rd, Atlanta, Georgia 30333 Place, Glasgow, Scotland G12 8TA, United Kingdom VICTORIA GIRARD LIESELOTTE CNOPS bioMérieux SA, R&D Microbiology, 3 Route de Port Institute of Tropical Medicine, Clinical Sciences, Michaud, 38390 La Balme Les Grottes, France Kronenburgstraat 43/3, Antwerp, 2000, Belgium RICHARD GOERING KARISSA D. CULBREATH Department of Medical Microbiology and Immunology, Department of Pathology, University of New Mexio Health Creighton University School of Medicine, Omaha, NE 68178 Sciences Center, and TriCore Reference Laboratories, Albuquerque, NM 87102 NATASHA GOUS Faculty of Health Sciences, University of the Witwatersrand, BRAD CUNNINGHAM 7 York Road, Third Floor, Room 3B22, Parktown, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa 7 York Road, Third Floor, Room 3B22, Parktown, Johannesburg, South Africa GILBERT GREUB Institute of Microbiology and Infectious Diseases Service, DANIEL J.
DIEKEMA University of Lausanne and University Hospital Center, University of Iowa Carver College of Medicine, Division of Lausanne, Switzerland Infectious Diseases, 200 Hawkins Drive, Iowa City, IA 52242 ELIZABETH A.