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. Hayden
St. 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
Cover: courtesy of Jared Tipton, Cepheid, Sunnyvale, California
Copyright © 2016 by ASM Press. ASM Press is a registered trademark of the American Society for Microbiology. All rights reserved. No part of this publication may be reproduced or transmitted in whole or in part or reutilized 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: Persing, David H., editor.
Title: Molecular microbiology : diagnostic principles and practice / editors: David H. Persing [and seven others].
Description: 3rd ed. | Washington, DC : ASM Press, [2016] | ?2016
Identifiers: LCCN 2016012321 (print) | LCCN 2016014483 (ebook) | ISBN 9781555819088 | ISBN 9781683673286 ()
Subjects: LCSH: Diagnostic microbiology. | Molecular microbiology. | Molecular diagnosis.
Classification: LCC QR67 .M65 2016 (print) | LCC QR67 (ebook) | DDC 616.9/041—dc23
LC record available at http://lccn.loc.gov/2016012321
doi:10.1128/9781555819071
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., N.W., Washington, DC 20036-2904, USA.
Send orders to: ASM Press, P.O. Box 605, Herndon, VA 20172, USA.
Phone: 800-546-2416; 703-661-1593. Fax: 703-661-1501.
E-mail: books@asmusa.org
Online: http://estore.asm.org
CONTENTS
Contributors
Preface
section I
NOVEL AND EMERGING TECHNOLOGIES
1 Nucleic Acid Amplification Methods Overview
FREDERICK S. NOLTE AND CARL T. WITTWER
2 Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory
KARISSA D. CULBREATH, KEITH E. SIMMON, AND CATHY A. PETTI
3 Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health
M. E. TÖRÖK AND S. J. PEACOCK
4 Digital PCR and Its Potential Application to Microbiology
JIM F. HUGGETT, JEREMY A. GARSON, AND ALEXANDRA S. WHALE
5 Massively Parallel DNA Sequencing and Microbiology
ULF GYLLENSTEN, RUSSELL HIGUCHI, AND DAVID PERSING
6 Next-Generation Sequencing
CHARLES CHIU AND STEVE MILLER
7 Pathogen Discovery
EFREM S. LIM AND DAVID WANG
8 Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Microbial Identification in Clinical Microbiology
ALEX VAN BELKUM, VICTORIA GIRARD, MAUD ARSAC, AND ROBIN PATEL
9 Multiplex Technologies
KEVIN ALBY AND MELISSA B. MILLER
section II
METAGENOMICS: IMPLICATIONS FOR DIAGNOSTICS
10 The Skin Microbiome: Insights into Potential Impact on Diagnostic Practice
ELIZABETH A. GRICE
11 The Gastrointestinal Microbiome
ABRIA MAGEE, JAMES VERSALOVIC, AND RUTH ANN LUNA
12 The Vaginal Microbiome
DAVID N. FREDRICKS
13 Microbial Communities of the Male Urethra
BARBARA VAN DER POL AND DAVID E. NELSON
14 The Human Virome in Health and Disease
KRISTINE M. WYLIE AND GREGORY A. STORCH
section III
HEALTH CARE-ASSOCIATED INFECTIONS
15 Molecular Detection of Staphylococcus aureus Colonization and Infection
KATHY A. MANGOLD AND LANCE R. PETERSON
16 Molecular Diagnostics for Clostridium difficile
FRÉDÉRIC BARBUT AND CURTIS J. DONSKEY
17 Overview of Molecular Diagnostics in Multiple-Drug-Resistant Organism Prevention: Focus on Multiple-Drug-Resistant Gram-Negative Bacterial Organisms
KAEDE V. SULLIVAN AND DANIEL J. DIEKEMA
18 Detection of Vancomycin-Resistant Enterococci
ALLISON J. MCGEER AND BARBARA M. WILLEY
section IV
MOLECULAR DIAGNOSTICS AND PUBLIC HEALTH
19 The Impact of Molecular Diagnostics on Surveillance of Foodborne Infections
JOHN BESSER, HEATHER CARLETON, RICHARD GOERING, AND PETER GERNER-SMIDT
20 Role of Molecular Methods in Improving Public Health Surveillance of Infections Caused by Antimicrobial-Resistant Bacteria in Health Care and Community Settings
FRED C. TENOVER
21 Molecular Diagnostics: Huge Impact on the Improvement of Public Health in China
HUI WANG, BIN CAO, YAWEI ZHANG, AND SHUGUANG LI
22 Surveillance and Epidemiology of Norovirus Infections
JOHN P. HARRIS
23 Molecular Diagnostic Assays for the Detection and Control of Zoonotic Diseases
J. SCOTT WEESE
section V
SYNDROMIC DIAGNOSTICS
24 Molecular Approaches to the Diagnosis of Meningitis and Encephalitis
KAREN C. BLOCH AND YI-WEI TANG
25 Using Nucleic Acid Amplification Techniques in a Syndrome-Oriented Approach: Detection of Respiratory Agents
KATHERINE LOENS AND MARGARETA IEVEN
26 Molecular and Mass Spectrometry Detection and Identification of Causative Agents of Bloodstream Infections
ONYA OPOTA, KATIA JATON, GUY PROD’HOM, AND GILBERT GREUB
27 Molecular Diagnosis of Gastrointestinal Infections
BENJAMIN A. PINSKY AND NIAZ BANAEI
28 Diagnostic Approaches to Genitourinary Tract Infections
CLAIRE C. BRISTOW AND JEFFREY D. KLAUSNER
29 Syndromic Diagnostic Approaches to Bone and Joint Infections
ALEXANDER J. MCADAM
section VI
VIROLOGY
30 Molecular Detection and Characterization of Human Immunodeficiency Virus Type 1
ANGELA M. CALIENDO AND COLLEEN S. KRAFT
31 Molecular Detection and Characterization of Hepatitis C Virus
MICHAEL S. FORMAN AND ALEXANDRA VALSAMAKIS
32 Molecular Detection and Characterization of Hepatitis B Virus
JEFFREY J. GERMER AND JOSEPH D. C. YAO
33 Molecular Detection of Human Papillomaviruses
DENISE I. QUIGLEY AND ELIZABETH R. UNGER
34 Molecular Diagnostics for Viral Infections in Transplant Recipients
MATTHEW J. BINNICKER AND RAYMUND R. RAZONABLE
section VII
FUNGI AND PROTOZOA
35 Molecular Detection and Identification of Fungal Pathogens
KATRIEN LAGROU, JOHAN MAERTENS, AND MARIE PIERRE HAYETTE
36 Molecular Approaches for Diagnosis of Chagas’ Disease and Genotyping of Trypanosoma cruzi
PATRICIO DIOSQUE, NICOLAS TOMASINI, AND MICHEL TIBAYRENC
37 Molecular Approaches for Diagnosis of Malaria and the Characterization of Genetic Markers for Drug Resistance
LISA C. RANFORD-CARTWRIGHT AND LAURA CIUFFREDA
38 Molecular Detection of Gastrointestinal Parasites
JACO J. VERWEIJ, ALEX VAN BELKUM, AND C. RUNE STENSVOLD
section VIII
POINT-OF-CARE/NEAR-CARE DIAGNOSTICS
39 Molecular Diagnostics and the Changing Face of Point-of-Care
DAVID L. DOLINGER AND ANNE M. WHALEN
40 Point-of-Care Technologies for the Diagnosis of Active Tuberculosis
GRANT THERON
41 Molecular Diagnostics for Use in HIV/AIDS Care and Treatment in Resource-Limited Settings
MAURINE M. MURTAGH
42 Rapid Point-of-Care Diagnosis of Malaria and Dengue Infection
LIESELOTTE CNOPS, MARJAN VAN ESBROECK, AND JAN JACOBS
section IX
THE HOST AND HOST RESPONSE
43 Implications of Pharmacogenetics for Antimicrobial Prescribing
AR KAR AUNG, ELIZABETH J. PHILLIPS, TODD HULGAN, AND DAVID W. HAAS
44 Exploiting MicroRNA (miRNA) Profiles for Diagnostics
ABHIJEET BAKRE AND RALPH A. TRIPP
45 Host Response in Human Immunodeficiency Virus Infection
PAUL J. MCLAREN AND AMALIO TELENTI
46 Biomarkers of Gastrointestinal Host Responses to Microbial Infections
RANA E. EL FEGHALY, HANSRAJ BANGAR, AND DAVID B. HASLAM
section X
INFORMATION TECHNOLOGY
47 Point-of-Care Medical Device Connectivity: Developing World Landscape
JEFF BAKER
48 WHONET: Software for Surveillance of Infecting Microbes and Their Resistance to Antimicrobial Agents
JOHN STELLING AND THOMAS F. O’BRIEN
49 Cloud-Based Surveillance, Connectivity, and Distribution of the GeneXpert Analyzers for Diagnosis of Tuberculosis (TB) and Multiple-Drug-Resistant TB in South Africa
WENDY S. STEVENS, BRAD CUNNINGHAM, NASEEM CASSIM, NATASHA GOUS, AND LESLEY E. SCOTT
section XI
QUALITY ASSURANCE
50 Molecular Method Verification
DONNA M. WOLK AND ELIZABETH M. MARLOWE
51 Molecular Microbiology Test Quality Assurance and Monitoring
MATTHEW J. BANKOWSKI
52 Proficiency Testing and External Quality Assessment for Molecular Microbiology
ROBERTA M. MADEJ
53 Practices of Sequencing Quality Assurance
KARA L. NORMAN AND DAVID M. DINAUER
54 Verification and Validation of Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry-Based Protocols
MATTHEW L. FARON, BLAKE W. BUCHAN, AND NATHAN A. LEDEBOER
section XII
THE BUSINESS OF DIAGNOSTICS
55 Improved Diagnostics in Microbiology: Developing a Business Case for Hospital Administration
ELIZABETH M. MARLOWE, SUSAN M. NOVAK-WEEKLEY, AND MARK LAROCCO
56 Molecular Diagnostics and the Changing Legal Landscape
MARK L. HAYMAN, JING WANG, AND JEFFREY M. LIBBY
Index
CONTRIBUTORS
KEVIN ALBY
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
MAUD ARSAC
bioMérieux SA, R&D Microbiology, 3 Route de Port Michaud, 38390 La Balme Les Grottes, France
AR KAR AUNG
Department of General Medicine and Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
JEFF BAKER
JESA Consulting, 63 Putnam Street, Suite 203, Saratoga Springs, NY 12866
ABHIJEET BAKRE
University of Georgia, Dept. of Infectious Diseases, Athens, GA 30602
NIAZ BANAEI
Stanford University School of Medicine, Stanford, CA 94305, and Clinical Microbiology Laboratory, Stanford Hospital & Clinics and Lucile Packard Children’s Hospital, Palo Alto, CA 94304
HANSRAJ BANGAR
Division of Infectious Disease, Cincinnati Children Hospital Medical Center, Cincinnati, OH 45229
MATTHEW J. BANKOWSKI
Diagnostic Laboratory Services, Inc. (The Queen’s Medical Center), Microbiology Department, Aiea, HI 96701, and John A. Burns School of Medicine and the University of Hawaii at Manoa, Department of Pathology, Honolulu, HI 96813
FRÉDÉRIC BARBUT
UHLIN (Unité d’Hygiène et de Lutte contre les Infections Nosocomiales), National Reference Laboratory for Clostridium difficile, Groupe Hospitalier de l’Est Parisien (HUEP), Site Saint-Antoine, 75012 Paris, France
JOHN BESSER
Enteric Disease Laboratory Branch, Centers for Disease Control & Prevention, 1600 Clifton Rd, Atlanta, GA 30333
MATTHEW J. BINNICKER
Mayo Clinic, Clinical Microbiology, 200 First Street SW - Hilton 454, Rochester, MN 55905
KAREN C. BLOCH
Vanderbilt University Medical Center, A-2200 MCN, Nashville, TN 37232
CLAIRE C. BRISTOW
Division of Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA 92093
BLAKE W. BUCHAN
Department of Pathology, Medical College of Wisconsin, 9200 West Wisconsin Ave., Milwaukee, WI 53226
ANGELA M. CALIENDO
Department of Medicine, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903
BIN CAO
China-Japan Friendship Hospital, Beijing, China 100029
HEATHER CARLETON
Enteric Disease Laboratory Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd., Atlanta, GA 30333
NASEEM CASSIM
Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Third Floor, Room 3B22, Parktown, Johannesburg, South Africa
CHARLES CHIU
University of California, San Francisco, Laboratory Medicine, 185 Berry Street, Suite 290, Box #0134, San Francisco, CA 94107
LAURA CIUFFREDA
University of Glasgow, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, 120 University Place, Glasgow, Scotland G12 8TA, United Kingdom
LIESELOTTE CNOPS
Institute of Tropical Medicine, Clinical Sciences, Kronenburgstraat 43/3, Antwerp, 2000, Belgium
KARISSA D. CULBREATH
Department of Pathology, University of New Mexio Health Sciences Center, and TriCore Reference Laboratories, Albuquerque, NM 87102
BRAD CUNNINGHAM
Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Third Floor, Room 3B22, Parktown, Johannesburg, South Africa
DANIEL J. DIEKEMA
University of Iowa Carver College of Medicine, Division of Infectious Diseases, 200 Hawkins Drive, Iowa City, IA 52242
DAVID M. DINAUER
Thermo Fisher Scientific, 9099 N Deerbrook Trail, Brown Deer, WI 53223
PATRICIO DIOSQUE
Unidad de Epidemiología Molecular, Instituto de Patología Experimental, CONICET, Argentina
DAVID L. DOLINGER
FIND, Geneve, Geneva CH1211, Switzerland
CURTIS J. DONSKEY
Infectious Diseases Section 1110(W), Cleveland Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH 44106
RANA E. EL FEGHALY
Department of Pediatrics, Division of Infectious Diseases, University of Mississippi Medical Center, Jackson, MS 39216
MATTHEW L. FARON
Department of Pathology, Medical College of Wisconsin, 9200 West Wisconsin Ave., Milwaukee, WI 53226
MICHAEL S. FORMAN
Department of Pathology, The Johns Hopkins Hospital, 600 North Wolfe Street, Meyer B1-193, Baltimore, MD 21287
DAVID N. FREDRICKS
Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109
JEREMY A. GARSON
Research Department of Infection, Division of Infection and Immunity, UCL, London, United Kingdom
JEFFREY J. GERMER
Division of Clinical Microbiology, Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905
PETER GERNER-SMIDT
Enteric Disease Laboratory Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, Georgia 30333
VICTORIA GIRARD
bioMérieux SA, R&D Microbiology, 3 Route de Port Michaud, 38390 La Balme Les Grottes, France
RICHARD GOERING
Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178
NATASHA GOUS
Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Third Floor, Room 3B22, Parktown, Johannesburg, South Africa
GILBERT GREUB
Institute of Microbiology and Infectious Diseases Service, University of Lausanne and University Hospital Center, Lausanne, Switzerland
ELIZABETH A. GRICE
University of Pennsylvania, Perelman School of Medicine, Department of Dermatology, 421 Curie Blvd, 1007 BRB II/III, Philadelphia, PA 19104
ULF GYLLENSTEN
Uppsala University, Department of Immunology, Genetics and Pathology, Science of Life Laboratory Uppsala, Biomedical Center, Box 815, SE-751 08 Uppsala, Sweden
DAVID W. HAAS
Vanderbilt Health - One Hundred Oaks, 719 Thompson Lane, Suite 47183, Nashville, TN 37204
JOHN P. HARRIS
Public Health England, Centre for Infectious Disease Surveillance and Control, 61 Colindale Avenue, Colindale, London, NW9 5EQ, United Kingdom
DAVID B. HASLAM
Division of Infectious Disease, Cincinnati Children Hospital Medical Center, Cincinnati, OH 45229
MARIE PIERRE HAYETTE
University Hospital of Liège, Liège, Belgium
MARK L. HAYMAN
Intellectual Property Practice Group, Morgan Lewis & Bockius LLP, One Federal Street, Boston, MA 02110
RUSSELL HIGUCHI
Cepheid, 904 Caribbean Dr., Sunnyvale, CA 94089
JIM F. HUGGETT
Molecular and Cell Biology, LGC, Queens Road, Teddington, Middlesex, TW11 0LY, United Kingdom
TODD HULGAN
Vanderbilt University School of Medicine, Department of Medicine, A2200 MCN, 1161 21st Avenue South, Nashville, TN 37232
MARGARETA IEVEN
University Hospital Antwerp, Department of Medical Microbiology, Wilrijkstraat 10, Antwerp, 2650, Belgium
JAN JACOBS
Institute of Tropical Medicine, Clinical Sciences, Kronenburgstraat 43/3, Antwerp, 2000, Belgium
KATIA JATON
Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
JEFFREY D. KLAUSNER
Division of Infectious Diseases, Department of Medicine, University of California Los Angeles, and Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90024
COLLEEN S. KRAFT
Department of Pathology and Laboratory Medicine, Division of Infectious Diseases, Emory University, 1364 Clifton Rd, NE, Atlanta, GA 30322
KATRIEN LAGROU
KU Leuven— University of Leuven, Department of Microbiology and Immunology, and University Hospitals Leuven, Department of Laboratory Medicine and National Reference Center for Mycosis, B-3000 Leuven, Belgium
MARK LAROCCO
MTL Consulting, Erie, PA 16506
NATHAN A. LEDEBOER
Department of Pathology, Medical College of Wisconsin, 9200 West Wisconsin Ave., Milwaukee, WI 53226
SHUGUANG LI
Peking University People’s Hospital, Beijing, China 100044
JEFFREY M. LIBBY
Mendel Biological Solutions, LLP, 3935 Point Eden Way, Hayward, CA 94545
EFREM S. LIM
Washington University in St. Louis, Department of Molecular Microbiology and Pathology & Immunology, 660 S. Euclid Avenue, Campus Box 8230, Saint Louis, MO 63110
KATHERINE LOENS
University Hospital Antwerp, Department of Medical Microbiology, Wilrijkstraat 10, Antwerp, 2650, Belgium
RUTH ANN LUNA
Department of Pathology & Immunology, Baylor College of Medicine, 1102 Bates Street, Feigin Center Suite 830, Houston, TX 77030
ROBERTA M. MADEJ
Alta Bates Summit Medical Center, Clinical Laboratory-Microbiology, Berkeley, CA 94705
JOHAN MAERTENS
KU Leuven— University of Leuven, Department of Microbiology and Immunology, and University Hospitals Leuven, Department of Hematology, B-3000 Leuven, Belgium
ABRIA MAGEE
Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
KATHY A. MANGOLD
NorthShore University HealthSystem, Department of Pathology and Laboratory Medicine, 2650 Ridge Ave., Burch Bldg., Room 116, Evanston, IL 60201
ELIZABETH M. MARLOWE
The Permanente Medical Group, Berkeley, CA 94710
ALEXANDER J. MCADAM
Infectious Diseases Diagnostic Laboratory, Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA 02115
ALLISON J. MCGEER
Infection Control, Room 210, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
PAUL J. MCLAREN
School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
STEVE MILLER
University of California, San Francisco, Laboratory Medicine, 185 Berry Street, Suite 290, Box #0100, San Francisco, CA 94107
MELISSA B. MILLER
Clinical Microbiology Laboratory, UNC Hospitals, 101 Manning Drive, East Wing 1033, Chapel Hill, NC 27514
MAURINE M. MURTAGH
The Murtagh Group, LLC, 2134 Stockbridge Avenue, Woodside, CA 94062
DAVID E. NELSON
Indiana University School of Medicine, Department of Microbiology & Immunology, Indianapolis, IN 46202
FREDERICK S. NOLTE
Medical University of South Carolina, Department of Pathology and Laboratory Medicine, 171 Ashley Avenue, MSC 908, Charleston, SC 29425
KARA L. NORMAN
Department of Research and Development, Thermo Fisher Quality Controls, Thermo Fisher Scientific, 6010 Egret Court, Benicia, CA 94510
SUSAN M. NOVAK-WEEKLEY
Southern California Permanente Medical Group, Microbiology, 11668 Sherman Way, North Hollywood, CA 91605
THOMAS F. O’BRIEN
Brigham and Women’s Hospital, Microbiology Laboratory, WHO Collaborating Centre for Surveillance of Antimicrobial Resistance, 75 Francis Street, Boston, MA 02115
ONYA OPOTA
Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
ROBIN PATEL
Mayo Clinic, Division of Clinical Microbiology, Division of Infectious Diseases, Rochester, MN 55905
S. J. PEACOCK
University of Cambridge, Department of Medicine, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ, United Kingdom
DAVID PERSING
Cepheid, 904 Caribbean Dr., Sunnyvale, CA 94089
LANCE R. PETERSON
NorthShore University HealthSystem, Department of Pathology and Laboratory Medicine, 2650 Ridge Ave., Burch Bldg., Room 116, Evanston, IL 60201
CATHY A. PETTI
4HealthSpring Global, Inc., Bradenton, FL 34209
ELIZABETH J. PHILLIPS
Vanderbilt University, 1493 Willowbrooke Circle, Franklin, TN 37069
BENJAMIN A. PINSKY
Stanford University School of Medicine, Stanford, CA 94305, and Clinical Virology Laboratory, Stanford Hospital & Clinics and Lucile Packard Children’s Hospital, Palo Alto, CA 94304
GUY PROD’HOM
Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
DENISE I. QUIGLEY
Cytogenetics and Molecular Genetics Laboratory, Kaiser Permanente North West Regional Laboratory, 13705 North East Airport Way, Portland, OR 97230
LISA C. RANFORD-CARTWRIGHT
University of Glasgow, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, 120 University Place, Glasgow, Scotland G12 8TA, United Kingdom
RAYMUND R. RAZONABLE
Mayo Clinic, Clinical Microbiology, 200 First Street SW - Hilton 454, Rochester, MN 55905
LESLEY E. SCOTT
Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Third Floor, Room 3B22, Parktown, Johannesburg, South Africa
KEITH E. SIMMON
Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108
JOHN STELLING
Brigham and Women’s Hospital, Microbiology Laboratory, WHO Collaborating Centre for Surveillance of Antimicrobial Resistance, 75 Francis Street, Boston, MA 02115
C. RUNE STENSVOLD
Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
WENDY S. STEVENS
Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Third Floor, Room 3B22, Parktown, Johannesburg, South Africa
GREGORY A. STORCH
Washington University School of Medicine, Pediatrics, 660 S Euclid Avenue, Campus Box 8116, St. Louis, MO 63110
KAEDE V. SULLIVAN
University of Pennsylvania, Pathology & Laboratory Medicine, 34th Street & Civic Center Blvd., Main Building, Room 5112A, Philadelphia, PA 19104
YI-WEI TANG
Memorial Sloan-Kettering Cancer Center, Clinical Microbiology Service, 1275 York Avenue, S328, New York, NY 10065
AMALIO TELENTI
J. Craig Venter Institute, La Jolla, CA 92037
FRED C. TENOVER
Cepheid, 904 Caribbean Drive, Sunnyvale, CA 94089
GRANT THERON
DST/NRF of Excellence for Biomedical Tuberculosis Research, and MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa; Lung Infection and Immunity Unit, Department of Medicine, University of Cape Town, Observatory, Cape Town, South Africa
MICHEL TIBAYRENC
Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), IRD Center, Montpellier, France
NICOLAS TOMASINI
Unidad de Epidemiología Molecular, Instituto de Patología Experimental, CONICET, Argentina, Salta, Argentina
M. E. TÖRÖK
University of Cambridge, Department of Medicine, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ, United Kingdom
RALPH A. TRIPP
University of Georgia, Animal Health Research Center, 111 Carlton Street, Athens, GA 30602
ELIZABETH R. UNGER
Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, MS G41, Atlanta, GA 30333
ALEXANDRA VALSAMAKIS
Department of Pathology, The Johns Hopkins Hospital, 600 North Wolfe Street, Meyer B1-193, Baltimore, MD 21287
ALEX VAN BELKUM
bioMérieux SA, R&D Microbiology, 3 Route de Port Michaud, 38390 La Balme Les Grottes, France
BARBARA VAN DER POL
The University of Alabama at Birmingham School of Medicine, Department of Medicine, 703 19th Street South, Birmingham, AL 35294
MARJAN VAN ESBROECK
Institute of Tropical Medicine, Clinical Sciences, Kronenburgstraat 43/3, Antwerp, 2000, Belgium
JAMES VERSALOVIC
Texas Children’s Hospital, Pathology, 1102 Bates Avenue, Houston, TX 77030
JACO J. VERWEIJ
St. Elisabeth Hospital, Laboratory of Medical Microbiology and Immunology, Tilburg, Netherlands
DAVID WANG
Washington University in St. Louis, Department of Molecular Microbiology and Pathology & Immunology, 660 South Euclid Avenue, Campus Box 8230, Saint Louis, MO 63110
HUI WANG
Peking University People’s Hospital, Beijing, China, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, P.R. China
JING WANG
Intellectual Property Practice Group, Morgan Lewis & Bockius LLP, One Federal Street, Boston, MA 02110
J. SCOTT WEESE
Dept of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G2W1, Canada
ALEXANDRA S. WHALE
Molecular and Cell Biology, LGC, Queens Road, Teddington, Middlesex, TW11 0LY, United Kingdom
ANNE M. WHALEN
FIND, Chemin des Mines 9, CH-1211, Geneva, Switzerland
BARBARA M. WILLEY
Department of Microbiology, Room 1480, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
CARL T. WITTWER
University of Utah, Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132
DONNA M. WOLK
Geisinger Health System, Department of Laboratory Medicine, and Weis Center for Research, Danville, PA 17822-0131, and Wilkes University, Wilkes-Barre, PA 18701
KRISTINE M. WYLIE
Washington University School of Medicine, Pediatrics, 660 S Euclid Avenue, Campus Box 8116, Saint Louis, MO 63110
JOSEPH D. C. YAO
Division of Clinical Microbiology, Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905
YAWEI ZHANG
Peking University People’s Hospital, Beijing, China 100044
PREFACE
In the 5 years since the 2011 edition of this book, the molecular diagnostics landscape has changed dramatically. In the 1990s, molecular diagnostics was the domain of only a few reference laboratories; it took almost 20 years for these techniques to make their way into about half of the CLIA high-complexity laboratories in the United States. The full potential of this technology was slow to be realized largely because the methods used by these laboratories were not capable of delivering on-demand results or being conducted at the point of care. Over the past year, with the advent of CLIA-waived molecular testing spurred on by the inexorable force of innovation, molecular diagnostics have become increasingly democratized to the extent that physician office laboratories and sexual health clinics are now performing molecular testing on the premises, often delivering results in minutes or a few hours.
Laboratory professionals may at times find themselves a bit bewildered in this rapidly evolving landscape. Adding to this, enter next-generation sequencing (NGS) technology, as described in several chapters in this book (chapters 2, 3, 5, 6, 10–14, and 53). NGS-based analysis of microbial genomes and populations is in some ways similar to where PCR was in 1987: full of opportunities and challenges. For the first time, identification of the full range of pathogens—viruses, bacteria, fungi, and protozoa—can be addressed by using the same core technology. Microbial population analysis can be carried out at unprecedented depth, opening up the field of metagenomics (chapters 10–14). Whole-genome analysis goes beyond organism identification to predict drug resistance and detect pathogenic determinants. As diagnosticians, it seems likely that as this field evolves, so will our job descriptions. Still, much progress remains to be made before NGS can move beyond its current status as a research tool. NGS systems need to become more automated and less expensive to operate. The analysis of complex data sets provided by these systems needs to be simplified; the interpretation of results cannot require a PhD in bioinformatics for delivery of routine results. However, as complex as it is now, NGS too will eventually become democratized by the integration of workflow automation, improvements in sequencing technology, and information technology (IT).
Speaking of which, IT itself is about to play an increasing role in how and to whom our results are delivered (section X). A rapid molecular result is only as good as the downstream action taken in the treatment and management of patients. As we speak, patients in London, along with providers, are getting “push notifications” of results from their sexual health tests, resulting in a dramatically shortened time to therapy. Cloud-based aggregation of molecular test data is providing snapshots of emerging pathogens and drug resistance in real time by collecting de-identified test data directly from testing platforms. From the respiratory cloud to the digital cloud, we are watching the emergence of a new generation of global surveillance capabilities which will be of enormous public health benefit. Rapid detection technologies are also likely to evolve in the direction of on-demand multiplexing for simultaneous detection of treatment-informing targets. The convergence of rapid molecular assays with improvements in IT to deliver actionable information to health care providers is becoming a reality.
In 2015, the White House announced a $20 million prize for innovative diagnostic tests that will lead to more precise antimicrobial therapeutic decisions. In addition, the United Kingdom has announced the Longitude Prize, a challenge with a £10 million award for developing a point-of-care diagnostic test that also will identify when antibiotics are needed and which one to use. Thus, it seems that the importance of molecular diagnostic testing is finally being appreciated at the highest levels, especially to address the global problem of antimicrobial resistance. Let’s not disappoint them.
David H. Persing, MD, PhD
Executive Vice President
Chief Medical and Technology Officer
Cepheid, Sunnyvale, California
Fred C. Tenover, PhD
Vice President, Scientific Affairs
Cepheid, Sunnyvale, California
section I
NOVEL AND EMERGING TECHNOLOGIES