Manual of Commercial Methods in Clinical Microbiology

651 Pages·2016·71.21 MB·English

by  A. L. Truant

Manual of Commercial Methods in Clinical Microbiology
Dedication
This book is dedicated to the memory of Stephen D. Allen, MD, gentleman, scientist, innovator,
pathologist, clinical microbiologist and anaerobist, author and teacher, mentor, colleague, Hoosier,
and friend.
Manual of Commercial
Methods in Clinical
Microbiology
International Edition
Editor‐in‐Chief
Allan L. Truant
Associate Editors
Yi‐Wei Tang
Ken B. Waites
Cécile Bébéar
Robert P. Rennie
Second Edition
Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved
Published by John Wiley & Sons, Inc., Hoboken, New Jersey
Published simultaneously in Canada
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Library of Congress Cataloging‐in‐Publication Data:
Names: Truant, Allan L., editor.
Title: Manual of Commercial Methods in Clinical Microbiology / Allan L. Truant, editor-in-chief.
Other titles: Commercial methods in clinical microbiology
Description: 2nd edition. | Hoboken, New Jersey : John Wiley & Sons, Inc., [2016] | Includes bibliographical
references and index.
Identifiers: LCCN 2015047743 (print) | LCCN 2015048299 (ebook) | ISBN 9781118131121 (cloth) |
ISBN 9781119021865 (pdf) | ISBN 9781119021841 (epub)
Subjects: | MESH: Equipment and Supplies | Microbiological Techniques | Catalogs, Commercial | Catalogs
Classification: LCC QR46 (print) | LCC QR46 (ebook) | NLM QW 26 | DDC 616.9/041–dc23
LC record available at http://lccn.loc.gov/2015047743
Cover credit: Getty/nobeastsofierce
Set in 10.5/12.5pt Minion by SPi Global, Pondicherry, India
10 9 8 7 6 5 4 3 2 1
Contents
Important Notice, xiii 2.2 Automated blood culture systems, 12
2.2.1 BacT/Alert, 13
Preface to the Second Edition, xiv
2.2.2 BACTEC 9000 series, 15
Foreword, xvi
2.2.3 VersaTREK blood culture system, 17
Acknowledgments, xvii 2.3 Molecular and other methods, 18
Rising Sun Chair, xviii 2.4 Future directions, 19
References, 19
Contributors, xix
3 Rapid Devices and Instruments for the
1 Role of the US Food and Drug Administration in the Identification of Aerobic Bacteria, 21
Regulation of Clinical Microbiology Devices, 1 Laura J. Chandler, P. Rocco LaSala, and
Kathleen B. Whitaker, Sally A. Hojvat, and Susan Whittier
Estelle Russek‐Cohen 3.1 Introduction, 21
1.1 Historical overview of in vitro diagnostics, 1 3.2 Major methods currently available, 21
1.1.1 Device classification via the MDA of 1976, 1 3.2.1 Conventional identification methods:
1.2 Current microbiology device review regulatory phenotypic testing with biochemicals, 21
pathways: practical considerations, 2 3.2.2 Molecular identification methods, 21
1.2.1 Premarket notification 510(k), 2 3.2.3 Fatty acid analysis with gas chromatography, 22
1.2.2 De novo petitions, 3 3.2.4 Protein mass spectrometry, 22
1.2.3 Premarket application, 4 3.2.5 Automated systems for the phenotypic
1.2.4 Major elements of an IVD submission to the identification of aerobic bacteria, 22
FDA, 5 3.3 Commercial systems for identification of
1.3 Assay performance characteristics: “Statistics 101” Gram‐positive organisms, 29
for diagnostic device developers, 7 3.3.1 Commercial identification systems for
1.3.1 Sensitivity/specificity, 7 aerobic Gram‐positive cocci, 29
1.3.2 Prevalence, negative predictive values, and 3.3.2 Commercial identification systems
positive predictive values, 7 for aerobic Gram‐positive Bacilli, 37
1.4 Common issues with new FDA submissions, 8 3.4 Commercial systems for identification of
1.4.1 IVD labeling, 9 Gram‐negative organisms, 38
1.4.2 New technologies, 9 3.4.1 Manual systems, 38
1.4.3 How have FDA regulations and policies 3.4.2 Automated systems for the identification of
fostered preparedness for new and Gram‐negative bacteria, 38
emerging pathogens and other public health 3.4.3 Identification methods for selected members
emergencies?, 9 of the family Enterobacteriaceae, 40
References, 10 3.4.4 Identification of selected Gram‐negative
organisms (non‐Enterobacteriaceae), 42
2 Commercial Blood Culture Systems and 3.4.5 Identification of selected fastidious
Methods, 11 Gram‐negative organisms, 44
Michael L. Wilson, Melvin P. Weinstein, and 3.5 Commercial methods for identification of
L. Barth Reller microorganisms directly in blood culture
2.1 Manual blood cultures, 11 bottles, 46
2.1.1 SEPTI‐CHEK, 11 3.5.1 BD GeneOhm StaphSR
2.1.2 Oxoid Signal, 12 (Becton Dickinson), 46
2.1.3 Isolator, 12 3.5.2 Xpert MRSA/SA, 46
v
vi Contents
3.5.3 PNA‐FISH probes, 47 5 Rapid Antigen Devices and Instruments for the
3.5.4 Verigene Staphylococcus Blood Detection and Identification of Viruses, 87
Culture (BC‐S) nucleic acid test, 47 Wallace H. Greene, Marilyn A. Menegus,
3.5.5 Biofire BCID Panel, 48 and Allan L. Truant
3.6 Commercial molecular methods 5.1 Influenza viruses, 88
for identification of bacteria isolated 5.1.1 BD Veritor System for rapid detection
in culture, 48 of influenza A and B, 90
3.6.1 GenProbe hybridization probes, 49 5.1.2 Sofia Influenza A & B, 90
3.7 Emerging technologies for the identification of 5.1.3 3M Rapid Detection Flu A+B Test, 91
organisms: mass spectrometry, 49 5.2 Respiratory syncytial virus, 91
3.7.1 MALDI‐ToF/MS, 49 5.3 Immunofluorescence staining of respiratory
References, 49 viruses, 92
5.4 Herpes simplex virus, varicella
4 Rapid Devices and Instruments for the
zoster virus, cytomegalovirus, 93
Identification of Anaerobic Bacteria, 56
5.5 Gastrointestinal viruses, 94
Christopher L. Emery, Maria D. Appleman,
References, 95
Jean A. Siders, and Thomas E. Davis
4.1 Introduction and clinical considerations, 56
6 Molecular Tests for the Identification of Viruses, 97
4.2 Steps in the diagnosis of anaerobic bacterial
Scott Duong and Christine C. Ginocchio
infections, 57
6.1 Introduction, 97
4.2.1 Collection, transport, and
6.2 Respiratory viral infections, 97
storage of specimens, 58
6.2.1 Background, 97
4.2.2 Incubation, inspection and
6.2.2 Detection of respiratory viruses, 98
subculture of colonies, 59
6.2.3 Commercially available
4.2.3 Presumptive identification of anaerobes, 60
in vitro diagnostic tests, 100
4.2.4 Phenotypic identification procedures, 61
6.2.4 Laboratory developed, investigational,
4.2.5 Alternative procedures for characterization
and research‐use only tests, 103
of anaerobes, 62
6.3 Enteric viruses, 105
4.3 Commercial kit requiring
6.3.1 Background, 105
24 h of anaerobic incubation, 64
6.3.2 Molecular assays for enteric viruses, 106
4.4 Commercial enzyme kits for identification after
6.4 Enterovirus and parechovirus, 107
four hours of aerobic incubation, 64
6.4.1 Background, 107
4.4.1 RapID ANA II, 65
6.4.2 Assays for enterovirus and
4.4.2 Vitek 2 ANC, 67
parechovirus, 107
4.4.3 Microscan Rapid Anaerobe Panel, 67
6.5 Herpesviruses, 108
4.4.4 Rapid ID 32A, 68
6.5.1 Background, 108
4.4.5 BBL Crystal Anaerobe
6.5.2 Molecular assays for qualitative detection
identification system, 69
of herpesviruses, 109
4.4.6 Interpretation of identification results
6.6 Viral infections associated with
obtained using commercial kits, 70
transplantation, 109
4.5 Identification by gene sequencing, 71
6.6.1 Background, 109
4.6 Identification by chemical methods, 71
6.6.2 Molecular assays for transplantation
4.6.1 Mass spectrometry systems, 71
monitoring, 111
4.6.2 Matrix‐assisted laser desorption ionization
6.7 Implementation and additional
time of flight, 72
considerations, 112
4.6.3 PCR combined with ESI/MS, 73
References, 113
4.6.4 Gas chromatography, 73
4.6.5 The Biolog AN MicroPlate, 74 7 Viral Hepatitis, 121
4.7 Immunodiagnostic and molecular methods for Emily Jeanne Cartwright and Yun F. (Wayne) Wang
diagnosis of Clostridium difficile infection, 74 7.1 Introduction/background, 121
4.7.1 Tests for glutamate dehydrogenase, 75 7.2 Clinical manifestations, epidemiology, and
4.7.2 Enzyme immunoassays for diagnostic considerations by virus, 121
toxin A and toxin B, 78 7.2.1 Hepatitis A virus, 121
4.7.3 Molecular tests, 81 7.2.2 Hepatitis B virus, 123
References, 82 7.2.3 Hepatitis D virus, 123
Contents vii
7.2.4 Hepatitis C virus, 124 10.5 Clinical symptoms and sequelae, 178
7.2.5 Hepatitis E virus, 126 10.6 Treatment, 179
7.3 Commercial methods, 127 10.7 Laboratory testing for
7.3.1 Hepatitis A virus, 128 C. trachomatis, 179
7.3.2 Hepatitis B virus, 128 References, 183
7.3.3 Hepatitis D virus, 129
11 Rickettsiae and Tick‐Borne Diseases, 184
7.3.4 Hepatitis C virus, 130
Natalie Williams‐Bouyer, Donald H. Bouyer,
7.3.5 Hepatitis E virus, 131
and Michael J. Loeffelholz
7.3.6 Approaches for global health, 131
11.1 Introduction, 184
7.4 Summary, 131
11.2 Overview of tick‐borne diseases, 184
References, 132
11.2.1 Ticks as vectors for infectious disease
8 Human Papillomaviruses, 135 transmission, 184
N. Esther Babady 11.2.2 Rickettsial infections, 184
8.1 Background, 135 11.2.3 Other tick‐borne diseases, 186
8.1.1 Low‐risk HPV and related 11.3 Newly emerging tick‐borne disease, 191
infections, 135 11.3.1 Novel phlebovirus, 191
8.1.2 High‐risk HPV and related References, 191
infections, 135
12 Mycoplasma, 195
8.1.3 Testing utility and recommendations, 136
Ken B. Waites and Cécile Bébéar
8.2 Commercial assays, 136
12.1 Introduction and clinical considerations, 195
8.2.1 Non‐nucleic acid amplification tests, 136
12.1.1 Mycoplasmas and ureaplasmas as
8.2.2 Nucleic acid amplification tests, 138
human pathogens, 195
8.2.3 Molecular genotyping assays, 141
12.1.2 Indications for diagnostic testing, 196
8.3 Current challenges and future directions, 143
12.2 Culture‐based diagnosis, 197
8.3.1 Current challenges, 143
12.2.1 Specimens appropriate for culture, 197
8.3.2 Future directions, 144
12.2.2 Specimen collection and transport, 198
References, 144
12.2.3 Commercial growth media
9 Human Immunodeficiency Virus, 149
and diagnostic kits, 198
Richard L. Hodinka
12.3 Serological diagnosis, 202
9.1 Introduction, 149
12.3.1 Cold agglutinins, 202
9.2 Markers of HIV infection, 150
12.3.2 Complement fixation, 203
9.3 HIV screening, 151
12.3.3 Commercial serological assay formats, 203
9.4 Laboratory‐based immunoassays, 152
12.3.4 Indirect immunofluorescence assays, 203
9.5 Rapid, less‐sophisticated immunoassays, 154
12.3.5 Particulate antigen–antibody assays, 203
9.6 Specimen matrices for HIV screening, 157
12.3.6 Enzyme‐linked immunosorbent
9.7 Confirmatory and
assays, 205
supplemental tests, 157
12.3.7 Genital mycoplasma assays, 205
9.8 Serological testing of neonates, 159
12.4 Molecular detection systems, 206
9.9 p24 Antigen detection, 160
12.4.1 Commercial molecular assays for
9.10 Qualitative molecular detection, 161
M. pneumoniae, 206
9.11 Quantification of HIV RNA, 162
12.4.2 Commercial molecular assays
9.12 Phenotypic and genotypic assays for drug
for genital mycoplasmas and
resistance, 165
ureaplasmas, 208
9.12.1 Phenotypic assays, 166
12.5 Antimicrobial susceptibility testing, 209
9.12.2 Genotypic assays, 166
12.6 Future directions, 210
9.12.3 Summary, 167
References, 211
References, 167
10 Chlamydia, 175 13 Commercial Methods for Identification
Claudiu I. Bandea, Robert C. Jerris, and Susceptibility Testing of Fungi, 214
and Carolyn M. Black Stephen A. Moser and Jason Wicker
10.1 Introduction, 175 13.1 Direct examination and
10.2 Epidemiology, 176 detection methods, 214
10.3 Biology, 177 13.1.1 Cryptococcus spp., 214
10.4 Natural history, 178 13.1.2 Candida spp., 217
viii Contents
13.1.3 Aspergillus, 218 14.4.1 GeneXpert MTB/RIF Test, 274
13.1.4 1,3‐β‐d‐glucan, 219 14.4.2 AMPLIFIED MTD2 Test, 274
13.1.5 Endemic mycoses, 219 14.4.3 COBAS TaqMan MTB Test, 274
13.2 Culture and detection, 220 14.4.4 LCx Mycobacterium tuberculosis
13.2.1 Fungal blood cultures, 220 assay, 275
13.2.2 Manual systems, 220 14.4.5 Clinical evaluation of direct tuberculosis
13.2.3 Continuously monitored automated tests, 275
blood‐culture systems, 222 14.5 Blood‐culture recovery of mycobacteria, 275
13.3 Identification systems, 224 14.6 Mycobacteria‐culturing methods and
13.3.1 Media for isolation and systems, 276
identification, 224 14.6.1 BD Septi‐Chek AFB System, 276
13.3.2 Rapid identification and screens, 226 14.6.2 BACTEC 460TB System, 276
13.3.3 Commercial kits for identification 14.6.3 BACTEC MGIT 960 System, 276
of yeasts and yeast‐like 14.6.4 BacT/Alert 3D System, 277
organisms, 229 14.6.5 VersaTREK System, 277
13.3.4 Automated systems, 230 14.6.6 Clinical evaluation of mycobacterial
13.4 Molecular testing, 236 recovery systems, 278
13.4.1 Accuprobe, 236 14.7 Identification of mycobacteria, 278
13.4.2 Candida peptide nucleic acid 14.7.1 Biochemicals, reagents, and
fluorescence in situ hybridization, 237 media, 279
13.4.3 PCR‐electrospray ionization/MS, 240 14.7.2 Nucleic acid probe from
13.4.4 LightCycler SeptiFast Test Gen‐Probe, 279
MGRADE, 240 14.7.3 16S rRNA gene sequencing by
13.4.5 Dermatophyte PCR kit, 241 MicroSEQ 500, 279
13.4.6 MycAssay, 241 14.7.4 Other identification methods, 279
13.4.7 Luminex xTAG technology, 243 14.8 Susceptibility tests for mycobacteria, 280
13.4.8 SepsiTest and Universal Microbe 14.8.1 Traditional assays, 280
Detection systems, 243 14.8.2 BBL Sensi‐Disk, 280
13.4.9 Pyrosequencing, 244 14.8.3 Automated broth culturing and testing
13.4.10 Fast MicroSeq D2 LSU rDNA Fungal systems, 280
Identification Kit, 245 14.8.4 Susceptibility tests for rapidly growing
13.4.11 VYOO system, 246 mycobacteria, 281
13.4.12 DNA extraction/PCR 14.8.5 Susceptibility by Etest, 281
amplification, 246 14.8.6 Gene‐sequence‐based drug resistance
13.5 Susceptibility testing, 248 tests, 281
13.5.1 Sensititre YeastOne, 248 14.9 Immunodiagnosis of tuberculosis, 281
13.5.2 Etest, 250 14.10 Conclusion, 281
13.5.3 Agar disk diffusion, 253 References, 281
13.5.4 Neo‐Sensitabs tablet diffusion
15 Diagnostic Medical Parasitology, 284
assay, 257
Lynne S. Garcia and Gary W. Procop
13.5.5 Screening with CHROMagar, 258
15.1 Diagnostic parasitology testing, 284
13.5.6 Vitek 2, 258
15.1.1 General comments, 284
13.5.7 ATB Fungus 2, 260
15.1.2 Specific options, 285
13.5.8 MALDI‐ToF/MS, 260
15.1.3 Diagnostic medical parasitology, 287
13.5.9 Miscellaneous susceptibility
15.2 Solicitation of product
methods, 261
information, 287
References, 261
15.3 Specimen collection systems, 287
14 Mycobacteria, 273 15.4 Fresh stool specimen collection, 287
Xiang Yang Han 15.5 Preservation of stool specimens, 289
14.1 Introduction, 273 15.5.1 Formalin, 289
14.2 Specimen processing, 273 15.5.2 Merthiolate–iodine–formalin, 292
14.3 Acid‐fast staining reagents, 273 15.5.3 Sodium acetate–acetic acid–
14.4 Direct detection of mycobacteria from formalin, 292
clinical specimens, 274 15.5.4 Schaudinn’s fluid, 292