Important Notice, xiii
Preface to the Second Edition, xiv
Foreword, xvi
Acknowledgments, xvii
Rising Sun Chair, xviii
Contributors, xix
1 Role of the US Food and Drug Administration in the Regulation of Clinical Microbiology Devices, 1
Kathleen B. Whitaker, Sally A. Hojvat, and Estelle Russek-Cohen
1.1 Historical overview of in vitro diagnostics, 1
1.2 Current microbiology device review regulatory pathways: practical considerations, 2
1.3 Assay performance characteristics: Statistics 101 for diagnostic device developers, 7
1.4 Common issues with new FDA submissions, 8
References, 10
2 Commercial Blood Culture Systems and Methods, 11
Michael L. Wilson, Melvin P. Weinstein, and L. Barth Reller
2.2 Automated blood culture systems, 12
2.3 Molecular and other methods, 18
2.4 Future directions, 19
References, 19
3 Rapid Devices and Instruments for the Identification of Aerobic Bacteria, 21
Laura J. Chandler, P. Rocco LaSala, and Susan Whittier
3.1 Introduction, 21
3.2 Major methods currently available, 21
3.3 Commercial systems for identification of Gram-positive organisms, 29
3.4 Commercial systems for identification of Gram-negative organisms, 38
3.5 Commercial methods for identification of microorganisms directly in blood culture bottles, 46
3.6 Commercial molecular methods for identification of bacteria isolated in culture, 48
3.7 Emerging technologies for the identification of organisms: mass spectrometry, 49
References, 49
4 Rapid Devices and Instruments for the Identification of Anaerobic Bacteria, 56
Christopher L. Emery, Maria D. Appleman, Jean A. Siders, and Thomas E. Davis
4.1 Introduction and clinical considerations, 56
4.2 Steps in the diagnosis of anaerobic bacterial infections, 57
4.3 Commercial kit requiring 24 h of anaerobic incubation, 64
4.4 Commercial enzyme kits for identification after four hours of aerobic incubation, 64
4.5 Identification by gene sequencing, 71
4.6 Identification by chemical methods, 71
4.7 Immunodiagnostic and molecular methods for diagnosis of Clostridium difficile infection, 74
References, 82
5 Rapid Antigen Devices and Instruments for the Detection and Identification of Viruses, 87
Wallace H. Greene, Marilyn A. Menegus, and Allan L. Truant
5.1 Influenza viruses, 88
5.2 Respiratory syncytial virus, 91
5.3 Immunofluorescence staining of respiratory viruses, 92
5.4 Herpes simplex virus, varicella zoster virus, cytomegalovirus, 93
5.5 Gastrointestinal viruses, 94
References, 95
6 Molecular Tests for the Identification of Viruses, 97
Scott Duong and Christine C. Ginocchio
6.1 Introduction, 97
6.2 Respiratory viral infections, 97
6.3 Enteric viruses, 105
6.4 Enterovirus and parechovirus, 107
6.5 Herpesviruses, 108
6.6 Viral infections associated with transplantation, 109
6.7 Implementation and additional considerations, 112
References, 113
7 Viral Hepatitis, 121
Emily Jeanne Cartwright and Yun F. (Wayne) Wang
7.1 Introduction/background, 121
7.2 Clinical manifestations, epidemiology, and diagnostic considerations by virus, 121
7.3 Commercial methods, 127
7.4 Summary, 131
References, 132
8 Human Papillomaviruses, 135
N. Esther Babady
8.1 Background, 135
8.2 Commercial assays, 136
8.3 Current challenges and future directions, 143
References, 144
9 Human Immunodeficiency Virus, 149
Richard L. Hodinka
9.1 Introduction, 149
9.2 Markers of HIV infection, 150
9.3 HIV screening, 151
9.4 Laboratory-based immunoassays, 152
9.5 Rapid, less-sophisticated immunoassays, 154
9.6 Specimen matrices for HIV screening, 157
9.7 Confirmatory and supplemental tests, 157
9.8 Serological testing of neonates, 159
9.9 p24 Antigen detection, 160
9.10 Qualitative molecular detection, 161
9.11 Quantification of HIV RNA, 162
9.12 Phenotypic and genotypic assays for drug resistance, 165
References, 167
10 Chlamydia, 175
Claudiu I. Bandea, Robert C. Jerris, and Carolyn M. Black
10.1 Introduction, 175
10.2 Epidemiology, 176
10.3 Biology, 177
10.4 Natural history, 178
10.5 Clinical symptoms and sequelae, 178
10.6 Treatment, 179
10.7 Laboratory testing for C. trachomatis, 179
References, 183
11 Rickettsiae and Tick-Borne Diseases, 184
Natalie Williams-Bouyer, Donald H. Bouyer, and Michael J. Loeffelholz
11.1 Introduction, 184
11.2 Overview of tick-borne diseases, 184
11.3 Newly emerging tick-borne disease, 191
References, 191
12 Mycoplasma, 195
Ken B. Waites and Cécile Bébéar
12.1 Introduction and clinical considerations, 195
12.2 Culture-based diagnosis, 197
12.3 Serological diagnosis, 202
12.4 Molecular detection systems, 206
12.5 Antimicrobial susceptibility testing, 209
12.6 Future directions, 210
References, 211
13 Commercial Methods for Identification and Susceptibility Testing of Fungi, 214
Stephen A. Moser and Jason Wicker
13.1 Direct examination and detection methods, 214
13.2 Culture and detection, 220
13.3 Identification systems, 224
13.4 Molecular testing, 236
13.5 Susceptibility testing, 248
References, 261
14 Mycobacteria, 273
Xiang Yang Han
14.1 Introduction, 273
14.2 Specimen processing, 273
14.3 Acid-fast staining reagents, 273
14.4 Direct detection of mycobacteria from clinical specimens, 274
14.5 Blood-culture recovery of mycobacteria, 275
14.6 Mycobacteria-culturing methods and systems, 276
14.7 Identification of mycobacteria, 278
14.8 Susceptibility tests for mycobacteria, 280
14.9 Immunodiagnosis of tuberculosis, 281
14.10 Conclusion, 281
References, 281
15 Diagnostic Medical Parasitology, 284
Lynne S. Garcia and Gary W. Procop
15.1 Diagnostic parasitology testing, 284
15.2 Solicitation of product information, 287
15.3 Specimen collection systems, 287
15.4 Fresh stool specimen collection, 287
15.5 Preservation of stool specimens, 289
15.6 Intestinal tract specimens (stool), 294
15.7 Ova and parasite examination, 297
15.8 Molecular methods, 297
15.9 Other diagnostic methods, 303
15.10 Collection of specimens from other body sites, 303
15.11 Blood collection, 303
15.12 Malaria rapid diagnostic tests, 305
References, 307
16 Molecular Microbiology, 309
Raghava Potula and Yi-Wei Tang
16.1 Introduction, 309
16.2 Specimen processing and nucleic acid extraction platforms, 309
16.3 Amplification methods and platforms, 310
16.4 Amplicon detection and identification platforms, 313
16.5 Future directions, 316
16.6 Summary, 316
References, 316
17 Automated Immunoassay Analyzers, 319
Richard L. Hodinka and Matthew J. Binnicker
References, 333
18 Molecular Typing Instruments and Methods, 336
Ruth Ann Luna
18.1 Introduction, 336
18.2 Background, 336
18.3 Current molecular typing methodologies, 337
18.4 Comparison of typing techniques, 340
18.5 Summary, 343
References, 343
19 Commercial Methods in Clinical Veterinary Microbiology, 346
Thomas J. Inzana, Xiang-Jin Meng, Tanja Opriessnig, and Lora Ballweber
19.1 Collection and transportation of clinical samples, 347
19.2 Selection of diagnostic laboratories and tests, 348
19.3 Pathology and histopathology, 349
19.4 Quality control of veterinary diagnostic assays: sensitivity and specitivity, 349
19.5 Veterinary virology, 350
19.6 Veterinary bacteriology, 359
19.7 Veterinary mycology, 365
19.8 Veterinary parasitology, 366
Acknowledgements, 371
References, 371
20 Microbiology Laboratory Information Systems, 377
Raymond D. Aller and Vincent Salazar
20.1 In general, microbiology laboratory information systems fit one of three categories, 377
20.2 What are the key features of software to support management of microbiology?, 378
20.3 Microbiology information systems have evolved over several decades, 380
20.4 Criteria for comparison of current systems, 382
20.5 Specialized software, 382
20.6 Selecting an information system for your laboratory, 383
20.7 Cases, 383
20.8 Management of the laboratory information system, 384
20.9 Personnel management, 384
References, 385
21 Emerging Infectious Diseases, 386
Brett Laurence, Julie Collins, Carolyn Fernandes, Rafik Samuel, and Byungse Suh
21.1 Introduction, 386
21.2 Plasmodium knowlesi, 386
21.3 Clostridium difficile, 389
21.4 Pandemic H1N1 influenza, 391
21.5 Escherichia coli O104:H4, 393
21.6 Cryptococcus gattii, 394
21.7 Borrelia miyamotoi, 396
21.8 Rickettsia parkeri, 397
21.9 Mycobacterium lepromatosis, 398
21.10 Bocavirus, 400
21.11 Human metapneumovirus, 400
21.12 Severe fever with thrombocytopenia syndrome virus, 402
21.13 Zika virus, 403
References, 404
22 Automated and Manual Systems for Antimicrobial Susceptibility Testing of Bacteria, 414
Alan T. Evangelista and James A. Karlowsky
22.1 Introduction, 414
22.2 Evaluation of commercial AST performance, 415
22.3 Automated broth microdilution AST systems, 415
22.4 Semiautomated and manual broth microdilution AST systems, 422
22.5 Manual and semiautomated agar antimicrobial gradient diffusion and disk diffusion susceptibility tests, 423
22.6 Phenotypic detection of antimicrobial resistance using chromogenic media, 425
22.7 Genotypic detection of antimicrobial resistance determinants in positive blood cultures, 427
22.8 Next generation methods for antimicrobial susceptibility testing, 428
References, 430
23 Bioterrorism, 433
James W. Snyder and Michael A. Pentella
23.1 Introduction, 433
23.2 History of bioterrorism, 433
23.3 Bioterrorism in the future, 434
23.4 Laboratory Response Network, 435
23.5 Rapid methods, 436
23.6 Conclusion, 436
References, 436
24 Clinical Microbiology: Looking Ahead, 438
Natalie N. Whitfield, Raquel M. Martinez, and Donna M. Wolk
24.1 Introduction, 438
24.2 Connectivity between extraction and amplification platforms, 439
24.3 Polymerase chain reaction and RT-PCR: detection and characterization, 441
24.4 Other amplification methods, 447
24.5 Probe technology, 448
24.6 Mass spectrometry, 449
24.7 DNA sequencing, 451
24.8 Emerging technology, 452
24.9 Other strategies and concepts that will impact clinical microbiology, 459
24.10 Some new responsibilities for the coming years, 460
24.11 Summary, 462
References, 463
International Section, 473
Introduction, 473
Allan L. Truant, Yi-Wei Tang, Ken B. Waites, Cécile Bébéar, and Robert Rennie
25 Clinical Microbiology In Vitro Diagnostic Medical Devices in Argentina: Regulatory Requirements And Product Information, 475
Marcela Echavarria and Mariela Aranda
25.1 History, 475
25.2 Regulation of clinical microbiology in vitro diagnostic medical devices in Argentina, 477
References, 481
26 Clinical Microbiology In Vitro Diagnostics in Australia: Regulatory Requirements and Product Information, 483
Carola Venturini, Vitali Sintchenko, and Jonathan R. Iredell
26.1 The Therapeutic Goods Administration, 483
26.2 National Pathology Accreditation Advisory Council, 486
26.3 National Association of Testing Authorities, 486
26.4 RCPA quality assurance programs, 487
26.5 Manufacturers and suppliers of IVDs, 487
References, 489
27 Clinical Microbiology In Vitro Diagnostic Devices in Canada: Regulatory Requirements and Product Information, 491
James A. Karlowsky
References, 493
28 Clinical Microbiology In Vitro Diagnostics in China: Regulatory Requirements and Product Information, 494
Shangwei Wu, Weiwei Zhao, Hongbo Li, and Dongfeng Tan
28.1 The regulatory requirements for clinical microbiology in vitro diagnostics products in China, 494
28.2 IVD product review: devices and instruments, 495
References, 506
29 Clinical Microbiology In Vitro Diagnostic Medical Devices in France: Regulatory Requirements and Product Information, 507
Frederique Gouriet
29.1 Regulatory requirements, 507
29.2 European Directive 98/79/EC, 507
29.3 Directive 98/79/EC in France, 514
29.4 The implications of the regulatory level authorities, 514
29.5 Assessment procedures, 514
Reference, 514
30 Clinical Microbiology In Vitro Diagnostic Medical Devices in India: Regulatory Requirements and Product Information, 515
Abhijit Chaudhury
References, 519
Websites for reference, 519
31 Clinical Microbiology In Vitro Diagnostics in Italy: Regulatory Requirements and Product Information, 520
Simone Ambretti, Mariapaola Landini, Davide Gibellini, and Tiziana Lazzarotto
31.1 Introduction, 520
31.2 National classification of medical devices, 520
31.3 Assessment procedures for IVD medical devices, 521
31.4 Registration for manufacturers of IVD medical devices, 524
Bibliography, 524
32 Clinical Microbiology In Vitro Diagnostics in Japan: Regulatory Requirements and Product Information, 525
Koji Kawakami and Yukie Yamauchi
32.1 The regulatory structure of pharmaceuticals and clinical trials in Japan, 525
32.2 The regulatory structure of in vitro diagnostic testing in Japan, 525
32.3 Marketing of IVD reagents in Japan, 526
32.4 Clinical efficiency study/correlation study, 527
32.5 Marketing approval, 530
32.6 National Health Insurance coverage of IVD reagents, 530
Bibliography, 530
33 Clinical Microbiology In Vitro Diagnostic Medical Devices in the Republic of Korea: Regulatory Requirements and Product Information, 531
Jeong Hwan Shin
Bibliography, 534
34 Clinical Microbiology In Vitro Diagnostic Medical Devices in South Africa: Regulatory Requirements and Product Information, 535
Abdool Kader Peer
34.1 Regulatory requirements, 535
34.2 Product information, 536
Reference, 536
35 Clinical Microbiology In Vitro Diagnostic Medical Devices in the UK: Regulatory Requirements and Product Information, 537
Timothy D. McHugh, Jim F. Huggett, and Simon Rattenbury
35.1 Background, 537
35.2 Definitions, 537
35.3 Conformity assessment, 545
35.4 Other considerations, 545
Bibliography, 545
Appendix: Manufacturers, Distributors and Vendors, 546
Raquel DeLeon-Gonsalves and Allan L. Truant
Index, 581
