Manual of Commercial Methods in Clinical Microbiology

The Editor-in-Chief, Allan L. Truant is a Professor of Pathology and Laboratory Medicine, Microbiology and Immunology, and Internal Medicine at the Lewis Katz School of Medicine at Temple University, and Director of Clinical Microbiology, Immunology and Virology Laboratories at the Temple University Hospital in Philadelphia, PA.

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