Manual of Commercial Methods in Clinical Microbiology

The Manual of Commercial Methods in Clinical Microbiology 2nd Edition, International Edition reviews in detail the current state of the art in each of the disciplines of clinical microbiology, and reviews the sensitivities, specificities and predictive values, and subsequently the effectiveness, of commercially available methods – both manual and automated. This text allows the user to easily summarize the available methods in any particular field, or for a specific pathogen – for example, what to use for an Influenza test, a Legionella test, or what instrument to use for identification or for an antibiotic susceptibility test. The Manual of Commercial Methods in Clinical Microbiology, 2nd Edition, International Edition presents a wealth of relevant information to clinical pathologists, directors and supervisors of clinical microbiology, infectious disease physicians, point-of-care laboratories, professionals using industrial applications of diagnostic microbiology and other healthcare providers. The content will allow professionals to analyze all commercially available methods to determine which works best in their particular laboratory, hospital, clinic, or setting. Updated to appeal to an international audience, The Manual of Commercial Methods in Clinical Microbiology, 2nd Edition, International Edition is an invaluable reference to those in the health science and medical fields.

Table of Contents:
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