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, xiiiPreface to the Second Edition, xivForeword, xviAcknowledgments, xviiRising Sun Chair, xviiiContributors, xix1 Role of the US Food and Drug Administration in the Regulation of Clinical Microbiology Devices, 1Kathleen B. Whitaker, Sally A. Hojvat, and Estelle Russek-Cohen1.1 Historical overview of in vitro diagnostics, 11.2 Current microbiology device review regulatory pathways: practical considerations, 21.3 Assay performance characteristics: “Statistics 101” for diagnostic device developers, 71.4 Common issues with new FDA submissions, 8References, 102 Commercial Blood Culture Systems and Methods, 11Michael L. Wilson, Melvin P. Weinstein, and L. Barth Reller2.2 Automated blood culture systems, 122.3 Molecular and other methods, 182.4 Future directions, 19References, 193 Rapid Devices and Instruments for the Identification of Aerobic Bacteria, 21Laura J. Chandler, P. Rocco LaSala, and Susan Whittier3.1 Introduction, 213.2 Major methods currently available, 213.3 Commercial systems for identification of Gram-positive organisms, 293.4 Commercial systems for identification of Gram-negative organisms, 383.5 Commercial methods for identification of microorganisms directly in blood culture bottles, 463.6 Commercial molecular methods for identification of bacteria isolated in culture, 483.7 Emerging technologies for the identification of organisms: mass spectrometry, 49References, 494 Rapid Devices and Instruments for the Identification of Anaerobic Bacteria, 56Christopher L. Emery, Maria D. Appleman, Jean A. Siders, and Thomas E. Davis4.1 Introduction and clinical considerations, 564.2 Steps in the diagnosis of anaerobic bacterial infections, 574.3 Commercial kit requiring 24 h of anaerobic incubation, 644.4 Commercial enzyme kits for identification after four hours of aerobic incubation, 644.5 Identification by gene sequencing, 714.6 Identification by chemical methods, 714.7 Immunodiagnostic and molecular methods for diagnosis of Clostridium difficile infection, 74References, 825 Rapid Antigen Devices and Instruments for the Detection and Identification of Viruses, 87Wallace H. Greene, Marilyn A. Menegus, and Allan L. Truant5.1 Influenza viruses, 885.2 Respiratory syncytial virus, 915.3 Immunofluorescence staining of respiratory viruses, 925.4 Herpes simplex virus, varicella zoster virus, cytomegalovirus, 935.5 Gastrointestinal viruses, 94References, 956 Molecular Tests for the Identification of Viruses, 97Scott Duong and Christine C. Ginocchio6.1 Introduction, 976.2 Respiratory viral infections, 976.3 Enteric viruses, 1056.4 Enterovirus and parechovirus, 1076.5 Herpesviruses, 1086.6 Viral infections associated with transplantation, 1096.7 Implementation and additional considerations, 112References, 1137 Viral Hepatitis, 121Emily Jeanne Cartwright and Yun F. (Wayne) Wang7.1 Introduction/background, 1217.2 Clinical manifestations, epidemiology, and diagnostic considerations by virus, 1217.3 Commercial methods, 1277.4 Summary, 131References, 1328 Human Papillomaviruses, 135N. Esther Babady8.1 Background, 1358.2 Commercial assays, 1368.3 Current challenges and future directions, 143References, 1449 Human Immunodeficiency Virus, 149Richard L. Hodinka9.1 Introduction, 1499.2 Markers of HIV infection, 1509.3 HIV screening, 1519.4 Laboratory-based immunoassays, 1529.5 Rapid, less-sophisticated immunoassays, 1549.6 Specimen matrices for HIV screening, 1579.7 Confirmatory and supplemental tests, 1579.8 Serological testing of neonates, 1599.9 p24 Antigen detection, 1609.10 Qualitative molecular detection, 1619.11 Quantification of HIV RNA, 1629.12 Phenotypic and genotypic assays for drug resistance, 165References, 16710 Chlamydia, 175Claudiu I. Bandea, Robert C. Jerris, and Carolyn M. Black10.1 Introduction, 17510.2 Epidemiology, 17610.3 Biology, 17710.4 Natural history, 17810.5 Clinical symptoms and sequelae, 17810.6 Treatment, 17910.7 Laboratory testing for C. trachomatis, 179References, 18311 Rickettsiae and Tick-Borne Diseases, 184Natalie Williams-Bouyer, Donald H. Bouyer, and Michael J. Loeffelholz11.1 Introduction, 18411.2 Overview of tick-borne diseases, 18411.3 Newly emerging tick-borne disease, 191References, 19112 Mycoplasma, 195Ken B. Waites and Cécile Bébéar12.1 Introduction and clinical considerations, 19512.2 Culture-based diagnosis, 19712.3 Serological diagnosis, 20212.4 Molecular detection systems, 20612.5 Antimicrobial susceptibility testing, 20912.6 Future directions, 210References, 21113 Commercial Methods for Identification and Susceptibility Testing of Fungi, 214Stephen A. Moser and Jason Wicker13.1 Direct examination and detection methods, 21413.2 Culture and detection, 22013.3 Identification systems, 22413.4 Molecular testing, 23613.5 Susceptibility testing, 248References, 26114 Mycobacteria, 273Xiang Yang Han14.1 Introduction, 27314.2 Specimen processing, 27314.3 Acid-fast staining reagents, 27314.4 Direct detection of mycobacteria from clinical specimens, 27414.5 Blood-culture recovery of mycobacteria, 27514.6 Mycobacteria-culturing methods and systems, 27614.7 Identification of mycobacteria, 27814.8 Susceptibility tests for mycobacteria, 28014.9 Immunodiagnosis of tuberculosis, 28114.10 Conclusion, 281References, 28115 Diagnostic Medical Parasitology, 284Lynne S. Garcia and Gary W. Procop15.1 Diagnostic parasitology testing, 28415.2 Solicitation of product information, 28715.3 Specimen collection systems, 28715.4 Fresh stool specimen collection, 28715.5 Preservation of stool specimens, 28915.6 Intestinal tract specimens (stool), 29415.7 Ova and parasite examination, 29715.8 Molecular methods, 29715.9 Other diagnostic methods, 30315.10 Collection of specimens from other body sites, 30315.11 Blood collection, 30315.12 Malaria rapid diagnostic tests, 305References, 30716 Molecular Microbiology, 309Raghava Potula and Yi-Wei Tang16.1 Introduction, 30916.2 Specimen processing and nucleic acid extraction platforms, 30916.3 Amplification methods and platforms, 31016.4 Amplicon detection and identification platforms, 31316.5 Future directions, 31616.6 Summary, 316References, 31617 Automated Immunoassay Analyzers, 319Richard L. Hodinka and Matthew J. BinnickerReferences, 33318 Molecular Typing Instruments and Methods, 336Ruth Ann Luna18.1 Introduction, 33618.2 Background, 33618.3 Current molecular typing methodologies, 33718.4 Comparison of typing techniques, 34018.5 Summary, 343References, 34319 Commercial Methods in Clinical Veterinary Microbiology, 346Thomas J. Inzana, Xiang-Jin Meng, Tanja Opriessnig, and Lora Ballweber19.1 Collection and transportation of clinical samples, 34719.2 Selection of diagnostic laboratories and tests, 34819.3 Pathology and histopathology, 34919.4 Quality control of veterinary diagnostic assays: sensitivity and specitivity, 34919.5 Veterinary virology, 35019.6 Veterinary bacteriology, 35919.7 Veterinary mycology, 36519.8 Veterinary parasitology, 366Acknowledgements, 371References, 37120 Microbiology Laboratory Information Systems, 377Raymond D. Aller and Vincent Salazar20.1 In general, microbiology laboratory information systems fit one of three categories, 37720.2 What are the key features of software to support management of microbiology?, 37820.3 Microbiology information systems have evolved over several decades, 38020.4 Criteria for comparison of current systems, 38220.5 Specialized software, 38220.6 Selecting an information system for your laboratory, 38320.7 Cases, 38320.8 Management of the laboratory information system, 38420.9 Personnel management, 384References, 38521 Emerging Infectious Diseases, 386Brett Laurence, Julie Collins, Carolyn Fernandes, Rafik Samuel, and Byungse Suh21.1 Introduction, 38621.2 Plasmodium knowlesi, 38621.3 Clostridium difficile, 38921.4 Pandemic H1N1 influenza, 39121.5 Escherichia coli O104:H4, 39321.6 Cryptococcus gattii, 39421.7 Borrelia miyamotoi, 39621.8 Rickettsia parkeri, 39721.9 Mycobacterium lepromatosis, 39821.10 Bocavirus, 40021.11 Human metapneumovirus, 40021.12 Severe fever with thrombocytopenia syndrome virus, 40221.13 Zika virus, 403References, 40422 Automated and Manual Systems for Antimicrobial Susceptibility Testing of Bacteria, 414Alan T. Evangelista and James A. Karlowsky22.1 Introduction, 41422.2 Evaluation of commercial AST performance, 41522.3 Automated broth microdilution AST systems, 41522.4 Semiautomated and manual broth microdilution AST systems, 42222.5 Manual and semiautomated agar antimicrobial gradient diffusion and disk diffusion susceptibility tests, 42322.6 Phenotypic detection of antimicrobial resistance using chromogenic media, 42522.7 Genotypic detection of antimicrobial resistance determinants in positive blood cultures, 42722.8 Next generation methods for antimicrobial susceptibility testing, 428References, 43023 Bioterrorism, 433James W. Snyder and Michael A. Pentella23.1 Introduction, 43323.2 History of bioterrorism, 43323.3 Bioterrorism in the future, 43423.4 Laboratory Response Network, 43523.5 Rapid methods, 43623.6 Conclusion, 436References, 43624 Clinical Microbiology: Looking Ahead, 438Natalie N. Whitfield, Raquel M. Martinez, and Donna M. Wolk24.1 Introduction, 43824.2 Connectivity between extraction and amplification platforms, 43924.3 Polymerase chain reaction and RT-PCR: detection and characterization, 44124.4 Other amplification methods, 44724.5 Probe technology, 44824.6 Mass spectrometry, 44924.7 DNA sequencing, 45124.8 Emerging technology, 45224.9 Other strategies and concepts that will impact clinical microbiology, 45924.10 Some new responsibilities for the coming years, 46024.11 Summary, 462References, 463International Section, 473Introduction, 473Allan L. Truant, Yi-Wei Tang, Ken B. Waites, Cécile Bébéar, and Robert Rennie25 Clinical Microbiology In Vitro Diagnostic Medical Devices in Argentina: Regulatory Requirements And Product Information, 475Marcela Echavarria and Mariela Aranda25.1 History, 47525.2 Regulation of clinical microbiology in vitro diagnostic medical devices in Argentina, 477References, 48126 Clinical Microbiology In Vitro Diagnostics in Australia: Regulatory Requirements and Product Information, 483Carola Venturini, Vitali Sintchenko, and Jonathan R. Iredell26.1 The Therapeutic Goods Administration, 48326.2 National Pathology Accreditation Advisory Council, 48626.3 National Association of Testing Authorities, 48626.4 RCPA quality assurance programs, 48726.5 Manufacturers and suppliers of IVDs, 487References, 48927 Clinical Microbiology In Vitro Diagnostic Devices in Canada: Regulatory Requirements and Product Information, 491James A. KarlowskyReferences, 49328 Clinical Microbiology In Vitro Diagnostics in China: Regulatory Requirements and Product Information, 494Shangwei Wu, Weiwei Zhao, Hongbo Li, and Dongfeng Tan28.1 The regulatory requirements for clinical microbiology in vitro diagnostics products in China, 49428.2 IVD product review: devices and instruments, 495References, 50629 Clinical Microbiology In Vitro Diagnostic Medical Devices in France: Regulatory Requirements and Product Information, 507Frederique Gouriet29.1 Regulatory requirements, 50729.2 European Directive 98/79/EC, 50729.3 Directive 98/79/EC in France, 51429.4 The implications of the regulatory level authorities, 51429.5 Assessment procedures, 514Reference, 51430 Clinical Microbiology In Vitro Diagnostic Medical Devices in India: Regulatory Requirements and Product Information, 515Abhijit ChaudhuryReferences, 519Websites for reference, 51931 Clinical Microbiology In Vitro Diagnostics in Italy: Regulatory Requirements and Product Information, 520Simone Ambretti, Mariapaola Landini, Davide Gibellini, and Tiziana Lazzarotto31.1 Introduction, 52031.2 National classification of medical devices, 52031.3 Assessment procedures for IVD medical devices, 52131.4 Registration for manufacturers of IVD medical devices, 524Bibliography, 52432 Clinical Microbiology In Vitro Diagnostics in Japan: Regulatory Requirements and Product Information, 525Koji Kawakami and Yukie Yamauchi32.1 The regulatory structure of pharmaceuticals and clinical trials in Japan, 52532.2 The regulatory structure of in vitro diagnostic testing in Japan, 52532.3 Marketing of IVD reagents in Japan, 52632.4 Clinical efficiency study/correlation study, 52732.5 Marketing approval, 53032.6 National Health Insurance coverage of IVD reagents, 530Bibliography, 53033 Clinical Microbiology In Vitro Diagnostic Medical Devices in the Republic of Korea: Regulatory Requirements and Product Information, 531Jeong Hwan ShinBibliography, 53434 Clinical Microbiology In Vitro Diagnostic Medical Devices in South Africa: Regulatory Requirements and Product Information, 535Abdool Kader Peer34.1 Regulatory requirements, 53534.2 Product information, 536Reference, 53635 Clinical Microbiology In Vitro Diagnostic Medical Devices in the UK: Regulatory Requirements and Product Information, 537Timothy D. McHugh, Jim F. Huggett, and Simon Rattenbury35.1 Background, 53735.2 Definitions, 53735.3 Conformity assessment, 54535.4 Other considerations, 545Bibliography, 545Appendix: Manufacturers, Distributors and Vendors, 546Raquel DeLeon-Gonsalves and Allan L. TruantIndex, 581

"The second edition of the Manual of Commercial Methods in Clinical Microbiology: International Edition is intended to be a current reference of commercially available tests, devices, and instruments used in clinical microbiology. The first edition contained 18 chapters that focused on US regulatory issues, rapid detection systems for bacteria and viruses, blood culture systems, diagnostic parasitology, automated serology, susceptibility testing, molecular methods, laboratory information systems, and specific pathogens such as HIV, Chlamydia, Mycoplasma, Mycobacterium, and emerging organisms. The second edition has been greatly updated and expanded to 35 chapters including new chapters on virology, viral hepatitis, automated molecular typing systems, specific pathogens such as human papillomavirus and rickettsiae, tickborne diseases, and bioterrorism. Additionally, there are 11 new chapters containing a synopsis of international clinical microbiology products and the regulatory requirements of selected countries including several in Europe and Asia, as well as Canada, Australia, South Africa, and Argentina.The content of this book focuses primarily on human clinical microbiology; however, both the first and second editions include a chapter on Commercial Methods in Clinical Veterinary Microbiology coauthored by microbiologists from 3 colleges of veterinary medicine. That chapter is an informed summary that reveals issues associated with the use of human diagnostic systems in veterinary microbiology and includes references that document the accuracy of such systems when used to analyze samples of various animal origins....Although the majority of the book focuses on available tests for human pathogens, a reasonable amount of the reference information will be useful for veterinary diagnostic microbiologists. The inclusion of the chapter on veterinary clinical veterinary microbiology integrates the reference material in an informative manner. It is a comprehensive reference of available commercial diagnostic systems for laboratory managers seeking tools for enhancing efficiency and accuracy." (Journal of the American Veterinary Medical Association, 15th Dec 2017)