Your essential guide to the design, operation, management, and health care integration of the modern molecular microbiology laboratory. This comprehensive resource offers definitive guidance on the operational and interpretive aspects of clinical molecular microbiology. Tailored for medical laboratory professionals, it provides practical "how-to" guidance for establishing, maintaining, and advancing molecular microbiology testing services and details the unique expertise required to support infectious disease diagnostics. The Manual offers a clear and practical roadmap for topics ranging from…mehr
Your essential guide to the design, operation, management, and health care integration of the modern molecular microbiology laboratory. This comprehensive resource offers definitive guidance on the operational and interpretive aspects of clinical molecular microbiology. Tailored for medical laboratory professionals, it provides practical "how-to" guidance for establishing, maintaining, and advancing molecular microbiology testing services and details the unique expertise required to support infectious disease diagnostics. The Manual offers a clear and practical roadmap for topics ranging from selecting appropriate technologies, instruments, and analytic pipelines to navigating complex interpretive challenges and positioning diagnostic testing services for future clinical and population health needs. Beginning with foundational technologies and their clinical applications, this book offers accessible overviews of each method's potential, implications, and emerging roles. Subsequent sections dive meticulously into details of laboratory setup, design, and operations, empowering readers with hands-on insights for routine and advanced testing methods, including advanced sequencing technologies. It also tackles the nuanced challenges of interpreting and reporting results from cutting-edge diagnostics, including those focused on antimicrobial resistance and metagenomics. The final section explores the broader impact of molecular microbiology on value-based care, with discussions on clinical management, laboratory stewardship, and the future of molecular diagnostics in public health. Comprehensive and forward-looking, the Manual of Molecular Microbiology equips readers with both foundational knowledge and practical expertise, making it an indispensable reference for today's clinical laboratory professionals.
Randall T. Hayden, St. Jude Children's Research Hospital, Memphis, TN, USA. Karen C. Carroll, The Johns Hopkins University School of Medicine, Baltimore, MD, USA. John P. Dekker, National Institutes of Health, Bethesda, MD, USA. Alexander J. McAdam, Boston Children's Hospital, Boston, MA, USA. Donna M. Wolk, Geisinger, Diagnostic Medicine Institute, Danville, PA; The Geisinger Commonwealth School of Medicine, Scranton, PA, USA.
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Contributors vii Preface xi Author and Editor Conflicts of Interest xiii Section I Technologies and Clinical Applications 1 1 Real-Time PCR 3 Jocelyn Hauser, Eleanor Powell, And N. Esther Babady 2 Digital PCR 18 Alexandra S. Whale, Denise M. O'sullivan, And Jim F. Huggett 3 Isothermal Nucleic Acid Amplification Technologies and CRISPR-Cas-Based Nucleic Acid Detection Strategies for Infectious Diseases Diagnostics 30 Benjamin M. Liu 4 Strain Typing (Bacterial, Viral, Fungal, and Mycobacterial) 48 Helena M.b. Seth-smith, Ashley M. Rooney, And Adrian Egli 5 Antimicrobial Resistance Genotyping 74 Heba H. Mostafa and Patricia J. Simner 6 Broad-Range Diagnostic Amplification and Detection 94 Øyvind Kommedal and Ruben Dyrhovden 7 Characterization of the Human Microbiome in Health and Disease 110 Chin Yee Tan and Neeraj K. Surana 8 Host Transcriptomics: Clinical Applications 127 Asuncion Mejias and Octavio Ramilo 9 Organism Transcriptomics 137 Aryeh Solomon and Roi Avraham Section II Design, Implementation, and Operations: General 145 10 Laboratory Design for Molecular Technologies 147 Erin Graf 11 Sample Selection, Preservation, Transport, and Storage 153 James J. Dunn and Erin H. Graf 12 Nucleic Acid Extraction and Purity, Including Performance Considerations of Different Extraction Chemistries 164 Bijal A. Parikh and Neil W. Anderson 13 Selection of Nucleic AcidAmplification Systems: In Vitro Diagnostic Tests 174 Cecilia M. Thompson, Heba H. Mostafa, And Kyle G. Rodino 14 Selection of Nucleic Acid Amplification Systems: Laboratory Developed Tests 180 Meghan W. Starolis 15 Verification, Validation, and Quality Assurance for Nucleic Acid Amplification Tests 189 Paige M.k. Larkin, Ninad Mehta, And Rebekah M. Martin 16 Molecular Microbiology Standardization 203 Jerry Boonyaratanakornkit Section III Design, Implementation, and Operations: Sequencing-Based Technologies 215 17 Sequencing Platforms 217 Hege Vangstein Aamot, Jacob Moran-Gilad, and John W. A. Rossen 18 Nucleic Acid Extraction and Next-Generation Sequencing Library Prep 232 Abraham G. Moller, David C. Gaston, And Augusto Dulanto Chiang 19 Considerations of Depth, Coverage, and Other Read Quality Metrics 244 Derek D. N. Smith and Andrea D. Tyler 20 Pipelines and Databases-Genome Assembly and Analysis from Bacterial Isolates 262 Natalie Scherff, Hauke Tönnies, Gabriel Elias Wagner, and Alexander Mellmann 21 Analysis of Metagenomic Next-Generation Sequencing Data Obtained from Clinical Samples 278 Brian O'donovan, Steve Miller, And Katrina Kalantar 22 Pipelines and Databases- Microbiome Analysis 296 Jonathan Sanders, Huang Lin, Qiyun Zhu, And James T. Morton 23 Validation and Quality Control of Next-Generation Sequencing Assays 314 Robert Schlaberg 24 Application-Specific Considerations for Clinical and Epidemiologic Sequencing 335 Lydia A. Krasilnikova, Mohamad R. A. Sater, and Melis N. Anahtar 25 Generation and Analysis of Host Transcriptomics and Development of Host-Response Based Signatures 352 Emily C. Lydon, Katrina L. Kalantar, And Charles R. Langelier Section IV Special Challenges in Result Interpretation and Reporting 361 26 Bacterial Antimicrobial Susceptibility Testing 363 Romney Humphries 27 Public Health Surveillance 378 Allen Bateman and Sara J. Blosser 28 Considerations in Molecular Strain Typing for Bacteria, Fungi, and Viruses 391 S. Wesley Long 29 Considerations in Result Interpretation and Reporting for Untargeted and Broadly Targeted Pathogen Detection Sequencing Assays 398 Heather L. Glasgow and Steve Miller 30 Considerations in Result Interpretation and Reporting for Microbiome Analysis 407 Arryn Craney 31 Clinical Interpretation of Ultrasensitive Molecular Assays 422 Daniel A. Ortiz and Blake W. Buchan Section V Molecular Microbiology's Impact on Value-based Care 439 32 Clinical Interpretation and Diagnostic Management 441 Swathi Gowtham 33 The Role of Clinical Microbiology in Antimicrobial and Diagnostic Stewardship 456 Amy J. Mathers 34 Evidence-Based Assay Deployment- Support of Population Health Initiatives 467 Susan M. Benson 35 Evidence-Based Assay Deployment- Precision Medicine Initiatives 475 Julie Hirschhorn and Haluk Kavus 36 Evidence-Based Assay Deployment- Infrastructure, Documentation, and Strategy 483 Natalie N. Whitfield and Donna M. Wolk Index 499
Contributors vii Preface xi Author and Editor Conflicts of Interest xiii Section I Technologies and Clinical Applications 1 1 Real-Time PCR 3 Jocelyn Hauser, Eleanor Powell, And N. Esther Babady 2 Digital PCR 18 Alexandra S. Whale, Denise M. O'sullivan, And Jim F. Huggett 3 Isothermal Nucleic Acid Amplification Technologies and CRISPR-Cas-Based Nucleic Acid Detection Strategies for Infectious Diseases Diagnostics 30 Benjamin M. Liu 4 Strain Typing (Bacterial, Viral, Fungal, and Mycobacterial) 48 Helena M.b. Seth-smith, Ashley M. Rooney, And Adrian Egli 5 Antimicrobial Resistance Genotyping 74 Heba H. Mostafa and Patricia J. Simner 6 Broad-Range Diagnostic Amplification and Detection 94 Øyvind Kommedal and Ruben Dyrhovden 7 Characterization of the Human Microbiome in Health and Disease 110 Chin Yee Tan and Neeraj K. Surana 8 Host Transcriptomics: Clinical Applications 127 Asuncion Mejias and Octavio Ramilo 9 Organism Transcriptomics 137 Aryeh Solomon and Roi Avraham Section II Design, Implementation, and Operations: General 145 10 Laboratory Design for Molecular Technologies 147 Erin Graf 11 Sample Selection, Preservation, Transport, and Storage 153 James J. Dunn and Erin H. Graf 12 Nucleic Acid Extraction and Purity, Including Performance Considerations of Different Extraction Chemistries 164 Bijal A. Parikh and Neil W. Anderson 13 Selection of Nucleic AcidAmplification Systems: In Vitro Diagnostic Tests 174 Cecilia M. Thompson, Heba H. Mostafa, And Kyle G. Rodino 14 Selection of Nucleic Acid Amplification Systems: Laboratory Developed Tests 180 Meghan W. Starolis 15 Verification, Validation, and Quality Assurance for Nucleic Acid Amplification Tests 189 Paige M.k. Larkin, Ninad Mehta, And Rebekah M. Martin 16 Molecular Microbiology Standardization 203 Jerry Boonyaratanakornkit Section III Design, Implementation, and Operations: Sequencing-Based Technologies 215 17 Sequencing Platforms 217 Hege Vangstein Aamot, Jacob Moran-Gilad, and John W. A. Rossen 18 Nucleic Acid Extraction and Next-Generation Sequencing Library Prep 232 Abraham G. Moller, David C. Gaston, And Augusto Dulanto Chiang 19 Considerations of Depth, Coverage, and Other Read Quality Metrics 244 Derek D. N. Smith and Andrea D. Tyler 20 Pipelines and Databases-Genome Assembly and Analysis from Bacterial Isolates 262 Natalie Scherff, Hauke Tönnies, Gabriel Elias Wagner, and Alexander Mellmann 21 Analysis of Metagenomic Next-Generation Sequencing Data Obtained from Clinical Samples 278 Brian O'donovan, Steve Miller, And Katrina Kalantar 22 Pipelines and Databases- Microbiome Analysis 296 Jonathan Sanders, Huang Lin, Qiyun Zhu, And James T. Morton 23 Validation and Quality Control of Next-Generation Sequencing Assays 314 Robert Schlaberg 24 Application-Specific Considerations for Clinical and Epidemiologic Sequencing 335 Lydia A. Krasilnikova, Mohamad R. A. Sater, and Melis N. Anahtar 25 Generation and Analysis of Host Transcriptomics and Development of Host-Response Based Signatures 352 Emily C. Lydon, Katrina L. Kalantar, And Charles R. Langelier Section IV Special Challenges in Result Interpretation and Reporting 361 26 Bacterial Antimicrobial Susceptibility Testing 363 Romney Humphries 27 Public Health Surveillance 378 Allen Bateman and Sara J. Blosser 28 Considerations in Molecular Strain Typing for Bacteria, Fungi, and Viruses 391 S. Wesley Long 29 Considerations in Result Interpretation and Reporting for Untargeted and Broadly Targeted Pathogen Detection Sequencing Assays 398 Heather L. Glasgow and Steve Miller 30 Considerations in Result Interpretation and Reporting for Microbiome Analysis 407 Arryn Craney 31 Clinical Interpretation of Ultrasensitive Molecular Assays 422 Daniel A. Ortiz and Blake W. Buchan Section V Molecular Microbiology's Impact on Value-based Care 439 32 Clinical Interpretation and Diagnostic Management 441 Swathi Gowtham 33 The Role of Clinical Microbiology in Antimicrobial and Diagnostic Stewardship 456 Amy J. Mathers 34 Evidence-Based Assay Deployment- Support of Population Health Initiatives 467 Susan M. Benson 35 Evidence-Based Assay Deployment- Precision Medicine Initiatives 475 Julie Hirschhorn and Haluk Kavus 36 Evidence-Based Assay Deployment- Infrastructure, Documentation, and Strategy 483 Natalie N. Whitfield and Donna M. Wolk Index 499
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