Description
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.
Table of Contents
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
