Manual of Molecular Microbiology

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