Preface
Acknowledgments
Chapter 1. Introduction and Historical Perspective
1.1. Introduction to Molecular Epidemiology
1.2. Historical Perspectives
1.3. Landmark Molecular Epidemiologic Studies
1.4. What Makes Modern Molecular Tools Different?
1.5. How Modern Molecular Epidemiology Differs From Traditional Epidemiologic Studies Using Laboratory Methods
1.6. Overview of this Textbook
Chapter 2. How Molecular Tools Enhance Epidemiologic Studies
2.1. What is Misclassification Bias?
2.2. How Reducing Misclassification via Molecular Tools Enhances Epidemiologic Studies
2.3. Ways Molecular Tools Advance the Science of Epidemiology
Chapter 3. Applications of Molecular Tools to Infectious Disease Epidemiology
3.1. Outbreak Investigation
3.2. Surveillance
3.3. Transmission System
3.4. Increase Understanding of the Epidemiology of Infectious Diseases
3.5. Identify Previously Unknown or Uncultivable Infectious Microbes
3.6. Provide Insight into Pathogen Gene Function and Host–Pathogen Interaction
Chapter 4. A Primer of Epidemiologic Study Designs
4.1. Experiment
4.2. Cohort Study
4.3. Cross-Sectional Study
4.4. Case–Control Study
4.5. Ecologic Study
4.6. Biases
Chapter 5. A Primer of Molecular Biology
5.1. Central Dogma and Some Caveats
5.2. Material Tested Using Molecular Tools
5.3. Gene Variants, SNPS, Insertions, Deletions, and Frameshift Mutations
5.4. Extrachromosomal Elements and Transposons
5.5. Recombination
5.6. Horizontal Gene Transfer
5.7. An Introduction to Common Molecular Methods
5.8. Sorting by Size, Charge, and Other Characteristics
5.9. Polymerase Chain Reaction
5.10. Sequencing
5.11. Hybridization/antigen–Antibody Reactions
Chapter 6. Molecular Tools
6.1. Molecular Tools and Epidemiology
6.2. The “OMICS¿
6.3. Genomics
6.4. Transcriptomics
6.5. Proteomics
6.6. Metabolomics
6.7. Epigenomics
6.8. Interactomics
6.9. Metagenomics and Metatranscriptomics
6.10. Selecting the Correct Technique for the Research Question
Chapter 7. Omics Analyses in Molecular Epidemiologic Studies
7.1. Bioinformatics, Genetic Sequences, and Molecular Epidemiology
7.2. Assemble Gene Sequences
7.3. Compare and Analyze Genetic Sequence
7.4. Gene Mapping
7.5. Bioinformatics, Microarrays, and Application to Molecular Epidemiology
7.6. Determining Similarity and Relatedness
7.7. Analyses of Microbiome Data
7.8. Documenting Genetic, Molecular, and Epidemiologic Data Sets
Chapter 8. Determining the Reliability and Validity and Interpretation of a Measure in the Study Populations
8.1. Identify All Data Handling and Processing Steps, from Specimen Collection to Recording Data in a Database
8.2. Assess the Potential for Error at Each Step, and the Error Tolerance
8.3. Determine the Reliability of the Selected Measure Across a Range of Values
8.4. Determine the Validity of the Selected Measure
8.5. Determine the Intralaboratory and Interlaboratory Reliability
8.6. Determine the Appropriate Interpretation of the Measurement
8.7. Using Stored Materials
Chapter 9. Designing and Implementing a Molecular Epidemiologic Study
9.1. Operationalizing a Research Question
9.2. Study Design Trade-Offs Associated with Including Molecular Tools
9.3. Constraints on the Study Protocol Imposed by Molecular Testing
9.4. Choosing Measures of Exposure and Outcome
9.5. Using a Commercial Kit
9.6. Molecular Fingerprinting
Chapter 10. Study Conduct
10.1. Documentation of All Protocols and Operating Procedures
10.2. Regular Meetings with Study Personnel
10.3. Training and Retraining of Study Personnel
10.4. Quality Control and Quality Assurance
10.5. Specimen Handling and Storage
10.6. Interim Data Analysis
10.7. Types of Interim Data Analysis
Chapter 11. Think About Data Analysis When Planning a Study
11.1. Data Analysis and Study Design
11.2. Estimating the Required Sample Size and (Conversely) Determining if the Conducted Study was Sufficiently Large
11.3. Data Structure
11.4. Data Cleaning
11.5. General Analytic Strategies
11.6. Molecular Level
11.7. Interactions of Microbes and Host
11.8. Human–Human Interactions
11.9. Interactions of Human Populations
Chapter 12. Human and Animal Subject Protection, Biorepositories, Biosafety Considerations, and Professional Ethics
12.1. What is Research?
12.2. Why Researchers are Obligated to Behave Ethically
12.3. Protection of Human Subjects
12.4. Studies Using Previously Collected Data
12.5. Ethical Issues Associated With Biorepositories
12.6. Public Data Access
12.7. Shipping of Materials Between Institutions
12.8. Protection of Animal Subjects
12.9. Biological Safety
12.10. Professional Ethics
Chapter 13. Future Directions
13.1. Methodological Development
13.2. Surveillance
13.3. Transmission
13.4. Interactions
13.5. Closing Thoughts
Index
