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9780470600115

Bacterial Population Genetics in Infectious Disease

by ; ;
  • ISBN13:

    9780470600115

  • ISBN10:

    047060011X

  • Format: eBook
  • Copyright: 2010-03-01
  • Publisher: Wiley-Blackwell
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Summary

This book is a unique synthesis of the major concepts and methods in bacterial population genetics in infectious disease, a field that is now about 35 yrs old. Emphasis is given to explaining population-level processes that shape genetic variation in bacterial populations and statistical methods of analysis of bacterial genetic data. A "how to" of bacterial population genetics, which covers an extremely large range of organisms Expanding area of science due to high-throughput genome sequencing of bacterial pathogens Covers both fundamental approaches to analyzing bacterial population structures with conceptual background in bacterial population biology Detailed treatment of statistical methods Glossary of terms in bacterial population genetics

Table of Contents

Foreword
Preface
Contributors
Concepts and Methods in Bacterial Population Genetics
The Coalescent of Bacterial Populations
Background and Motivation
Population Reproduction Models
Time and the Effective Population Size
The Genealogy of a Sample of Size n
From Coalescent Time to Real Time
Mutations
Demography
Recombination and Gene Conversion
Summary
Linkage, Selection, and the Clonal Complex
Introduction-Historical Overview
Recombination, Linkage, and Substructure
Neutrality versus Selection
Clustering Techniques
Sequence-Based Analysis of Bacterial Population Structures
Introduction
Alignments
Phylogenetic Methods
Measures of Uncertainty
Beyond the Tree Model
Genetic Recombination and Bacterial Population Structure
Introduction
Constraints on LGT
Infl uences of LGT on Sequence Analyses
The Detection of Individual LGT Events
The Estimation of Homologous Recombination Rates
Properly Accounting for LGT During Sequence Analyses
Questions Relating Directly to LGT
Statistical Methods for Detecting the Presence of Natural Selection in Bacterial Populations
Introduction
Natural Selection
Statistical Methods for Detecting the Presence of Natural Selection
Statistical Methods for Bacterial Populations
An Example
Discussion and Perspective
Demographic Infl uences on Bacterial Population Structure
Bacterial Population Size
Measures of Genetic Diversity
The Concept of Effective Population Size
Inferring Past Demography from Genetic Sequence Data
Population Subdivision
What is a Bacterial Population?
Conclusion
Population Genomics of Bacteria
Introduction
Classical Bacterial Population Genetics
The Genomics Era
Bacterial Population Genomics
Next-Gen Bacterial Population Genomics
Next-Gen Genomics Technology
Next-Gen Genomic Data Analysis
Conclusions/Future Prospects
The Use of MLVA and SNP Analysis to Study the Population Genetics of Pathogenic Bacteria
Introduction
MLVA and Other DNA Fragment-Based Methods
SNP and DNA Sequence-Based Methods
Conclusion
Population Genetics of Select Bacterial Pathogens
Population Genetics of Bacillus : Phylogeography of Anthrax in North America
Introduction
History of Anthrax in North America
The Anthrax Districts after 1944
Molecular Genotyping of B. anthracis
Genotypes within the Anthrax Districts in North America
Phylogenetic Resolution within the WNA Lineage
Phylogeographic Resolution within the Ames Lineage
Additional B. anthracis Genotypes in North America
Conclusions
Population Genetics of Campylobacter
Introduction
Human Infection
Genetic Structure
Models of Campylobacter Evolution
Clades and Species
Conclusion
Population Genetics of Enterococcus
Introduction
Antibiotic Resistance
Vancomycin Resistance
VRE: A Zoonosis or Not?
Population Structure and Genetic Evolution: Similarities and Differences Between E. faecium and E. faecalis
What Is Driving GD in E. faecium and E. faecalis ?
The Accessory Genome of E. faecium and E. faecalis
Summary, Conclusions, and Future Perspectives
Population Biology of Lyme Borreliosis Spirochetes
Introduction
Genome Organization of LB Spirochetes
Genotyping of LB Spirochetes and Phylogenetic Tools
Population Biology and Evolution of LB Spirochetes
Do LB Species Exist?
Future Research Avenues
Population Genetics of Neisseria meningitidis
Introduction
A Brief History of Typing of Meningococci
Species Separation
Sampling Strategies
The Clonal Complexes of Meningococci
Forces Shaping the Meningococcal Metalineage
Virulence, a Mysterious Trait
Population Effect of Meningococcal Vaccines
Antibiotic Resistance and Meningococcal Lineages
Concluding Remarks
Population Genetics of Pathogenic Escherichia coli
Introduction
E. coli Population Genetics: Clonal or not Clonal?
The E. coli Phylogenetic Structure
The Evolutionary History of a Host-Specifi c Obligate Pathogen: The Shigella and EIEC Case Study
What Makes You an Opportunistic Pathogen?
The Virulence Resistance Trade-off
Concluding Remarks
Population Genetics of Salmonella : Selection for Antigenic Diversity
Introduction
Generation Timescale Diversifi cation
Antigenic Diversity in Salmonella
Why Are Diverse H and O Antigens Maintained in Salmonella ?
Conclusions
Population Genetics of Staphylococcus
Introduction
Overview of The Staphylococcal Population Structure
Staphylococcal Population Structure in Specific Disease Contexts
Origin and Maintenance of Staphylococcal Genetic Variation
Macroevolutionary Considerations and Concluding Remarks
Appendix 1-Diversity and Differentiation
Population Genetics of Streptococcus
Habitats, Transmission, and Disease
Classical Strain Typing
Multilocus Sequence Typing (MLST) Based on Housekeeping Genes
Species Boundaries and Gene Flow
Niche-driving Genes
Bacterial Population Dynamics and Selection
Machinery of Genetic Change, Revisited
Population Genetics of Vibrios
Introduction
V. cholerae
V. parahaemolyticus
V. vulnificus
Conclusions
References
Index
Table of Contents provided by Publisher. All Rights Reserved.

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