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 organismsExpanding area of science due to high-throughput genome sequencing of bacterial pathogensCovers both fundamental approaches to analyzing bacterial population structures with conceptual background in bacterial population biologyDetailed treatment of statistical methods
Foreword.
Preface.
Contributors.
Part I Concepts and Methods in Bacterial Population Genetics.
1 The Coalescent of Bacterial Populations.
1.1 Background and Motivation.
1.2 Population Reproduction Models.
1.3 Time and the Effective Population Size.
1.4 The Genealogy of a Sample of Sizen.
1.5 From Coalescent Time to Real Time.
1.6 Mutations.
1.7 Demography.
1.8 Recombination and Gene Conversion.
1.9 Summary.
2 Linkage, Selection, and the Clonal Complex.
2.1 IntroductionHistorical Overview.
2.2 Recombination, Linkage, and Substructure.
2.3 Neutrality versus Selection.
2.4 Clustering Techniques.
3 Sequence-Based Analysis of Bacterial Population Structures.
3.1 Introduction.
3.2 Alignments.
3.3 Phylogenetic Methods.
3.4 Measures of Uncertainty.
3.5 Beyond the Tree Model.
4 Genetic Recombination and Bacterial Population Structure.
4.1 Introduction.
4.2 Constraints on LGT.
4.3 Infl uences of LGT on Sequence Analyses.
4.4 The Detection of Individual LGT Events.
4.5 The Estimation of Homologous Recombination Rates.
4.6 Properly Accounting for LGT During Sequence Analyses.
4.7 Questions Relating Directly to LGT.
5 Statistical Methods for Detecting the Presence of Natural Selection in Bacterial Populations.
5.1 Introduction.
5.2 Natural Selection.
5.3 Statistical Methods for Detecting the Presence of Natural Selection.
5.4 Statistical Methods for Bacterial Populations.
5.5 An Example.
5.6 Discussion and Perspective.
6 Demographic Infl uences on Bacterial Population Structure.
6.1 Bacterial Population Size.
6.2 Measures of Genetic Diversity.
6.3 The Concept of Effective Population Size.
6.4 Inferring Past Demography from Genetic Sequence Data.
6.5 Population Subdivision.
6.6 What is a Bacterial Population?
6.7 Conclusion.
7 Population Genomics of Bacteria.
7.1 Introduction.
7.2 Classical Bacterial Population Genetics.
7.3 The Genomics Era.
7.4 Bacterial Population Genomics.
7.5 Next-Gen Bacterial Population Genomics.
7.6 Next-Gen Genomics Technology.
7.7 Next-Gen Genomic Data Analysis.
7.8 Conclusions/Future Prospects.
8 The Use of MLVA and SNP Analysis to Study the Population Genetics of Pathogenic Bacteria.
8.1 Introduction.
8.2 MLVA and Other DNA Fragment-Based Methods.
8.3 SNP and DNA Sequence-Based Methods.
8.4 Conclusion.
Part II Population Genetics of Select Bacterial Pathogens.
9 Population Genetics ofBacillus: Phylogeography of Anthrax in North America.
9.1 Introduction.
9.2 History of Anthrax in North America.
9.3 The Anthrax Districts after 1944.
9.4 Molecular Genotyping ofB. anthracis.
9.5 Genotypes within the Anthrax Districts in North America.
9.6 Phylogenetic Resolution within the WNA Lineage.
9.7 Phylogeographic Resolution within the Ames Lineage.
9.8 AdditionalB. anthracis Genotypes in North America.
9.9 Conclusions.
10 Population Genetics ofCampylobacter.
10.1 Introduction.
10.2 Human Infection.
10.3 Genetic Structure.
10.4 Models ofCampylobacter Evolution.
10.5 Clades and Species.
10.6 Conclusion.
11 Population Genetics ofEnterococcus.
11.1 Introduction.
11.2 Antibiotic Resistance.
11.3 Vancomycin Resistance.
11.4 VRE: A Zoonosis or Not?
11.5 Population Structure and Genetic Evolution: Similarities and Differences BetweenE. faecium andE. faecalis.
11.6 What Is Driving GD inE. faecium andE. faecalis?
11.7 The Accessory Genome ofE. faecium andE. faecalis.
11.8 Summary, Conclusions, and Future Perspectives.
12 Population Biology of Lyme Borreliosis Spirochetes.
12.1 Introduction.
12.2 Genome Organization of LB Spirochetes.
12.3 Genotyping of LB Spirochetes and Phylogenetic Tools.
12.4 Population Biology and Evolution of LB Spirochetes.
12.5 Do LB Species Exist?
12.6 Future Research Avenues.
13 Population Genetics ofNeisseria meningitidis.
13.1 Introduction.
13.2 A Brief History of Typing of Meningococci.
13.3 Species Separation.
13.4 Sampling Strategies.
13.5 The Clonal Complexes of Meningococci.
13.6 Forces Shaping the Meningococcal Metalineage.
13.7 Virulence, a Mysterious Trait.
13.8 Population Effect of Meningococcal Vaccines.
13.9 Antibiotic Resistance and Meningococcal Lineages.
13.10 Concluding Remarks.
14 Population Genetics of PathogenicEscherichia coli.
14.1 Introduction.
14.2E. coli Population Genetics: Clonal or not Clonal?
14.3 TheE. coli Phylogenetic Structure.
14.4 The Evolutionary History of a Host-Specifi c Obligate Pathogen: TheShigella and EIEC Case Study.
14.5 What Makes You an Opportunistic Pathogen?
14.6 The Virulence Resistance Trade-off.
14.7 Concluding Remarks.
15 Population Genetics ofSalmonella: Selection for Antigenic Diversity.
15.1 Introduction.
15.2 Generation Timescale Diversifi cation.
15.3 Antigenic Diversity inSalmonella.
15.4 Why Are Diverse H and O Antigens Maintained inSalmonella?
15.5 Conclusions.
16 Population Genetics ofStaphylococcus.
16.1 Introduction.
16.2 Overview of The Staphylococcal Population Structure.
16.3 Staphylococcal Population Structure in Specific Disease Contexts.
16.4 Origin and Maintenance of Staphylococcal Genetic Variation.
16.5 Macroevolutionary Considerations and Concluding Remarks.
Appendix 1Diversity and Differentiation.
17 Population Genetics ofStreptococcus.
17.1 Habitats, Transmission, and Disease.
17.2 Classical Strain Typing.
17.3 Multilocus Sequence Typing (MLST) Based on Housekeeping Genes.
17.4 Species Boundaries and Gene Flow.
17.5 Niche-driving Genes.
17.6 Bacterial Population Dynamics and Selection.
17.7 Machinery of Genetic Change, Revisited.
18 Population Genetics of Vibrios.
18.1 Introduction.
18.2V. cholerae.
18.3V. parahaemolyticus .
18.4V. vulnificus.
18.5 Conclusions.
References.
Index.
