Bacterial Population Genetics in Infectious Disease -- Contents -- Foreword -- Preface -- Contributors -- Part I: Concepts and Methods in Bacterial Population Genetics -- Chapter 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 SIZE n -- 1.5 FROM COALESCENT TIME TO REAL TIME -- 1.6 MUTATIONS -- 1.7 DEMOGRAPHY -- 1.8 RECOMBINATION AND GENE CONVERSION -- 1.9 SUMMARY -- REFERENCES -- Chapter 2: Linkage, Selection, and the Clonal Complex -- 2.1 INTRODUCTION-HISTORICAL OVERVIEW -- 2.2 RECOMBINATION, LINKAGE, AND SUBSTRUCTURE -- 2.3 NEUTRALITY VERSUS SELECTION -- 2.4 CLUSTERING TECHNIQUES -- REFERENCES -- Chapter 33: 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 -- REFERENCES -- Chapter 4: Genetic Recombination and Bacterial Population Structure -- 4.1 INTRODUCTION -- 4.2 CONSTRAINTS ON LGT -- 4.3 INFLUENCES 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 -- REFERENCES -- Chapter 5: Statistical Methods for Detectingthe Presence of Natural Selectionin 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 -- REFERENCES -- Chapter 6: Demographic Influences 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 -- REFERENCES -- Chapter 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 -- REFERENCES -- Chapter 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 -- REFERENCES -- Part II: Population Genetics of Select Bacterial Pathogens -- Chapter 9: Population Genetics of Bacillus :Phylogeography of Anthraxin North America -- 9.1 INTRODUCTION -- 9.2 HISTORY OF ANTHRAX IN NORTH AMERICA -- 9.3 THE ANTHRAX DISTRICTS AFTER 1944 -- 9.4 MOLECULAR GENOTYPING OF B . 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 ADDITIONAL B . ANTHRACIS GENOTYPES IN NORTH AMERICA -- 9.9 CONCLUSIONS -- REFERENCES -- Chapter 10: Population Genetics of Campylobacter -- 10.1 INTRODUCTION -- 10.2 HUMAN INFECTION -- 10.3 GENETIC STRUCTURE -- 10.4 MODELS OF CAMPYLOBACTER EVOLUTION -- 10.5 CLADES AND SPECIES -- 10.6 CONCLUSION -- REFERENCES -- Chapter 11: Population Genetics of Enterococcus -- 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 BETWEEN E. FAECIUMAND E. FAECALIS -- 11.6 WHAT IS DRIVING GD IN E. FAECIUM AND E. FAECALIS ?.

11.7 THE ACCESSORY GENOME OF E. FAECIUM AND E. FAECALIS -- 11.8 SUMMARY, CONCLUSIONS, AND FUTURE PERSPECTIVES -- REFERENCES -- Chapter 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 -- REFERENCES -- Chapter 13: Population Genetics of Neisseria 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 -- REFERENCES -- Chapter 14: Population Genetics of Pathogenic Escherichia coli -- 14.1 INTRODUCTION -- 14.2 E. COLI POPULATION GENETICS: CLONAL OR NOT CLONAL? -- 14.3 THE E. COLI PHYLOGENETIC STRUCTURE -- 14.4 THE EVOLUTIONARY HISTORY OF A HOST-SPECIFIC OBLIGATE PATHOGEN: THE SHIGELLA AND EIEC CASE STUDY -- 14.5 WHAT MAKES YOU AN OPPORTUNISTIC PATHOGEN? -- 14.6 THE VIRULENCE RESISTANCE TRADE-OFF -- 14.7 CONCLUDING REMARKS -- REFERENCES -- Chapter 15: Population Genetics of Salmonella :Selection for Antigenic Diversity -- 15.1 INTRODUCTION -- 15.2 GENERATION TIMESCALE DIVERSIFICATION -- 15.3 ANTIGENIC DIVERSITY IN SALMONELLA -- 15.4 WHY ARE DIVERSE H AND O ANTIGENS MAINTAINED IN SALMONELLA ? -- 15.5 CONCLUSIONS -- REFERENCES -- Chapter 16: Population Genetics of Staphylococcus -- 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 -- REFERENCES -- APPENDIX 1-DIVERSITY AND DIFFERENTIATION -- Chapter 17: Population Genetics of Streptococcus -- 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 -- REFERENCES -- Chapter 18: Population Genetics of Vibrios -- 18.1 INTRODUCTION -- 18.2 V. CHOLERAE -- 18.3 V. PARAHAEMOLYTICUS -- 18.4 V. VULNIFICUS -- 18.5 CONCLUSIONS -- REFERENCES -- Index -- Color plates.