Bacterial Population Genetics in Infectious Disease

Bacterial Population Genetics in Infectious Disease......Page 2
Contents......Page 10
Foreword......Page 14
Preface......Page 18
Contributors......Page 20
Part I: Concepts and Methods in Bacterial Population Genetics......Page 22
1.1 BACKGROUND AND MOTIVATION......Page 24
1.2 POPULATION REPRODUCTION MODELS......Page 25
1.3 TIME AND THE EFFECTIVE POPULATION SIZE......Page 26
1.4 THE GENEALOGY OF A SAMPLE OF SIZE n......Page 29
1.6 MUTATIONS......Page 30
1.7 DEMOGRAPHY......Page 32
1.8 RECOMBINATION AND GENE CONVERSION......Page 34
1.9 SUMMARY......Page 38
REFERENCES......Page 39
2.1 INTRODUCTION—HISTORICAL OVERVIEW......Page 40
2.2 RECOMBINATION, LINKAGE, AND SUBSTRUCTURE......Page 41
2.3 NEUTRALITY VERSUS SELECTION......Page 46
2.4 CLUSTERING TECHNIQUES......Page 50
REFERENCES......Page 54
3.1 INTRODUCTION......Page 58
3.2 ALIGNMENTS......Page 59
3.3 PHYLOGENETIC METHODS......Page 64
3.4 MEASURES OF UNCERTAINTY......Page 70
3.5 BEYOND THE TREE MODEL......Page 74
REFERENCES......Page 79
4.1 INTRODUCTION......Page 82
4.2 CONSTRAINTS ON LGT......Page 83
4.3 INFLUENCES OF LGT ON SEQUENCE ANALYSES......Page 86
4.4 THE DETECTION OF INDIVIDUAL LGT EVENTS......Page 87
4.5 THE ESTIMATION OF HOMOLOGOUS RECOMBINATION RATES......Page 95
4.6 PROPERLY ACCOUNTING FOR LGT DURING SEQUENCE ANALYSES......Page 96
4.7 QUESTIONS RELATING DIRECTLY TO LGT......Page 97
REFERENCES......Page 101
5.1 INTRODUCTION......Page 108
5.3 STATISTICAL METHODS FOR DETECTING THE PRESENCE OF NATURAL SELECTION......Page 109
5.4 STATISTICAL METHODS FOR BACTERIAL POPULATIONS......Page 115
5.5 AN EXAMPLE......Page 119
5.6 DISCUSSION AND PERSPECTIVE......Page 120
REFERENCES......Page 121
6.1 BACTERIAL POPULATION SIZE......Page 124
6.2 MEASURES OF GENETIC DIVERSITY......Page 125
6.3 THE CONCEPT OF EFFECTIVE POPULATION SIZE......Page 127
6.4 INFERRING PAST DEMOGRAPHY FROM GENETIC SEQUENCE DATA......Page 132
6.5 POPULATION SUBDIVISION......Page 133
6.6 WHAT IS A BACTERIAL POPULATION?......Page 135
6.7 CONCLUSION......Page 136
REFERENCES......Page 137
7.1 INTRODUCTION......Page 142
7.2 CLASSICAL BACTERIAL POPULATION GENETICS......Page 143
7.3 THE GENOMICS ERA......Page 152
7.4 BACTERIAL POPULATION GENOMICS......Page 153
7.5 NEXT-GEN BACTERIAL POPULATION GENOMICS......Page 156
7.6 NEXT-GEN GENOMICS TECHNOLOGY......Page 158
7.7 NEXT-GEN GENOMIC DATA ANALYSIS......Page 162
7.8 CONCLUSIONS/FUTURE PROSPECTS......Page 167
REFERENCES......Page 168
8.1 INTRODUCTION......Page 174
8.2 MLVA AND OTHER DNA FRAGMENT-BASED METHODS......Page 175
8.3 SNP AND DNA SEQUENCE-BASED METHODS......Page 178
8.4 CONCLUSION......Page 183
REFERENCES......Page 184
Part II: Population Genetics of Select Bacterial Pathogens......Page 188
9.2 HISTORY OF ANTHRAX IN NORTH AMERICA......Page 190
9.3 THE ANTHRAX DISTRICTS AFTER 1944......Page 192
9.4 MOLECULAR GENOTYPING OF B . ANTHRACIS......Page 193
9.6 PHYLOGENETIC RESOLUTION WITHIN THE WNA LINEAGE......Page 195
9.7 PHYLOGEOGRAPHIC RESOLUTION WITHIN THE AMES LINEAGE......Page 197
9.8 ADDITIONAL B . ANTHRACIS GENOTYPES IN NORTH AMERICA......Page 198
REFERENCES......Page 199
10.1 INTRODUCTION......Page 202
10.2 HUMAN INFECTION......Page 203
10.3 GENETIC STRUCTURE......Page 204
10.4 MODELS OF CAMPYLOBACTER EVOLUTION......Page 208
10.5 CLADES AND SPECIES......Page 211
REFERENCES......Page 212
11.1 INTRODUCTION......Page 216
11.2 ANTIBIOTIC RESISTANCE......Page 217
11.3 VANCOMYCIN RESISTANCE......Page 218
11.5 POPULATION STRUCTURE AND GENETIC EVOLUTION:SIMILARITIES AND DIFFERENCES BETWEEN E. FAECIUMAND E. FAECALIS......Page 220
11.6 WHAT IS DRIVING GD IN E. FAECIUM AND E. FAECALIS ?......Page 226
11.7 THE ACCESSORY GENOME OF E. FAECIUM AND E. FAECALIS......Page 229
11.8 SUMMARY, CONCLUSIONS, AND FUTURE PERSPECTIVES......Page 232
REFERENCES......Page 233
12.1 INTRODUCTION......Page 238
12.2 GENOME ORGANIZATION OF LB SPIROCHETES......Page 240
12.3 GENOTYPING OF LB SPIROCHETES AND PHYLOGENETIC TOOLS......Page 243
12.4 POPULATION BIOLOGY AND EVOLUTION OF LB SPIROCHETES......Page 245
12.5 DO LB SPECIES EXIST?......Page 257
12.6 FUTURE RESEARCH AVENUES......Page 258
REFERENCES......Page 260
13.2 A BRIEF HISTORY OF TYPING OF MENINGOCOCCI......Page 268
13.3 SPECIES SEPARATION......Page 269
13.5 THE CLONAL COMPLEXES OF MENINGOCOCCI......Page 272
13.6 FORCES SHAPING THE MENINGOCOCCAL METALINEAGE......Page 277
13.7 VIRULENCE, A MYSTERIOUS TRAIT......Page 279
13.8 POPULATION EFFECT OF MENINGOCOCCAL VACCINES......Page 280
13.9 ANTIBIOTIC RESISTANCE AND MENINGOCOCCAL LINEAGES......Page 281
REFERENCES......Page 282
14.1 INTRODUCTION......Page 290
14.2 E. COLI POPULATION GENETICS: CLONAL OR NOT CLONAL?......Page 291
14.3 THE E. COLI PHYLOGENETIC STRUCTURE......Page 294
14.4 THE EVOLUTIONARY HISTORY OF A HOST-SPECIFIC OBLIGATE PATHOGEN: THE SHIGELLA AND EIEC CASE STUDY......Page 297
14.5 WHAT MAKES YOU AN OPPORTUNISTIC PATHOGEN?......Page 299
14.7 CONCLUDING REMARKS......Page 302
REFERENCES......Page 303
15.1 INTRODUCTION......Page 308
15.2 GENERATION TIMESCALE DIVERSIFICATION......Page 313
15.3 ANTIGENIC DIVERSITY IN SALMONELLA......Page 317
15.4 WHY ARE DIVERSE H AND O ANTIGENS MAINTAINED IN SALMONELLA ?......Page 322
REFERENCES......Page 332
16.1 INTRODUCTION......Page 342
16.2 OVERVIEW OF THE STAPHYLOCOCCAL POPULATION STRUCTURE......Page 343
16.3 STAPHYLOCOCCAL POPULATION STRUCTURE IN SPECIFIC DISEASE CONTEXTS......Page 348
16.4 ORIGIN AND MAINTENANCE OF STAPHYLOCOCCAL GENETIC VARIATION......Page 352
16.5 MACROEVOLUTIONARY CONSIDERATIONS AND CONCLUDING REMARKS......Page 356
REFERENCES......Page 357
APPENDIX 1—DIVERSITY AND DIFFERENTIATION......Page 363
17.1 HABITATS, TRANSMISSION, AND DISEASE......Page 366
17.2 CLASSICAL STRAIN TYPING......Page 368
17.3 MULTILOCUS SEQUENCE TYPING (MLST)BASED ON HOUSEKEEPING GENES......Page 371
17.4 SPECIES BOUNDARIES AND GENE FLOW......Page 375
17.5 NICHE-DRIVING GENES......Page 381
17.6 BACTERIAL POPULATION DYNAMICS AND SELECTION......Page 385
REFERENCES......Page 392
18.1 INTRODUCTION......Page 400
18.2 V. CHOLERAE......Page 403
18.3 V. PARAHAEMOLYTICUS......Page 410
18.4 V. VULNIFICUS......Page 413
REFERENCES......Page 418
Index......Page 424
Color plates......Page 442