Bacterial Population Genetics in Infectious Disease (eBook, PDF)
Redaktion: Robinson, D. Ashley; Falush, Daniel; Feil, Edward J
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Bacterial Population Genetics in Infectious Disease (eBook, PDF)
Redaktion: Robinson, D. Ashley; Falush, Daniel; Feil, Edward J
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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…mehr
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- Produktdetails
- Verlag: John Wiley & Sons
- Seitenzahl: 440
- Erscheinungstermin: 5. Mai 2010
- Englisch
- ISBN-13: 9780470600115
- Artikelnr.: 37297623
- Verlag: John Wiley & Sons
- Seitenzahl: 440
- Erscheinungstermin: 5. Mai 2010
- Englisch
- ISBN-13: 9780470600115
- Artikelnr.: 37297623
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 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. 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. 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 of Bacillus: 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 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. 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. 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. faecium and 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. 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 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. 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-Specifi c
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. 15 Population Genetics of Salmonella: Selection for
Antigenic Diversity. 15.1 Introduction. 15.2 Generation Timescale Diversifi
cation. 15.3 Antigenic Diversity in Salmonella. 15.4 Why Are Diverse H and
O Antigens Maintained in Salmonella? 15.5 Conclusions. 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. Appendix 1--Diversity and Differentiation. 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. 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.
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 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. 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. 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 of Bacillus: 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 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. 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. 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. faecium and 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. 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 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. 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-Specifi c
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. 15 Population Genetics of Salmonella: Selection for
Antigenic Diversity. 15.1 Introduction. 15.2 Generation Timescale Diversifi
cation. 15.3 Antigenic Diversity in Salmonella. 15.4 Why Are Diverse H and
O Antigens Maintained in Salmonella? 15.5 Conclusions. 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. Appendix 1--Diversity and Differentiation. 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. 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.