Genetics and Evolution of Infectious Diseases (eBook)

Cover Page 1
Genetics and Evolution of Infectious Diseases 4
Copyright Page 5
Contents 6
List of Contributors 14
Preface 20
Introduction 22
Part 1: Methodological/Generalist Chapters 24
Chapter 1 Virus Species 26
1.1 The Species Problem in Biology 26
1.2 Classes Versus Individuals 27
1.3 Species Taxa as Cluster Classes 27
1.4 Species: Concrete Versus Abstract Entities 28
1.5 The Nature of Viruses 29
1.6 Viruses Should not be Reduced to Virions 29
1.7 What is a Virus Species? 31
1.8 Species and Quasi-Species 32
1.9 Definition of Virus Species Versus Identification of Viruses 32
1.10 Using Viral Genomes to Define Virus Species 33
1.11 Names and Typography of Virus Species 35
Chapter 2 A Theory-Based Pragmatism for Discovering and Classifying Newly Divergent Bacterial Species 44
2.1 Introduction 44
2.2 Ecological Breadth of Recognized Species 47
2.3 Models of Bacterial Speciation 50
2.4 Algorithms for Identifying Ecotypes 54
2.5 Confirming the Ecological Distinctness of Ecotypes 55
2.6 Ecological Homogeneity within Ecotypes 57
2.7 Are Bacterial Ecotypes Cohesive? 58
2.8 Incorporating Ecology into Bacterial Systematics 59
Chapter 3 Population Structure of Pathogenic Bacteria 66
3.1 Introduction 66
3.2 Bacterial Population Structure by Other Means 67
3.3 What, if Anything, is a Bacterial Population? 71
3.4 Conclusions 75
Chapter 4 Epidemiology and Evolution of Fungal Pathogens in Plants and Animals 82
4.1 Introduction 82
4.2 Major Human and Animal Pathogenic Fungi 84
4.3 New and Emerging Mycoses 87
4.4 Plant Pathogenic Fungi 93
4.5 New and Emerging Plant Diseases 95
4.6 Modern Molecular Epidemiologic Tools for Investigating Fungal Diseases 97
4.7 Population Genetics of Pathogenic Fungi 101
4.8 Species and Speciation in Pathogenic Fungi 117
4.9 Mating and Pathogenesis 122
4.10 Genomics of Fungi: What makes a Fungus Pathogenic? 125
4.11 Conclusion 129
Chapter 5 Clonal Evolution 156
5.1 Introduction 156
5.2 Definitions 157
5.3 The Origin of Life, the Origin of Propagation and Recombination 158
5.4 Clonal Modes 159
5.5 Quantifying the Importance of Asexuality in the Biosphere 160
5.6 Genetic Consequences of Asexuality 160
5.7 Evolution and the Paradox of Sex 161
5.8 Clonal Microevolution 163
5.9 Conclusions 166
Chapter 6 Coevolution of Host and Pathogen 170
6.1 Coevolution of Host and Pathogen 170
6.2 The Process of Antagonistic Coevolution 176
6.3 Testing for Host–Pathogen Coevolution 179
6.4 Implications of Coevolution 185
6.5 Summary/Future Outlook 186
Chapter 7 Elucidating Human Migrations by Means of their Pathogens 196
7.1 Introduction 196
7.2 Using Pathogens as Genetic Tracers for Host History 197
7.3 Candidates 199
7.4 Conclusion 216
Chapter 8 Phylogenetic Analysis of Pathogens 226
8.1 Introduction 226
8.2 The Uses of Phylogenies 227
8.3 The Logic of Phylogeny Reconstruction 229
8.4 Characters and Samples 231
8.5 The Practice of Phylogeny Reconstruction 235
8.6 Choosing a Method 240
8.7 Phylogenetic Trees 242
8.8 Phylogenetic Networks 246
Chapter 9 Evolutionary Responses to Infectious Disease 256
9.1 Introduction 256
9.2 Parasites as Our Friends 257
9.3 Demography and Parasites 258
9.4 Agriculture 259
9.5 Some Lessons from Malaria 260
9.6 Disease and Standard of Living in Preindustrial Societies: A Simple Model 263
9.7 Population Limitation 264
9.8 Disease, Mating, and Reproductive Strategy 267
9.9 Prosperity and the Postindustrial Era Mortality Decline 268
Chapter 10 Infectious Disease Genomics 272
10.1 Introduction 272
10.2 Vaccine Target 274
10.3 Drug Target 276
10.4 Vector Control 276
10.5 Diagnostic Target and Pathogen Discovery 277
10.6 Conclusion 278
Chapter 11 Proteomics and Host–Pathogen Interactions: A Bright Future? 286
11.1 Introduction 286
11.2 Interest of Proteomics to Study Host–Pathogen Interactions 287
11.3 Retrospective Analysis of Previous Proteomics Studies 288
11.4 Pitfalls of the Current Conceptual Approach in many “Parasito-Proteomics” Studies 294
11.5 Toward New Conceptual Approaches to Decipher the Host–Parasite Interactions for Parasites with Short or Complex Life Cycle 295
11.6 Population Proteomics, an Emerging Discipline, to Study Host–Parasite Interactions 301
11.7 5-Year View 309
11.8 Conclusion 312
Glossary 313
Chapter 12 The Evolution of Antibiotic Resistance 328
12.1 Introduction 328
12.2 Mechanisms and Sources of Antibiotic Resistance 332
12.3 Evolution of Antibiotic-Resistance Genes 337
12.4 Limitations to Adaptation and the Cost of Resistance 343
12.5 Can the Evolution of Antibiotic Resistance be Predicted? 349
12.6 Conclusions and Perspectives 350
Glossary 351
Chapter 13 General Mechanisms of Antiviral Resistance 362
13.1 Introduction 362
13.2 Evolutionary Outcomes that have Enabled Viruses to Resist Control 366
13.3 One Principle Mechanism for Development of Resistance 369
13.4 Viruses with Segmented Genomes: Additional Resistance Mechanism 370
13.5 Evolution of Resistant Mutants 370
13.6 Illustrative Examples of Resistance to Specific Antiviral Drugs 371
13.7 Optimizing Drug Combinations to Avoid Resistance 376
13.8 Unexpected Consequences of Resistance Mutations 378
13.9 A Role for Compounds Targeting Host Proteins for Antiviral Therapy 380
13.10 Conclusion 381
Chapter 14 Evolution of Resistance to Insecticide in Disease Vectors 386
14.1 Introduction 386
14.2 Part 1: Insecticide Resistance: Definition and History 388
14.3 Part 2: Mechanisms of Resistance 394
14.4 Part 3: Treatment Practices and Resistance Management Strategies 409
14.5 Conclusion 416
Chapter 15 Genetics of Major Insect Vectors 434
15.1 Introduction 434
15.2 Genetics of Tsetse Flies, Glossina spp. (Diptera: Glossinidae), and African Trypanosomiasis 435
15.3 Genetics of the Triatominae (Hemiptera, Reduviidae) and Chagas Disease 449
15.4 The Anopheles gambiae Complex 469
Glossary 482
Chapter 16 Modern Morphometrics of Medically Important Insects 496
16.1 Introduction 496
16.2 Landmark-Based Geometric Morphometry 497
16.3 Nonenvironmental Sources of Metric Change 500
16.4 Environmental Sources of Metric Changes 503
16.5 The Regulation of Phenotype 506
16.6 Applications in Medical Entomology 508
16.7 Conclusion 517
Chapter 17 Multilocus Sequence Typing of Pathogens 526
17.1 Introduction 526
17.2 Molecular Design and Development of MLST 527
17.3 MLST Databases 531
17.4 Advantages and Disadvantages of MLST 531
17.5 Analytical Approaches 533
17.6 Applications of MLST 537
17.7 Conclusions and Prospects 540
Chapter 18 Omics, Bioinformatics, and Infectious Disease Research 546
18.1 The Need for Bioinformatics 546
18.2 Metagenomics 547
18.3 Comparative Genomics 548
18.4 Pan-Genomics 551
18.5 Transcriptomics 552
18.6 Proteomics 554
18.7 Structural Genomics/Proteomics 555
18.8 A “How-To” of Second-Generation Sequencing 556
18.9 Alignment or Assembly of Second-generation Sequences 557
18.10 Concluding Remarks 559
Chapter 19 Genomics of Infectious Diseases and Private Industry 564
19.1 Introduction 564
19.2 Customers and Their Needs 565
19.3 Technologies and Companies 568
19.4 Conclusion and Perspectives 574
Chapter 20 Current Progress in the Pharmacogenetics of Infectious Disease Therapy 578
20.1 Introduction 578
20.2 The Role of Pharmacogenetics in Communicable Diseases 579
20.3 Strategies for Investigating New Pharmacogenetic Associations 579
20.4 Implementation of Pharmacogenetics 581
20.5 Pharmacogenetics of HIV Therapy 583
20.6 Pharmacogenetics of Antimalarial Therapy 589
20.7 Pharmacogenetics of Antituberculosis Therapy 591
20.8 Summary and Perspective 591
Part 2: Specialized Chapters 602
Chapter 21 Genetic Exchange in Trypanosomatids and Its Relevance to Epidemiology 604
21.1 Introduction 604
21.2 Trypanosoma brucei 605
21.3 Trypanosoma cruzi 611
21.4 Leishmania 619
Chapter 22 Genomic Insights into the Past, Current and Future Evolution of Human Parasites of the Genus Plasmodium 630
22.1 Introduction 630
22.2 Evolution of Plasmodium: The Past 10 Million Years 637
22.3 Evolution of Plasmodium: The Twenty-First Century in Three Courses 644
22.4 Evolution of Plasmodium and the Eradication Agenda 650
Chapter 23 Integrated Genetic Epidemiology of Chagas Disease 660
23.1 What Is Integrated Genetic Epidemiology? 660
23.2 Chagas Disease: A Major Health Problem in Latin America and Other Countries 661
23.3 The Chagas Disease Cycle 661
23.4 Host Genetic Susceptibility to Chagas Disease 662
23.5 Vector Genetic Diversity 666
23.6 Parasite Genetic Diversity 666
23.7 Concluding Remarks 668
Glossary 668
Chapter 24 The Rise and Fall of the Mycobacterium tuberculosis Complex 674
24.1 Overview 674
24.2 Mycobacterium tuberculosis Complex: Definitions and Epidemiology 675
24.3 The Mycobacterium Genus 676
24.4 Mycobacterium tuberculosis Complex Evolution 680
24.5 Pending Questions and Concluding Thoughts 684
Glossary 686
Chapter 25 The Evolution and Dynamics of Methicillin-Resistant Staphylococcus aureus 692
25.1 Introduction 692
25.2 The Staphylococcal Cassette Chromosome mec 693
25.3 Molecular Epidemiology of MRSA 695
25.4 Evolution of Staphylococcus aureus and MRSA 700
25.5 Conclusion 704
Chapter 26 Origin and Emergence of HIV/AIDS 712
26.1 History of AIDS 712
26.2 HIV Is Closely Related to Simian Immunodeficiency Viruses (SIV) from Nonhuman Primates 714
26.3 HIV-1 Is Derived from SIVs Circulating among African Apes 718
26.4 Origin of HIV-2: An Other Emergence, an Other Epidemic 723
26.5 Ongoing Exposure of Humans to a Large Diversity of SIVs: Risk for a Novel HIV? 724
26.6 Conclusion 727
Chapter 27 Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology 734
27.1 A Brief History of SARS 734
27.2 SARS Coronavirus 736
27.3 The Animal Link 739
27.4 Natural Reservoirs of SARS-CoV 740
27.5 Molecular Evolution of SARS-CoV in Humans and Animals 742
27.6 Virus Surveillance in Wild Animals 746
27.7 Concluding Remarks 747
Chapter 28 Ecology and Evolution of Avian Influenza Viruses 752
28.1 Introduction to Influenza A Virus 752
28.2 Influenza Viruses in Birds 755
28.3 Evolutionary Genetics of Avian Influenza Viruses 761
28.4 Future Perspective 766