Genetics and Evolution of Infectious Diseases, 2nd Edition

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Genetics and Evolution of Infectious Diseases, 2nd Edition

By Michel Tibayrenc

Genetics and Evolution of Infectious Diseases, 2nd Edition PDF discusses the constantly evolving field of infectious diseases and their continued impact on the health of populations, especially in resource-limited areas of the world. Students in public health, biomedical professionals, clinicians, public health practitioners, and decisions-makers will find valuable information in this book that is relevant to the control and prevention of neglected and emerging worldwide diseases that are a major cause of global morbidity, disability, and mortality.

Although substantial gains have been made in public health interventions for the treatment, prevention, and control of infectious diseases during the last century, in recent decades the world has witnessed a worldwide human immunodeficiency virus (HIV) pandemic, increasing antimicrobial resistance, and the emergence of many new bacterial, fungal, parasitic, and viral pathogens.

The economic, social, and political burden of infectious diseases is most evident in developing countries which must confront the dual burden of death and disability due to infectious and chronic illnesses

Takes an integrated approach to infectious diseases
Includes contributions from leading authorities
Provides the latest developments in the field of infectious disease

Table of Contents

1. Recent Developments in the Definition and Official Names of Virus Species

1. Introduction
2. The Logic of Hierarchical Virus Classification
3. Bionominalism: Are Species Classes or Individuals?
4. The Virus Species Problem
5. Properties Used for Defining Virus Species and Identifying Individual Viruses
6. A Virus Species Cannot Be Defined Solely by the Properties of Viral Genomes
7. The New ICTV Definition of Virus Species
8. Non-Latinized Binomial Names for Virus Species
9. Discussion

2. A Theory-Based Pragmatism for Discovering and Classifying Newly Divergent Species of Bacterial Pathogens

1. Introduction
2. Ecological Breadth of Recognized Species
3. The Stable Ecotype Model of Bacterial Speciation
4. Demarcating Putative Ecotypes From Sequence Data
5. Ecological Diversity Within Putative Ecotypes
6. Models of Frequent Speciation
7. Other Models Where Ecotypes Are Not Discernible as Sequence Clusters
8. Are Bacterial Ecotypes Cohesive?
9. Incorporating Ecology Into Bacterial Systematics

3. Population Structure of Pathogenic Bacteria

1. Introduction
2. Recombination in Bacterial Populations
3. Evolutionary Processes Shape Intra- and Interhost Bacterial Population Structure
4. Genomic Analysis Tools for Studying Bacterial Population Structure
5. Conclusions

4. Epidemiology and Evolution of Fungal Pathogens in Plants and Animals

1. Introduction
2. New and Emerging Mycoses
3. Plant Pathogenic Fungi
4. New and Emerging Plant Diseases
5. Modern Molecular Epidemiological Tools for Investigating Fungal Diseases
6. Population Genetics of Pathogenic Fungi
7. Genomics of Fungi: What Makes a Fungus Pathogenic?
8. Conclusion

5. Clonal Evolution

1. Introduction
2. Definitions
3. The Origin of Life, the Origin of Propagation, and Recombination
4. Clonal Modes
5. Quantifying the Importance of Asexuality in the Biosphere
6. Genetic Consequences of Asexuality
7. Evolution and the Paradox of Sex
8. Clonal Microevolution
9. Conclusions
Abbreviation List

6. Coevolution of Host and Pathogen

1. Coevolution of Host and Pathogen
2. The Process of Antagonistic Coevolution
3. Testing for Host–Pathogen Coevolution
4. Implications of Coevolution
5. Summary/Future Outlook

7. Microbes as Tracers of Past Human Demography and Migrations

1. Introduction
2. Using Pathogens as Genetic Tracers for Host History
3. Candidates
4. Conclusion
Abbreviations

8. Phylogenetic Analysis of Pathogens

1. Introduction
2. The Uses of Phylogenies
3. The Logic of Phylogeny Reconstruction
4. Characters and Samples
5. The Practice of Phylogeny Reconstruction
6. Choosing a Method
7. Representing Phylogenies: Trees
8. Phylogenetic Networks

9. Evolutionary Responses to Infectious Disease

1. Introduction
2. Parasites as Our Friends
3. Demography and Parasites
4. Agriculture
5. Some Lessons From Malaria
6. Disease and Standard of Living in Preindustrial Societies: A Simple Model
7. Population Limitation
8. Disease, Mating, and Reproductive Strategy
9. Prosperity and the Postindustrial Era Mortality Decline

10. Infectious Disease Genomics

1. Introduction
2. Vaccine Target
3. New Drug Discovery
4. Drug Target
5. Therapeutic Response and Drug Resistance
6. Vector Control
7. Clinical Application
8. Conclusion

11. Proteomics and Host–Pathogen Interactions: A Bright Future?

1. Introduction
2. Interest of Proteomics to Study Host–Pathogen Interactions
3. Retrospective Analysis of Previous Proteomics Studies
4. Toward New Conceptual Approaches to Decipher the Host–Parasite Interactions for Parasites With Simple or Complex Life Cycle
5. Population Proteomics: An Emerging Discipline to Study Host–Parasite Interactions
6. Conclusion

12. The Evolution of Antibiotic Resistance

1. Introduction
2. Mechanisms and Sources of Antibiotic Resistance
3. Evolution of Antibiotic-Resistance Genes
4. Limitations to Adaptation and the Cost of Resistance
5. Can the Evolution of Antibiotic Resistance be Predicted?
6. Conclusions and Perspectives
Glossary
List of Abbreviations

13. Modern Morphometrics of Medically Important Arthropods

1. Introduction
2. Landmark-Based Geometric Morphometry
3. Pseudo-Landmark-Based Shape
4. Allometry
5. Measurement Error
6. Some Considerations About the Genetics of Metric Change
7. Phenotypic Plasticity
8. A Special Case of Shape Change: the Character Displacement
9. The Regulation of Phenotype
10. Applications in Medical Entomology
Glossary

14. Evolution of Resistance to Insecticide in Disease Vectors

1. Introduction
2. Insecticide Resistance: Definition and History
3. Mechanisms of Resistance
4. Conclusion

15. Genetics of Major Insect Vectors

1. Introduction
2. Genetics of Tsetse Flies and African Trypanosomiasis
3. Genetics of the Triatominae (Hemiptera, Reduviidae) and Chagas Disease
4. The Anopheles gambiae Complex
5. Genetics of the Order Ixodida
Glossary

16. Multilocus Sequence Typing of Pathogens: Methods, Analyses, and Applications

1. Introduction
2. Molecular Design and Development of Multilocus Sequence Typing
3. Multilocus Sequence Typing Databases
4. Advantages and Disadvantages of Multilocus Sequence Typing
5. Analytical Approaches
6. Applications of Multilocus Sequence Typing
7. Conclusions and Prospects

17. Next-Generation Sequencing, Bioinformatics, and Infectious Diseases

1. Analyzing Big Data
2. Comparative Genomics
3. Transcriptomics
4. Single-Cell Technologies
5. High-Throughput Sequencing
6. De Novo Genome Assembly
7. Whole-Genome Sequence Analysis
8. RNA-Seq (Transcriptomics)
9. Concluding Remarks

18. Genomics of Infectious Diseases and Private Industry

1. Introduction
2. Technologies and Instrument Platforms
3. Customers and Their Needs
4. Industry Landscape
5. Conclusion

19. Current Progress in the Pharmacogenetics of Infectious Disease Therapy

1. Introduction
2. Pharmacogenetics of HIV Therapy
3. Pharmacogenetics of Antimalarial Therapy
4. Pharmacogenetics of Antituberculous Therapy
5. Summary and Perspective

20. Genetic Exchange in Trypanosomatids and Its Relevance to Epidemiology

1. Introduction
2. Trypanosoma brucei
3. Trypanosoma cruzi
4. Leishmania
Abbreviations

21. Genomic Insights Into the Past, Current, and Future Evolution of Human Parasites of the Genus Plasmodium

1. Introduction
2. Evolution of Plasmodium: The Last 10Million Years
3. Evolution of Plasmodium: The 21st Century in Three Courses
4. Evolution of Plasmodium, and the Eradication Agenda

22. Integrated Genetic Epidemiology of Chagas Disease

1. What Is Integrated Genetic Epidemiology?
2. Chagas Disease: A Major Health Problem in Latin America and Other Countries
3. The Chagas Disease Cycle
4. Host Genetic Susceptibility to Chagas Disease
5. Vector Genetic Diversity
6. Parasite Genetic Diversity
7. Concluding Remarks
Glossary

23. Adaptive Evolution of the Mycobacterium tuberculosis Complex to Different Hosts

1. Overview: Disease and Mycobacterial Genetics
2. Host–Pathogen Coevolution of the Tubercle Bacillus
3. Evolution of the Mycobacterium tuberculosis Complex From a Genomic Perspective
4. Evolution in the Laboratory Environment and In Vitro Attenuation of Bacteria From the Mycobacterium tuberculosis Complex
5. Short-Term Evolution of Mycobacterium tuberculosis During Infection, Drug Treatment, and Disease
6. Adaptive Cues of the Mycobacterium tuberculosis Complex As the Most Successful Pathogens
7. Pending Questions and Concluding Remarks

24. The Evolution and Dynamics of Methicillin-Resistant Staphylococcus aureus

1. Introduction
2. The Staphylococcal Cassette Chromosome mec
3. Evolution of Staphylococcus aureus and MRSA
4. Molecular Epidemiology of MRSA
5. Conclusion

25. Origin and Emergence of HIV/AIDS

1. History of AIDS
2. Human Immunodeficiency Viruses Are Closely Related to Simian Immunodeficiency Virus From Nonhuman Primates
3. HIV-1 Is Derived From Simian Immunodeficiency Viruses Circulating Among African Apes
4. Origin of HIV-2: Another Emergence, Another Epidemic
5. Ongoing Exposure of Humans to a Large Diversity of Simian Immunodeficiency Viruses: Risk for a Novel HIV?
6. Conclusion

26. Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology

1. A Brief History of SARS
2. SARS Coronavirus
3. The Animal Link
4. Natural Reservoirs of SARS-CoV
5. Molecular Evolution of SARS-CoV in Humans and Animals
6. Coronavirus Surveillance in Wildlife Animals
7. Concluding Remarks

27. Ecology and Evolution of Avian Influenza Viruses

1. Introduction to Influenza A Virus
2. Influenza Viruses in Birds
3. Evolutionary Genetics of Avian Influenza Viruses
4. Future Perspective

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