Genetics and Evolution of Infectious Diseases / edited by Michel Tibayrenc.

Format:

Book

Contributor:

Tibayrenc, Michel, editor.

Language:

English

Subjects (All):

Communicable diseases.

Communicable diseases--Genetic aspects.

Physical Description:

1 online resource (1002 pages)

Edition:

Third edition.

Place of Publication:

Amsterdam, Netherlands : Elsevier, [2024]

Summary:

Genetics and Evolution of Infectious Diseases, Third Edition discusses the evolving field of infectious diseases and their continued impact on the health of populations, especially in resource-limited areas of the world where they must confront the dual burden of death and disability due to infectious and chronic illnesses.

Contents:

Front Cover

Genetics and Evolution of Infectious Diseases

Copyright

Contents

Contributors

1 - Methodological/Generalist Chapters

1 - A New Official Definition of Virus Species Has Led to a Controversial Linnaean Latinized Binomial Format of Vir ...

1. The Nature of Virus Classification

2. The Late Acceptance of the Species Concept in Virus Classification

3. Properties Used for Demarcating New Virus Species Are Not the Same as the Diagnostic Properties Used for Identifying the Me ...

4. Popular Anglicized Non-Latinized Virus Species Names Were Subsequently Abandoned

5. The ICTV Introduced Names of Virus Species that Correspond to the Italicized Version of the Virus Name, Thereby Creating Un ...

6. The New ICTV Definition of Virus Species Is at Odds with the Definition of Species in Other Biological Classifications

7. Adrian Gibbs Questions the Merits of a New ICTV Latinized Binomial Nomenclature for Virus Species Associated with Metagenom ...

8. Ontology and Epistemology of Viruses and Living Organisms

References

2 - A Completionist Approach to Discovering and Characterizing Bacterial Diversity

1. Introduction-Toward a Completionist Bacterial Systematics

2. Genomes Enable Completionist Systematics at the Species Level

3. The Ecological Breadth of Recognized Species Taxa

4. Sexual Isolation and Ecological Divergence in the Origins of Species-like Lineages That can Coexist Indefinitely

5. How Modes of Speciation Affect the Correspondence Between Sequence Clusters and Ecotypes

6. Genomes Enable Completionist Systematics at the Ecotype Level

7. Rapprochement Between Theory-based and Tradition-based Systematics of Bacteria

Acknowledgments

3 - Population Structure of Pathogenic Bacteria

1. Introduction.

2. Recombination and Selection in Bacterial Populations

2.1 Emergence and Persistence of Sequence Clusters

2.2 Heterogeneity in Recombination

2.3 The Structure of the Pan-genome of Species and Populations

2.4 Negative Frequency-Dependent Selection

3. Bacterial Population Structure Within and Between Hosts

3.1 Within-host Diversity and Bottlenecks Shape Transmission Dynamics

3.2 Between-host Evolution and Impact on Population Structure

4. Geography and Bacterial Population Structure

4.1 Bacterial Phylogeography and Migration Between Populations

4.2 Range Expansion as a Model of Geographic Spread

5. Conclusions

4 - Diverse Strategies and Evolutionary Histories of Fungal Pathogens

1. Introduction

2. A Brief Overview of Fungal Pathogens

2.1 Plant Pathogens

2.2 Animal Pathogens

3. Selected Examples of Human Pathogens

3.1 Major Pathogens: Candida, Cryptococcus, Aspergillus

3.2 Primary Pathogens: Blastomyces, Coccidioidomycosis, Paracoccidioides, Histoplasma, Pneumocystis

3.3 Emerging Fungal Pathogens

4. Facultative Pathogenesis and Adaptation Versus Exaptation

5. Virulence Factors

5.1 Conventional Virulence Factors

5.2 Thermotolerance

5.3 Extremotolerance

5.4 Resistance to Antifungals

6. Host and Environment Populations, and Emergence of New Fungal Pathogens

6.1 Population Genetics and Genomics

6.2 Recombination and Hybridization

6.3 Emergence of New Fungal Pathogens

7. Conclusions

Declaration of Competing Interest

5 - Molecular Epidemiology of Pathogenic Microorganisms and the Predominant Clonal Evolution Model

1. Introduction: What Is Molecular Epidemiology?

2. Brief Recall on the PCE Model

2.1 What Is, and what Is Not the PCE Model

2.2 Deep Phylogenies/Multigene Bifurcating Trees.

2.3 Other PCE Traits

2.4 Evolutionary Scales

The Russian Doll Model

2.5 Other Models of Pathogen Population Structure

2.6 The Problem of the Wahlund Effect∗: The "Starving Sex Hypothesis"

3. Bacterial Species

3.1 Escherichia coli

3.2 Neisseria meningitidis

4. Parasite Species

4.1 Leishmania donovani/infantum

4.2 Trypanosoma cruzi

5. Yeasts

5.1 The Cryptococcus neoformans/gattii Complex

6. Concluding Remarks

Glossary of Specialized Terms

6 - Parasite-Host Coevolution

2. Common Parasites and Their Definition/Description

2.1 Macroparasites

2.2 Microparasites

2.3 Endoparasites

2.4 Fungi

2.5 Protozoa

2.6 Bacteria

2.7 Ectoparasites

3. Viruses

4. Red Queen Hypothesis and the Evolutionary Arms Race

5. Rapidly Evolving Pathogens-RNA Viruses as a Model

6. Where Did Viruses Come From? Viral Evolution

7. How Do Viruses Evolve and Selection Pressures Not Just on Individual Pathogens With Mutations, but on Groups of Pathogens? ...

8. Phylogenetics Reveals Coevolutionary Patterns

9. Parasite-Host Relationships in Human Infectious Diseases

10. Parasite-Host Relationships in Animal Infectious Diseases

11. Host Immunogenetics Adaptations

12. Parasite Manipulation of Host Behavior

13. A Parasite-absent World

14. Conclusions

7 - Human Genetic Variability and Transmissible Diseases

2. A Population Genetics∗ Framework for the Study of Transmissible Diseases

2.1 Overall Genetic Variation Seems to be Greater Within Major Continental Groups Than Between Them

2.2 Clines∗ or Trees?

2.3 Additional Variability and Stratifications

2.4 Low-Frequency and Rare Variants

2.5 "Russian Doll" Patterns

2.6 Genetic Stratifications and Polygenic Scores∗.

2.7 We are All Half-Breed: Mixtures are Ubiquitous

2.8 If We are All Mestizos, Don't Human Populations Tend Toward Homogenization?

2.9 Ancestry Informative Markers and Self-Reported Ancestry

2.10 General Conclusions

3. Communicable Diseases: A Phenomenon of Co-Evolution Involving Two or Three Actors

3.1 The Considerable Role of Environment

3.2 Genetic Inequality and Transmissible Diseases

3.3 How do Humans Protect Themselves Against Pathogens?

3.4 Other Diseases

3.5 Pathogen Strains as Markers of Human Populations

3.6 Influence of Human Behavior on Transmissible Disease Epidemiology: The Baldwin Effect and the Niche Construction Theory

3.7 Transmissible Diseases and History

3.8 Archaic Adaptive Introgression

4. Conclusions on Human Genetic Variability and Susceptibility to Communicable Diseases

8 - Pathogens as Tracers of Past Human Demography and Migrations

2. Pathogen Genomics to Infer Host History

3. Bacteria

3.1 Helicobacter pylori

3.2 Mycobacterium tuberculosis

3.3 Mycobacterium leprae

4. Viruses

4.1 Human Polyomaviruses

4.2 Human Herpesviruses

5. Conclusion

9 - Evolutionary Responses to Infectious Disease

2. Parasites as Our Friends

3. Demography and Parasites

4. Agriculture

5. Some Lessons from Malaria

6. The Columbian Exchange

7. Disease and Standard of Living in Preindustrial Societies: A Simple Model

8. Population Limitation

9. Disease, Mating, and Reproductive Strategy

10. Prosperity and the Postindustrial Era Mortality Decline

10 - Infectious Disease Genomics

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: Still a Bright Future?

2. Interest of Proteomics to Study Host-(Vector)-Pathogen Interactions

3. Retrospective of Pioneering Proteomics Studies

3.1 Deciphering of the Molecular Strategies Involved in Pathogen Immune Evasion

3.2 Host Proteome Responses to Parasite Infection

3.3 Biomarkers Linked to Infection Process by a Pathogen Using SELDI-TOF-MS Technology

4. Evolution of Conceptual Approaches to Decipher the Host-Pathogen Interactions for Microorganisms With Simple or Complex Lif ...

4.1 From "Parasito-Proteomics" to "Pathogeno-Proteomics": An Holistic View to Disentangle the Hosts and Pathogens Genome Respon ...

4.2 Proteomics of Arthropod Vectors: Understanding the Role of Sialomes in the Host-Vector Interactions

4.3 Pitfalls of the Current Proteomics Approaches

4.4 Proteo-Genomics: Next-Generation Proteomics to Deepen the Characterization of Proteins, Their Biological Functions, and The ...

4.5 Host-Pathogen Interactomes

4.6 Population Proteomics, a Growing Discipline, to Study Host-Pathogen Interactions

4.6.1 Prospects With Population Proteomics for Any Living Organisms

4.6.2 Human Population Proteomics

5. Five-Year View

5.1 Metabolomics and Fluxomics, Key "Omics" Tools to Complete Deciphering of Host-Pathogen Crosstalks

5.2 Applied Outputs: New Diagnostic Tools and Identification of New Therapeutic Target

5.3 Bioterrorism and Proteomics

5.4 Environment and HostMicroorganisms Interactions

6. Conclusions

Glossary

Short Biographical Lines for Contributors

12 - Genomic Epidemiology and Surveillance of Antimicrobial Resistance

1. Antimicrobial Resistance: A Current Major Threat.

2. Genomic Epidemiology and Surveillance in the Fight Against AMR.

Notes:

Includes bibliographical references and index.

Description based on publisher supplied metadata and other sources.

Description based on print version record.

Other Format:

Print version: Tibayrenc, Michel Genetics and Evolution of Infectious Diseases

ISBN:

9780443288197

OCLC:

1446131029