Encyclopedia of Infectious Diseases: Modern Methodologies

Contributors.

Biographical.

Introduction: Infectious Diseases, the Major Challenge of Twenty-First Century Medicine.

1. Pulmonary Tuberculosis and Mycobacterium Tuberculosis: Modern Molecular Epidemiology and Perspectives (Sylvain Godreuil, Loubna Tazi, and Anne-Laure Bañuls).

1.1. Introduction.

1.2. General Points on Mycobacterium Tuberculosis (MTB) and Pulmonary Tuberculosis (PTB).

1.3. Genetics of MTB, Molecular Tools, and Population Structure.

1.4. Use of Molecular Epidemiology for Understanding Tuberculosis Transmission and Pathogenesis.

1.5. Urgent Needs for TB Control, Limitations, and New Issues for Molecular Epidemiology.

1.6. Conclusion and Perspectives.

2. Diseases that Threaten Livestock (J. Blancou and P.-C. Lefévre).

2.1. Introduction.

2.2. Animal Diseases Under Control.

2.3. Diseases that Are an Economic Burden and Hamper International Trade in Animals and Animal Products.

2.4. Animal Diseases that may Threaten Human Health.

2.5. Surveillance and Control of Transmissible Animal Diseases: Progress Expected from Modern Technologies.

3. HIV/AIDS Infection in the World with a Special Focus on Africa (C. Laurent, M. Peeters, and E. Delaporte).

3.1. Introduction.

3.2. Current State of the Epidemic.

3.3. Molecular Epidemiology.

3.4. Implication of HIV Variability on Pathogenesis, Treatment, Diagnosis, and Vaccine Development in Africa.

3.5. Access to Treatment.

3.6. Conclusion.

4. Molecular-Phylogenetic Strategies for Characterization of Uncultured Pathogens (Daniel N. Frank and Robert A. Feldman).

4.1. Introduction.

4.2. A Phylogenetic Framework for Culture-Independent Pathogen Detection.

4.3. Whole Genome Characterization of Uncultured Pathogens.

4.4. Future Perspectives.

5. Molecular or Immunological Tools for Efficient Control of Tuberculosis (J.L. Herrmann and P.H. Lagrange).

5.1. Introduction.

5.2. Definitions: Clinical Characteristics of Tuberculosis.

5.3. Molecular Epidemiology: Advantages and Drawbacks.

5.4. Immunological Epidemiology.

5.5. Conclusions.

6. Understanding Human Leishmaniasis:The Need for an Integrated Approach (M. Hide, B. Bucheton, S. Kamhawi, R. Bras-Gonçalves, S. Sundar, J.-L. Lemesre, and A.-L. Banuls).

6.1. Generalities on Leishmaniasis.

6.2. Impact of Sand Fly Vectors on Leishmaniasis.

6.3. Biodiversity and Genetics of Parasites: Implications in Virulence and Pathogenicity in Humans.

6.4. The Immune Response and Genetic Factors from the Mammalian Host.

6.5. The Need for an Integrated Approach: The Kala-Azar Example in India.

6.6. Conclusion.

7. Epidemics of Plant Diseases: Mechanisms, Dynamics and Management (Serge Savary).

7.1. Botanical Epidemiology.

7.2. Phenomenology of Botanical Epidemics.

7.3. Processes in Botanical Epidemics.

7.4. Factors Influencing Epidemics.

7.5. Some Simple Models in Botanical Epidemiology.

7.6. Refinement of Models.

7.7. Disease Management: A Brief Review of Principles.

7.8. Concluding Remarks.

8. Malaria Vaccines (Charles W.Todd,Venkatachalam Udhayakumar, Ananias A. Escalante, and Altaf A. Lal).

8.1. Introduction.

8.2. Malaria Vaccine Considerations.

8.3. Required Efficacy of Malaria Vaccines.

8.4. Duration of Protection.

8.5. Field Epidemiology Studies.

8.6. Selection of Vaccine Epitopes.

8.7. The Vaccine Target: Epitopes or Strains?

8.8. Cytoadherence and Variant Genes.

8.9. Limitations to Malaria Vaccine Development.

8.10. Adjuvants and Antigen Delivery Systems.

8.11. Multistage, Multiepitope Malaria Vaccine Candidate Antigens.

8.12. Description of FALVAC-1 Antigen.

8.13. Designing Artificial Recombinant Antigens.

9. The SARS Case Study:An Alarm Clock? (Gabriel Turinici and Antoine Danchin).

9.1. SARS: Definition and Clinical Aspects.

9.2. Mathematical Models for Epidemic Spread Propagation.

9.3. The Double Epidemic Model.

9.4. Conclusion.

10. Recombination and Its Role in the Evolution of Pathogenic Microbes (Philip Awadalla, Xin-zhuan Su, and Kate McGee).

10.1. Introduction.

10.2. The Evolutionary Costs and Benefits of Recombination.

10.3. Evolutionary Significance of Recombination in Pathogenic Microbes.

10.4. Recombination and Its Effects on Evolutionary Inferences within a Species.

10.5. Detecting and Estimating Recombination.

10.6. Conclusions.

11. Evolutionary History of the Malaria Parasites (Francisco J.Ayala).

11.1. Malaria’s Human Toll.

11.2. Evolutionary Origins of Plasmodium.

11.3. Human to Monkey or Monkey to Human?

11.4. Population Structure of P. falciparum.

11.5. Malaria’s Eve Hypothesis.

11.6. The Neolithic Revolution, Agriculture, and Climate Change.

11.7. Concluding Remarks.

12. Ecology Of Infectious Diseases: An Example with Two Vaccine-Preventable Infectious Diseases (H. Broutin, N. Mantilla-Beniers, and P. Rohani).

12.1. Introduction.

12.2. Concepts and Methods.

12.3. An Example with Two Directly Transmitted Diseases: Measles and Pertussis Dynamics.

12.4. Conclusion.

13. Influenza Evolution (Robin M. Bush).

13.1. Introduction.

13.2. The Influenza Virus.

13.3. Antigenic Shift and Antigenic Drift.

13.4. Host Specificity.

13.5. Avian Influenza.

13.6. Swine and Equine Influenza.

13.7. Human Influenza.

13.8. The Current Avian H5N1 Outbreak.

13.9. Evolution and Intervention.

14. Experimental Evolution of Pathogens (Vaughn S. Cooper).

14.1. Experimental Design.

14.2. Measuring Adaptation.

14.3. Experimental Evolution of Vesicular Stomatitis Virus (VSV).

14.4. In Vivo Evolution of Salmonella Typhimurium.

14.5. Experimental Evolution of Candida Albicans Antibiotic Resistance.

14.6. Future Prospects.

15. Evolution of Antigenic Variation (Steven A. Frank).

15.1. Introduction.

15.2. Why Do Parasites Vary?

15.3. Mechanisms that Generate Variation.

15.4. Interactions with Host Immunity.

15.5. Experimental Evolution.

15.6. Measuring Selection with Population Samples.

15.7. Shape, Charge, Binding Kinetics, and Evolution.

16. Hantavirus Coevolution with Their Rodent Hosts (Vincent Herbreteau, Heikki Henttonen, Kumiko Yoshimatsu, Jean-Paul Gonzalez,Yupin Suputtamongkol, and Jean-Pierre Hugot).

16.1. Introduction.

16.2. Generalities on Hantaviruses.

16.3. Serological Presence without Cases in Thailand.

16.4. Phylogeny of Hantaviruses.

16.5. Discussion.

16.6. Conclusion.

17. Phylogenetic Methods for the Analysis of Parasites and Pathogens (Jamie R. Stevens).

17.1. Introduction.

17.2. The Phylogenetic Process.

17.3. Methods of Comparing Phylogenies.

17.4. Dating Phylogenetic Trees.

17.5. Conclusion.

18. Parasites that Manipulate Their Hosts (Frédéric Thomas, Janice Moore, Robert Poulin, and Shelley Adamo).

18.1. Introduction.

18.2. Historical Overview.

18.3. Selected Examples of Manipulation.

18.4. How Does the Presence of a Parasite Alter Host Behavior?

18.5. Adaptive Versus Nonadaptive Changes.

18.6. Cost(s) of Manipulation for Parasites.

18.7. Mafia-Like Strategy of Manipulation.

18.8. Multiple Parasites within Manipulated Hosts.

18.9. How Complex are "Parasitically Modified Organisms"?

18.10. Intraspecific Variation in Manipulative Processes.

18.11. Manipulative Parasites and Ecosystem Functioning.

18.12. Concluding Remarks.

19. Human Genetic Diversity and the Spread of Infectious Diseases (M.Tibayrenc).

19.1. Introduction: Key Concepts.

19.2. Exploring the Genetic Background of Human Genetic Susceptibility to Infectious Diseases.

19.3. Human Diversity Revealed by Neutral/Historical Genetic Markers.

19.4. Genetically Driven Phenotypic Diversity.

19.5. Are Races and Ethnic Groups Biologically Meaningful and Medically Relevant?

19.6. Our Genetic Inheritance has been Sculpted by Infectious Diseases.

19.7. Major International Programs that will Boost Our Understanding of Human Genetic Diversity.

19.8. Conclusion.

20. Molecular Epidemiology and Evolutionary Genetics of Pathogens (M.Tibayrenc).

20.1. Introduction: Molecular Epidemiology (ME) and Evolutionary Genetics Are Inseparable.

20.3. The Modern Hypermarket of Molecular Technologies.

20.4. Survival Kit for Evolutionary Genetic Interpretation.

20.5. Conclusion.

21. The Need for Megatechnologies: Massive Sequencing, Proteomics and Bioinformatics (David G. Biron,Austin L. Hughes, Hugh D. Loxdale, and Hercules Moura).

21.1. Introduction.

21.2. The Pre-Genomic Era.

21.3. Genomic Era.

21.4. Post-Genomic Era.

21.5. Conclusion.

22. Mathematical Modeling of Infectious Diseases Dynamics (M. Choisy, J.-F. Guégan, and P. Rohani).

22.1. Introduction.

22.2. The Philosophy of Mathematical Modeling.

22.3. The Nature of Epidemiological Data.

22.4. Childhood Micro-Parasitic Infections.

22.5. A Simple Epidemic Model.

22.6. A Simple Endemic Model.

22.7. Endemo-Epidemic Models.

22.8. Data Analysis.

22.9. Applications to Vaccination Policies.

22.10. Conclusion.

22.11. Summary.

23. Using a Geographic Information System to Spatially Investigate Infectious Disease (A. Curtis, J.K. Blackburn, and Y. Sansyzbayev).

23.1. Introduction.

23.2. The Basic GIS: Individual Components.

23.3. Data Manipulation.

23.4. Spatial Analysis.

23.5. Spatial Visualization.

23.6. The Future of GIS.

24. Vector Control by Surveillance Networks: The ECLAT Program and Chagas (J.-P. Dujardin and C.J. Schofield).

24.1. Introduction.

24.2. Origin and Spread of Human Chagas Disease.

24.3. The Dispersal of the Main Vectors.

24.4. From Disease to Public Health Problem.

24.5. Control and Surveillance.

24.6. Vigilance and Research.

24.7. Conclusion.

25. Contributions of Morphometrics to Medical Entomology (J.-P. Dujardin and D.E. Slice).

25.1. Introduction.

25.2. Causes of Metric Variation?

25.3. Size and Shape.

25.4. Morphometrics and Medical Entomology.

25.5. Authors Contribution to Morphometrics Software.

25.6. Conclusion.

26. Surveillance of Vector-Borne Diseases Using Remotely Sensed Data (D.E. Gorla).

26.1. Vector-Borne Disease Surveillance.

26.2. Remote Sensing and Vector-Borne Diseases.

26.3. Identification of Vector Habitats.

26.4. Monitoring Environmental Changes for Disease Surveillance.

26.5. Early Warning Systems for Vector-Borne Disease Outbreaks.

27. Archaeological Epidemiology of Infectious Diseases: Fossil DNA (Felipe Guhl and Arthur Aufderheide).

27.1. Introduction.

27.2. Techniques and Procedures for Detecting Infectious Agents in Archaeology.

27.3. Epidemiology of Ancient Infectious Diseases.

27.4. Clues Regarding American Humans.

27.5. New Perspectives.

28. Insights Into Structure and Evolution of Bacterial Species That Are Revealed by Molecular Methods (P. Roumagnac, L. Gagnevin, O. Pruvost, and M.Achtman).

28.1. Introduction.

28.2. Methods that Index DNA Polymorphism.

28.3. Applications of Molecular Methods.

28.4. Conclusions.

29. Exploring Genetic Relatedness, Patterns of Evolutionary Descent, and the Population Genetics of Bacterial Pathogens Using Multilocus Sequence Typing (Brian G. Spratt,William P. Hanage, and Christophe Fraser).

29.1. Introduction.

29.2. Bacterial Population Structure and MLST.

29.3. MLST Data As a Resource for Bacterial Population Genetics.

29.4. Measuring Rates of Recombination from MLST Data.

29.5. Concluding Remarks.

30. Topical Debates Evaluation of Risks and Benefits of Consumption of Antibiotics: From Individual to Public Health (Fernando Baquero).

30.1. Antibiotics and Human Health.

30.2. The Determinants of Health: Conservation Medicine.

30.3. From Fears to Possibilities.

30.4. How Important Is Antibiotic Resistance As a Risk for Public Health?

30.5. Health Versus Resistance.

30.6. Changes in Antibiotic Consumer’s Behavior: Egoism Versus Altruism.

30.7. The Role of Worry in Individual Patient’s Behavior.

30.8. The Role of Worry in the Prescriber’s Behavior.

30.9. Individual Versus Society Components in Shaping Individual Risks.

30.10. Appropriate Demand of Antibiotics and the Individual Risk.

30.11. "MY" Utilization of Antibiotics: A Personal Decision.

30.12. The Individual Health Risks of Antibiotic Use.

30.13. The Individual Health Benefits of Antibiotic Use.

30.14. The Problem of Minimums: Minimal Benefits Versus Minimal Risks.

30.15. The Problem of Presumed Minimal Benefits that Might Become Significant Ones.

30.16. The Design of Observational–Ecological Experiments to Determine Attributable Risks and Benefits of the Use of Antibiotics.

30.17. Conclusion.

31. Epidemic Diseases in the Past: History, Philosophy, and Religious Thought (D. Buchillet).

31.1. Plague.

31.2. Smallpox.

31.3. Cholera.

31.4. Conclusion.

32. Fundamentals, Domains, and Diffusion of Disease Emergence: Tools and Strategies for a New Paradigm (Jean-Paul J. Gonzalez, Philippe Barbazan, François Baillon, Julien Capelle, Damien Chevallier, Jean-Paul Cornet, Florence Fournet,Vincent Herbreteau, Jean-Pierre Hugot, Meriadeg Le Gouilh, Eric Leroy, Bernard Mondet, Narong Nitatpattana, Stephane Rican, Gérard Salem, Wailarut Tuntrapasarat, and Marc Souris).

32.1. From Nosology to Concept.

32.2. Tools and Strategies: An Integrative Approach.

32.3. Emergence of Exemplary Diseases or Systems.

32.4. Concluding Remarks.

33. Epidemiology in a Changing World:The Need for a Bigger Picture! (J.-F. Guégan and G. Constantin de Magny).

33.1. Introduction.

33.2. The Interactions Between Human Populations and Natural Systems.

33.3. Dynamic Properties of Microbes, Their Hosts and the Environment.

33.4. The Ecology of Infectious Diseases in Practice.

33.5. Conclusion and Suggested Research Perspectives.

33.6. Summary.

34. Contributions of Social Anthropology to Malaria Control (Jaffré Yannick).

34.1. Introduction.

34.2. Six Proposals of Research and Control.

34.3. Anthropology for Improving the Offer of Health Care.

34.4. Three Operational Approaches.

35. The Neglected Diseases and Their Economic Determinants (Alvaro Moncayo and Mario Ortiz Yanine).

35.1. The "Neglected" Diseases, Criteria for Classification.

35.2. The Diseases.

35.3. The "Neglected" Diseases Burden.

35.4. The Economic Situation and Trends in the Affected Countries and Regions.

35.5. Economic Barriers for Development of Drugs, Vaccines and Vector Control Tools Against the "Neglected Diseases."

35.6. Future Perspectives.

36. The Challenge of Bioterrorism (Stephen A. Morse).

36.1. Introduction.

36.2. Definitions.

36.3. Threat Agents.

36.4. Impact of Biotechnology.

36.5. Scenarios.

36.6. Responses to Bioterrorism: Laboratory.

36.7. Responses to Bioterrorism: Epidemiology and Surveillance.

36.8. Molecular Epidemiology and Microbial Forensics.

36.9. Basic and Applied Research.

36.10. Limiting Access to Dangerous Pathogens.

36.11. Summary.

37. Needs for an Integrative Approach of Epidemics: The Example of Cholera (R. Piarroux and D. Bompangue).

37.1. Introduction.

37.2. Vibrio Cholerae and Its Natural Environment.

37.3. Cholera.

37.4. Man and Cholera Epidemics in the  Nineteenth and Twentieth Centuries.

37.5. Man, Society, and Cholera at the Beginning of the Twenty-First Century: Our Personal Experience of Cholera Management.

37.6. Conclusion.

38. Infectious Diseases: Market of the Future? (Jan Verhoef and Ad Fluit).

38.1. Introduction.

38.2. The Information and Communication Technology Revolution.

38.3. Internet Changing the Health Care  Delivery Landscape.

38.4. The Looming Biotech Revolution.

38.5. Rapid Diagnosis of Infection.

38.6. Laboratory Automation.

38.7. Market.

38.8. Future Market.

38.9. Anticipated Developments.

38.10. Novel Antibiotics.

38.11. New Classes of Antibiotics.

38.12. Pharmacogenomics.

38.13. Conclusion.

39. Mobilizing the Scientific Community for the Patient’s Benefit:At the Crossroads of Fundamental and Applied Science (K.Victoir).

39.1. What Are Neglected Diseases?

39.2. Conclusion.

40. Infectious Diseases and Arts (Pierre Vidal, Myrtille Tibayrenc, and Jean-Paul Gonzalez).

40.1. The Fine Arts: Pictorial Representations.

40.2. Literature.

40.3. Cinematographic Art: Movies and Diseases.

40.4. The Arts and Infectious Disease, in Conclusion.

Index.