Unlocking pathogen genotyping information for public health by mathematical modeling

Trends in Microbiology

Volumn 18, Issue 9, 2010, Pages 406-412

  Kretzschmar, Mirjam ^a,b   Gabriela M Gomes, M ^c   Coutinho, Roel A ^b,d   Koopman, James S ^e  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

^c INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^d ACADEMIC MEDICAL CENTER   (Netherlands)

^e UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INFLUENZA VACCINE; PERTUSSIS VACCINE; WART VIRUS VACCINE;

CHLAMYDIASIS; CONTACT EXAMINATION; DISEASE SURVEILLANCE; DISEASE TRANSMISSION; GENETIC DRIFT; GENOTYPE; GONORRHEA; HEPATITIS B; HEPATITIS C VIRUS; HOST PATHOGEN INTERACTION; HOST RESISTANCE; HUMAN IMMUNODEFICIENCY VIRUS; INFECTION CONTROL; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; MOLECULAR TYPING; NONHUMAN; PERTUSSIS; PHYLOGENY; PRIORITY JOURNAL; PUBLIC HEALTH; PUBLIC HEALTH SERVICE; REVIEW; SEASONAL INFLUENZA; SEQUENCE ANALYSIS; TUBERCULOSIS; WART VIRUS;

BACTERIA; COMMUNICABLE DISEASE CONTROL; COMMUNICABLE DISEASES; COMPUTATIONAL BIOLOGY; DISEASE NOTIFICATION; EUROPE; EVOLUTION, MOLECULAR; GENOTYPE; HUMANS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR EPIDEMIOLOGY; NETHERLANDS; PUBLIC HEALTH; VIRUSES;

EID: 77956184144     PISSN: 0966842X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tim.2010.06.008     Document Type: Review

References (46)

1. Grenfell B.T., et al. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 2004, 303:327-332.
2. Worobey M., et al. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 2008, 455:661-664.
3. Pybus O.G., et al. The hepatitis C virus epidemic among injecting drug users. Infect Genet. Evol. 2005, 5:131-139.
4. Smith D.J., et al. Mapping the antigenic and genetic evolution of influenza virus. Science 2004, 305:371-376.
5. de Jong J.C., et al. Antigenic and genetic evolution of swine influenza A (H3N2) viruses in Europe. J. Virol. 2007, 81:4315-4322.
6. Koelle K., et al. Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science 2006, 314:1898-1903.
7. Pybus O.G., Rambaut A. Evolutionary analysis of the dynamics of viral infectious disease. Nat. Rev. Genet. 2009, 10:540-550.
8. Eames K.T., Keeling M.J. Coexistence and specialization of pathogen strains on contact networks. Am. Nat. 2006, 168:230-241.
9. Koppelman M.H., Zaaijer H.L. Diversity and origin of hepatitis B virus in Dutch blood donors. J. Med. Virol. 2004, 73:29-32.
10. van Houdt R., et al. Effect of a targeted hepatitis B vaccination program in Amsterdam, The Netherlands. Vaccine 2007, 25:2698-2705.
11. Nieuwenhuis R.F., et al. Resurgence of lymphogranuloma venereum in Western Europe: an outbreak of Chlamydia trachomatis serovar l2 proctitis in The Netherlands among men who have sex with men. Clin. Infect. Dis. 2004, 39:996-1003.
12. Stene-Johansen K., et al. Molecular epidemiological studies show that hepatitis A virus is endemic among active homosexual men in Europe. J. Med. Virol. 2007, 79:356-365.
13. van de Laar T., et al. Evidence of a large, international network of HCV transmission in HIV-positive men who have sex with men. Gastroenterology 2009, 136:1609-1617.
14. Mellmann A., et al. Automated DNA sequence-based early warning system for the detection of methicillin-resistant Staphylococcus aureus outbreaks. PLoS Med. 2006, 3:e33.
15. Enright M.C., et al. The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proc. Natl. Acad. Sci. U. S. A. 2002, 99:7687-7692.
16. Russell C.A., et al. The global circulation of seasonal influenza A (H3N2) viruses. Science 2008, 320:340-346.
17. Pybus O.G., et al. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 2000, 155:1429-1437.
18. Nordborg M. Coalescent theory. Handbook of Statistical Genetics (3rd edition) 2007, 843-872. John Wiley and Sons. D.J. Balding (Ed.).
19. Wilson D.J., et al. Germs, genomes and genealogies. Trends Ecol. Evol. 2005, 20:39-45.
20. Volz E.M., et al. Phylodynamics of infectious disease epidemics. Genetics 2009, 183:1421-1430.
21. Gordo I., Campos P.R. Patterns of genetic variation in populations of infectious agents. BMC Evol. Biol. 2007, 7:116.
22. Gordo I., et al. Genetic diversity in the SIR model of pathogen evolution. PLoS One 2009, 4:e4876.
23. Pilcher C.D., et al. Brief but efficient: acute HIV infection and the sexual transmission of HIV. J. Infect. Dis. 2004, 189:1785-1792.
24. Jacquez J.A., et al. Role of the primary infection in epidemics of HIV infection in gay cohorts. J. Acquir. Immune Defic. Syndr. 1994, 7:1169-1184.
25. Brenner B.G., et al. High rates of forward transmission events after acute/early HIV-1 infection. J. Infect. Dis. 2007, 195:951-959.
26. Lewis F., et al. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med. 2008, 5:e50.
27. Volz E., Heckathorn D.D. Probability based estimation theory for respondent driven sampling. Journal of Official Statistics 2008, 24:79-97.
28. Diekmann O., et al. On the definition and the computation of the basic reproduction ratio R0 in models for infectious diseases in heterogeneous populations. J. Math. Biol. 1990, 28:365-382.
29. Abdul-Quader A.S., et al. Effectiveness of respondent-driven sampling for recruiting drug users in New York City: findings from a pilot study. J. Urban Health 2006, 83:459-476.
30. Resik S., et al. Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in Cuba. AIDS Res. Hum. Retroviruses 2007, 23:347-356.
31. Frost S.D., Volz E.M. Viral phylodynamics and the search for an 'effective number of infections'. Philos. Trans. R Soc. Lond. B Biol. Sci. 2010, 365:1879-1890.
32. Grundmann H., et al. How many infections are caused by patient-to-patient transmission in intensive care units?. Crit. Care Med. 2005, 33:946-951.
33. Pelupessy I., et al. How to assess the relative importance of different colonization routes of pathogens within hospital settings. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:5601-5605.
34. Kretzschmar M., et al. Vaccination against hepatitis B in low endemic countries. Epidemiol. Infect. 2002, 128:229-244.
35. Restif O., Grenfell B.T. Vaccination and the dynamics of immune evasion. J. R. Soc. Interface 2007, 4:143-153.
36. Hanage W.P. Serotype-specific problems associated with pneumococcal conjugate vaccination. Future Microbiol. 2008, 3:23-30.
37. Maiden M.C., et al. Effect of meningococcal serogroup C conjugate vaccines on carriage and herd immunity. J. Infect. Dis. 2008, 197:737-743.
38. Wheeler C.M., et al. Human papillomavirus genotype distributions: implications for vaccination and cancer screening in the United States. J. Natl. Cancer Inst. 2009, 101:475-487.
39. Mooi F.R., et al. Polymorphism in the Bordetella pertussis virulence factors P.69/pertactin and pertussis toxin in The Netherlands: temporal trends and evidence for vaccine-driven evolution. Infect. Immun. 1998, 66:670-675.
40. Muller J., et al. Contact tracing in stochastic and deterministic epidemic models. Math. Biosci. 2000, 164:39-64.
41. Fraser C., et al. Factors that make an infectious disease outbreak controllable. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:6146-6151.
42. Eames K.T., Keeling M.J. Contact tracing and disease control. Proc. Biol. Sci. 2003, 270:2565-2571.
43. Small P.M., et al. The epidemiology of tuberculosis in San Francisco. A population-based study using conventional and molecular methods. N. Engl. J. Med. 1994, 330:1703-1709.
44. Sintchenko V., Gilbert G.L. Utility of genotyping of Mycobacterium tuberculosis in the contact investigation: a decision analysis. Tuberculosis (Edinb.) 2007, 87:176-184.
45. Klovdahl A.S., et al. Networks and tuberculosis: an undetected community outbreak involving public places. Soc. Sci. Med. 2001, 52:681-694.
46. Sintchenko V., et al. Pathogen profiling for disease management and surveillance. Nat. Rev. Microbiol. 2007, 5:464-470.