Navigating the future of bacterial molecular epidemiology

Current Opinion in Microbiology

Volumn 13, Issue 5, 2010, Pages 640-645

  Baker, Stephen ^a   Hanage, William P ^b   Holt, Kathryn E ^c  

^a OXFORD UNIVERSITY CLINICAL RESEARCH UNIT   (Viet Nam)

^b ST MARY S HOSPITAL   (United Kingdom)

^c UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

BACTERIAL GENOME; BACTERIUM IDENTIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; INDEL MUTATION; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; MOLECULAR EPIDEMIOLOGY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PHYLOGENY; REVIEW; SALMONELLA TYPHI; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STAPHYLOCOCCUS AUREUS;

BACTERIA (MICROORGANISMS);

EID: 77957822719     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2010.08.002     Document Type: Review

References (35)

1. Lilienfeld A.M., Lilienfeld D.E. John Snow, the Broad Street pump and modern epidemiology. Int J Epidemiol 1984, 13:376-378.
2. Holden M.T., Feil E.J., Lindsay J.A., Peacock S.J., Day N.P., Enright M.C., Foster T.J., Moore C.E., Hurst L., Atkin R., et al. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci USA 2004, 101:9786-9791.
3. Baker S., Dougan G. The genome of Salmonella enterica serovar Typhi. Clin Infect Dis 2007, 45(Suppl. 1):S29-33.
4. Hanage W.P., Fraser C., Spratt B.G. The impact of homologous recombination on the generation of diversity in bacteria. J Theor Biol 2006, 239:210-219.
5. Maiden M.C., Bygraves J.A., Feil E., Morelli G., Russell J.E., Urwin R., Zhang Q., Zhou J., Zurth K., Caugant D.A., et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 1998, 95:3140-3145.
6. Aanensen D.M., Spratt B.G. The multilocus sequence typing network: mlst.net. Nucleic Acids Res 2005, 33:W728-733.
7. MacLean D., Jones J.D., Studholme D.J. Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol 2009, 7:287-296.
8. Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu Rev Microbiol 2008, 62:53-70.
9. Leimkugel J., Hodgson A., Forgor A.A., Pfluger V., Dangy J.P., Smith T., Achtman M., Gagneux S., Pluschke G. Clonal waves of Neisseria colonisation and disease in the African meningitis belt: eight-year longitudinal study in northern Ghana. PLoS Med 2007, 4:e101.
10. Suerbaum S., Achtman M. Helicobacter pylori: recombination, population structure and human migrations. Int J Med Microbiol 2004, 294:133-139.
11. Vesaratchavest M., Tumapa S., Day N.P., Wuthiekanun V., Chierakul W., Holden M.T., White N.J., Currie B.J., Spratt B.G., Feil E.J., et al. Nonrandom distribution of Burkholderia pseudomallei clones in relation to geographical location and virulence. J Clin Microbiol 2006, 44:2553-2557.
12. Parry C.M., Hien T.T., Dougan G., White N.J., Farrar J.J. Typhoid fever. N Engl J Med 2002, 347:1770-1782.
13. Kidgell C., Reichard U., Wain J., Linz B., Torpdahl M., Dougan G., Achtman M. Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old. Infect Genet Evol 2002, 2:39-45.
14. Roumagnac P., Weill F.X., Dolecek C., Baker S., Brisse S., Chinh N.T., Le T.A., Acosta C.J., Farrar J., Dougan G., et al. Evolutionary history of Salmonella typhi. Science 2006, 314:1301-1304.
15. Weill F.X., Tran H.H., Roumagnac P., Fabre L., Minh N.B., Stavnes T.L., Lassen J., Bjune G., Grimont P.A., Guerin P.J. Clonal reconquest of antibiotic-susceptible Salmonella enterica serotype Typhi in Son La Province, Vietnam. Am J Trop Med Hyg 2007, 76:1174-1181.
16. Le T.A., Fabre L., Roumagnac P., Grimont P.A., Scavizzi M.R., Weill F.X. Clonal expansion and microevolution of quinolone-resistant Salmonella enterica serotype typhi in Vietnam from 1996 to 2004. J Clin Microbiol 2007, 45:3485-3492.
17. Baker S., Holt K., van de Vosse E., Roumagnac P., Whitehead S., King E., Ewels P., Keniry A., Weill F.X., Lightfoot D., et al. High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia. J Clin Microbiol 2008, 46:1741-1746.
18. Vollaard A.M., Ali S., van Asten H.A., Widjaja S., Visser L.G., Surjadi C., van Dissel J.T. Risk factors for typhoid and paratyphoid fever in Jakarta, Indonesia. JAMA 2004, 291:2607-2615.
19. Baker S., Holt K., Whitehead S., Goodhead I., Perkins T., Stocker B., Hardy J., Dougan G. A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi. Mol Microbiol 2007, 66:1207-1218.
20. Holt K.E., Parkhill J., Mazzoni C.J., Roumagnac P., Weill F.X., Goodhead I., Rance R., Baker S., Maskell D.J., Wain J., et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 2008, 40:987-993.
21. Holt K., Baker S., Dongol S., Basnyat B., Adhikari N., Thorson S., Pulickal A., Song Y., Parkhill J., Farrar J., et al. High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children. BMC Infect Dis 2010, 10:144.
22. Kariuki S., Revathi G., Kiiru J., Mengo D.M., Mwituria J., Muyodi J., Munyalo A., Teo Y.Y., Holt K.E., Kingsley R.A., et al. Typhoid in Kenya is associated with a dominant multidrug resistant Salmonella Typhi haplotype that is also widespread in South East Asia. J Clin Microbiol 2010, 48(6):2171-2176.
23. Morgan M. Methicillin-resistant Staphylococcus aureus and animals: zoonosis or humanosis?. J Antimicrob Chemother 2008, 62:1181-1187.
24. Klein E., Smith D.L., Laxminarayan R. Hospitalizations and deaths caused by methicillin-resistant Staphylococcus aureus, United States, 1999-2005. Emerg Infect Dis 2007, 13:1840-1846.
25. Enright M.C., Day N.P., Davies C.E., Peacock S.J., Spratt B.G. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J Clin Microbiol 2000, 38:1008-1015.
26. Harmsen D., Claus H., Witte W., Rothganger J., Claus H., Turnwald D., Vogel U. Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J Clin Microbiol 2003, 41:5442-5448.
27. Katayama Y., Ito T., Hiramatsu K. A new class of genetic element, staphylococcus cassette chromosome mec, encodes methicillin resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2000, 44:1549-1555.
28. Enright M.C., Robinson D.A., Randle G., Feil E.J., Grundmann H., Spratt B.G. The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proc Natl Acad Sci USA 2002, 99:7687-7692.
29. Nubel U., Roumagnac P., Feldkamp M., Song J.H., Ko K.S., Huang Y.C., Coombs G., Ip M., Westh H., Skov R., et al. Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci USA 2008, 105:14130-14135.
30. Nubel U., Dordel J., Kurt K., Strommenger B., Westh H., Shukla S.K., Zemlickova H., Leblois R., Wirth T., Jombart T., et al. A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus. PLoS Pathog 2010, 6(4):e1000855.
31. Bartels M.D., Nanuashvili A., Boye K., Rohde S.M., Jashiashvili N., Faria N.A., Kereselidze M., Kharebava S., Westh H. Methicillin-resistant Staphylococcus aureus in hospitals in Tbilisi, the Republic of Georgia, are variants of the Brazilian clone. Eur J Clin Microbiol Infect Dis 2008, 27:757-760.
32. Feil E.J., Nickerson E.K., Chantratita N., Wuthiekanun V., Srisomang P., Cousins R., Pan W., Zhang G., Xu B., Day N.P., et al. Rapid detection of the pandemic methicillin-resistant Staphylococcus aureus clone ST 239, a dominant strain in Asian hospitals. J Clin Microbiol 2008, 46:1520-1522.
33. Harris S.R., Feil E.J., Holden M.T., Quail M.A., Nickerson E.K., Chantratita N., Gardete S., Tavares A., Day N., Lindsay J.A., et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327:469-474.
34. Grundmann H., Aanensen D.M., van den Wijngaard C.C., Spratt B.G., Harmsen D., Friedrich A.W. Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis. PLoS Med 2010, 7:e1000215.
35. Aanensen D.M., Huntley D.M., Feil E.J., al-Own F., Spratt B.G. EpiCollect: linking smartphones to web applications for epidemiology, ecology and community data collection. PLoS One 2009, 4:e6968.