Multi-locus sequence typing: A tool for global epidemiology

Trends in Microbiology

Volumn 11, Issue 10, 2003, Pages 479-487

  Urwin, Rachel ^a   Maiden, Martin C J ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENE; BACTERIAL INFECTION; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; BIOINFORMATICS; DATA BASE; EUKARYOTE; GENE LOCUS; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; PROKARYOTE; REVIEW;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 0141817852     PISSN: 0966842X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tim.2003.08.006     Document Type: Review

References (60)

1. van Belkum A., et al. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clin. Microbiol. Rev. 14:2001;547-560.
2. Achtman M. A surfeit of YATMs? J. Clin. Microbiol. 34:1996;1870.
3. Maiden M.C.J., et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. U. S. A. 95:1998;3140-3145.
4. Popoff M.Y., et al. Supplement 1997 (no. 41) to the Kauffmann-White scheme. Res. Microbiol. 149:1998;601-604.
5. Gupta S., Maiden M.C.J. Exploring the evolution of diversity in pathogen populations. Trends Microbiol. 9:2001;181-185.
6. Selander R.K., et al. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51:1986;873-884.
7. Enright M.C., Spratt B.G. Multilocus sequence typing. Trends Microbiol. 7:1999;482-487.
8. Jefferies J., et al. Automated pneumococcal MLST using liquid-handling robotics and a capillary DNA sequencer. Mol. Biotechnol. 24:2003;303-308.
9. Enright M.C., Spratt B.G. A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology. 144:1998;3049-3060.
10. Dingle K.E., et al. Multilocus sequence typing system for Campylobacter jejuni. J. Clin. Microbiol. 39:2001;14-23.
11. Suerbaum S., et al. Allelic diversity and recombination in Campylobacter jejuni. J. Bacteriol. 183:2001;2553-2559.
12. Kidgell C., et al. Salmonella typi, the causative agent of typhoid feaver, is approximately 50,000 years old. Infect. Genet. Evol. 2:2002;39-45.
13. Homan W.L., et al. Multilocus sequence typing scheme for Enterococcus faecium. J. Clin. Microbiol. 40:2002;1963-1971.
14. Feil E.J., et al. How clonal is Staphylococcus aureus? J. Bacteriol. 185:2003;3307-3316.
15. Meats E., et al. Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing. J. Clin. Microbiol. 41:2003;1623-1636.
16. Godoy D., et al. Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei. J. Clin. Microbiol. 41:2003;2068-2079.
17. Jones N., et al. Multilocus sequence typing system for group B Streptococcus. J. Clin. Microbiol. 41:2003;2530-2536.
18. Kotetishvili M., et al. Multilocus sequence typing has better discriminatory ability for typing Vibrio cholerae than does pulsed-field gel electrophoresis and provides a measure of phylogenetic relatedness. J. Clin. Microbiol. 41:2003;2191-2196.
19. Salcedo C., et al. Development of a multilocus sequence typing method for analysis of Listeria monocytogenes clones. J. Clin. Microbiol. 41:2003;757-762.
20. Holmes E.C., et al. The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol. Biol. Evol. 16:1999;741-749.
21. Bygraves J.A., et al. Population genetic and evolutionary approaches to the analysis of Neisseria meningitidis isolates belonging to the ET-5 complex. J. Bacteriol. 181:1999;5551-5556.
22. Enright M.C., et al. Molecular typing of bacteria directly from cerebrospinal fluid. Eur. J. Clin. Microbiol. Infect. Dis. 19:2000;627-630.
23. Kriz P., et al. Multilocus sequence typing of Neisseria meningitidis directly from cerebrospinal fluid. Epidemiol. Infect. 128:2002;157-160.
24. Jolley K.A., et al. Carried meningococci in the Czech Republic: a diverse recombining population. J. Clin. Microbiol. 38:2000;4492-4498.
25. Chan M.S., et al. Database-driven multi locus sequence typing (MLST) of bacterial pathogens. Bioinformatics. 17:2001;1077-1083.
26. Caugant D.A., et al. Genetic structure of Neisseria meningitidis populations in relation to serogroup, serotype, and outer membrane protein pattern. J. Bacteriol. 169:1987;2781-2792.
27. Dingle K.E., et al. Molecular characterisation of Campylobacter jejuni clones: a rational basis for epidemiological investigations. Emerg. Infect. Dis. 8:2002;949-955.
28. Huson D.H. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics. 14:1998;68-73.
29. Enright M.C., et al. The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proc. Natl. Acad. Sci. U. S. A. 99:2002;7687-7692.
30. Jolley K.A., et al. Sequence type analysis and recombinational tests (START). Bioinformatics. 17:2001;1230-1231.
31. Johnson C.N., et al. Genetic Relatedness of Levofloxacin-Nonsusceptible Streptococcus pneumoniae Isolates from North America. J. Clin. Microbiol. 41:2003;2458-2464.
32. de Sousa M.A., et al. Two international methicillin-resistant Staphylococcus aureus clones endemic in a university hospital in Patras. Greece. J. Clin. Microbiol. 41:2003;2027-2032.
33. Sadowy E., et al. Identification of multidrug-resistant Streptococcus pneumoniae strains isolated in Poland by multilocus sequence typing. Microb. Drug Resist. 9:2003;81-86.
34. Dicuonzo G., et al. Genotypes of invasive pneumococcal isolates recently recovered from Italian patients. J. Clin. Microbiol. 40:2002;3660-3665.
35. Shlush L.I., et al. Molecular epidemiological analysis of the changing nature of a meningococcal outbreak following a vaccination campaign. J. Clin. Microbiol. 40:2002;3565-3571.
36. Sa-Leao R., et al. Multilocus sequence typing of Streptococcus pneumoniae clones with unusual drug resistance patterns: genetic backgrounds and relatedness to other epidemic clones. J. Infect. Dis. 184:2001;1206-1210.
37. Crisostomo M.I., et al. The evolution of methicillin resistance in Staphylococcus aureus: similarity of genetic backgrounds in historically early methicillin-susceptible and -resistant isolates and contemporary epidemic clones. Proc. Natl. Acad. Sci. U. S. A. 98:2001;9865-9870.
38. Brueggemann A.B., et al. Clonal relationships between invasive and carriage Streptococcus pneumoniae and serotype- and clone-specific differences in invasive disease potential. J. Infect. Dis. 187:2003;1424-1432.
39. Meats E., et al. Stability of serotypes during nasopharyngeal carriage of Streptococcus pneumoniae. J. Clin. Microbiol. 41:2003;386-392.
40. Mayer L.W., et al. Outbreak of W135 meningococcal disease in 2000: not emergence of a new W135 strain but clonal expansion within the electophoretic type-37 complex. J. Infect. Dis. 185:2002;1596-1605.
41. Feil E.J., et al. Recombination within natural populations of pathogenic bacteria: short- term empirical estimates and long-term phylogenetic consequences. Proc. Natl. Acad. Sci. U. S. A. 98:2001;182-187.
42. Sreevatsan S., et al. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. U. S. A. 94:1997;9869-9874.
43. Achtman M., et al. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. U. S. A. 96:1999;14043-14048.
44. Suerbaum S., et al. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. U. S. A. 95:1998;12619-12624.
45. Achtman M., et al. Recombination and clonal groupings within Helicobacter pylori from different geographical regions. Mol. Microbiol. 32:1999;459-470.
46. Falush D., et al. Traces of human migrations in Helicobacter pylori populations. Science. 299:2003;1582-1585.
47. Falush D., et al. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc. Natl. Acad. Sci. U. S. A. 98:2001;15056-15061.
48. Tavanti, A. et al. Optimisation and validation of multilocus sequence typing for Candida albicans. J. Clin. Microbiol. (in press).
49. Bougnoux M.E., et al. Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. J. Clin. Microbiol. 40:2002;1290-1297.
50. Morehouse E.A., et al. Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone. Mol. Ecol. 12:2003;395-403.
51. Olive D.M., Bean P. Principles and applications of methods for DNA-based typing of microbial organisms. J. Clin. Microbiol. 37:1999;1661-1669.
52. Musser J.M. Molecular population genetic analysis of emerged bacterial pathogens: selected insights. Emerg. Infect. Dis. 2:1996;1-17.
53. Selander R.K., Levin B.R. Genetic diversity and structure in Escherichia coli populations. Science. 210:1980;545-547.
54. Dykhuizen D.E., et al. Borrelia burgdorferi is clonal: implications for taxonomy and vaccine development. Proc. Natl. Acad. Sci. U. S. A. 90:1993;10163-10167.
55. Boyd E.F., et al. Molecular genetic relationships of the salmonellae. Appl. Environ. Microbiol. 62:1996;804-808.
56. Maynard Smith J., et al. Localized sex in bacteria. Nature. 349:1991;29-31.
57. Maynard Smith J., et al. How clonal are bacteria? Proc. Natl. Acad. Sci. U. S. A. 90:1993;4384-4388.
58. Spratt B.G., et al. The relative contributions of recombination and point mutation to the diversification of bacterial clones. Curr. Opin. Microbiol. 4:2001;602-606.
59. Guttman D.S., Dykhuizen D.E. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science. 266:1994;1380-1383.
60. Feil E.J., Spratt B.G. Recombination and the population structures of bacterial pathogens. Annu. Rev. Microbiol. 55:2001;561-590.