Multilocus sequence typing for studying genetic relationships among Yersinia species

Journal of Clinical Microbiology

Volumn 43, Issue 6, 2005, Pages 2674-2684

  Kotetishvili, Mamuka ^a   Kreger, Arnold ^a   Wauters, Georges ^b   Morris Jr , J Glenn ^a   Sulakvelidze, Alexander ^a   Stine, O Colin ^a  

^a UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^b UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

O ANTIGEN;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; GENE LOCUS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC RECOMBINATION; GLNA GENE; GYRB GENE; MOLECULAR PHYLOGENY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PRIORITY JOURNAL; RECA GENE; RNA ANALYSIS; TAXONOMY; YERSINIA; YERSINIA ALDOVAE; YERSINIA BERCOVIERI; YERSINIA ENTEROCOLITICA; YERSINIA FREDERIKSENII; YERSINIA INTERMEDIA; YERSINIA KRISTENSENII; YERSINIA MOLLARETII; YERSINIA PESTIS; YERSINIA PSEUDOTUBERCULOSIS; YERSINIA ROHDEI; YERSINIA RUCKERI;

ANIMALS; BACTERIAL PROTEINS; BACTERIAL TYPING TECHNIQUES; DNA, BACTERIAL; DNA, RIBOSOMAL; DOGS; HUMANS; MOLECULAR SEQUENCE DATA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS); YERSINIA;

YERSINIA; YERSINIA ALDOVAE; YERSINIA BERCOVIERI; YERSINIA ENTEROCOLITICA; YERSINIA FREDERIKSENII; YERSINIA INTERMEDIA; YERSINIA KRISTENSENII; YERSINIA MOLLARETII; YERSINIA PESTIS; YERSINIA PSEUDOTUBERCULOSIS; YERSINIA ROHDEI; YERSINIA RUCKERI;

EID: 20444448503     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.43.6.2674-2684.2005     Document Type: Article

References (62)

1. Achtman, M., K. Zurth, G. Morelli, G. Torrea, A. Guiyoule, and E. Carniel. 1999. Yersihia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 96:14043-14048.
2. Adair, D. M., P. L. Worsham, K. K. Hill, A. M. Klevytska, P. J. Jackson, A. M. Friedlander, and P. Keim. 2000. Diversity in a variable-number tandem repeat from Yersinia pestis. J. Clin. Microbiol. 38:1516-1519.
3. Ahmad, S., W. G. Weisburg, and R. A. Jensen. 1990. Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria. J. Bacteriol. 172:1051-1061.
4. Aleksic, S. 1995. Occurrence of Y. enterocolitica antigens O:3, O:9 and O:8 in different Yersinia species, their corresponding H antigens and origin. Contrib. Microbiol. Immunol. 13:89-92.
5. Aleksic, S., and J. Bockemühl. 1999. Yersinia and other Enterobacteriaceae, p. 483-496. In P. R. Murray, E. J. Baron, M. A. Pfaller, F. C. Tenover, and R. H. Yolken (ed.), Manual of clinical microbiology, 7th ed. American Society for Microbiology, Washington, D.C.
6. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
7. Baker, P. M., and J. J. Farmer III. 1982. New bacteriophage typing system for Yersinia enterocolitica, Yersinia kristensenii, Yersinia frederiksenii, and Yersinia intermedia: correlation with serotyping, biotyping, and antibiotic susceptibility. J. Clin. Microbiol. 15:491-502.
8. Bercovier, H., H. H. Mollaret, J. M. Alonso, J. Brault, G. R. Fanning, A. G. Steigerwalt, and D. J. Brenner. 1980. Intra- and interspecies relatedness of Yersinia pestis by DNA hybridization and its relationship to Yersinia pseudotuberculosis. Curr. Microbiol. 4:225-229.
9. Blumberg, H. M., J. A. Kiehlbauch, and I. K. Wachsmuth. 1991. Molecular epidemiology of Yersinia enterocolitica O:3 infections: use of chromosomal DNA restriction fragment length polymorphisms of rRNA genes. J. Clin. Microbiol. 29:2368-2374.
10. Bottone, E. J. 1997. Yersinia enterocolitica: the charisma continues. Clin. Microbiol. Rev. 10:257-276.
11. Brenner, D. J., A. G. Steigerwalt, D. P. Falxo, R. E. Weaver, and G. R. Fanning. 1976. Characterization of Yersinia enterocolitica and Yersinia pseudotuberculosis by deoxyribonucleic acid hybridization and by biochemical reactions. Int. J. Syst. Bacteriol. 26:180-194.
12. Caugant, D. A., S. Aleksic, H. H. Mollaret, R. K. Selander, and G. Kapperud. 1989. Clonal diversity and relationships among strains of Yersinia enterocolitica. J. Clin. Microbiol. 27:2678-2683.
13. Cavalcanti, Y. V., N. C. Leal, and A. M. De Almeida. 2002. Typing of Yersinia pestis isolates from the state of Ceara, Brazil. Lett. Appl. Microbiol. 35:543-547.
14. Dang, H., and C. R. Lovell. 2000. Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl. Environ. Microbiol. 66:467-475.
15. Demarta, A., S. De Respinis, M. Dolina, and R. Peduzzi. 2004. Molecular typing of Yersinia frederiksenii strains by means of 16S rDNA and gyrB gene sequence analyses. FEMS Microbiol. Lett. 238:423-428.
16. Dolina, M., V. Gaia, and R. Peduzzi. 1995. Molecular typing of Yersinia frederiksenii strains by means of ribotyping and DNA-DNA hybridization. Contrib. Microbiol. Immunol. 13:140-144.
17. Dolina, M., and R. Peduzzi. 1993. Population genetics of human, animal, and environmental Yersinia strains. Appl. Environ. Microbiol. 59:442-450.
18. Enright, M. C., and B. G. Spratt. 1999. Multilocus sequence typing. Trends Microbiol. 7:482-487.
19. Ewing, B., and P. Greene. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8:175-185.
20. Ewing, B., and P. Greene. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8:186-194.
21. Ewing, W. H., A. J. Ross, D. J. Brenner, and G. R. Fanning. 1978. Yersinia ruckeri sp. nov., the redmouth (RM) bacterium. Int. J. Syst. Bacteriol. 28:37-44.
22. Garcia, J. A., L. Dominguez, J. L. Larsen, and K. Pedersen. 1998. Ribotyping and plasmid profiling of Yersinia ruckeri. J. Appl. Microbiol. 85:949-955.
23. Giacomelli, F., J. Wiener, J. B. Kruskal, J. V. Pomeranz, and A. V. Loud. 1971. Subpopulations of blood lymphocytes demonstrated by quantitative cytochemistry. J. Histochem. Cytochem. 19:426-433.
24. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
25. Goullet, P., and B. Picard. 1988. Characterization of Yersinia enterocolitica, Y. intermedia. Y. aldovae, Y. frederiksenii, Y. kristensenii and Y. pseudotuberculosis by electrophoretic polymorphism of acid phosphatase, esterases, and glutamate and malate dehydrogenases. J. Gen. Microbiol. 134:317-325.
26. Goullet, P., and B. Picard. 1984. Distinctive electrophoretic and isoelectric focusing patterns of esterases from Yersinia enterocolitica and Yersinia pseudotuberculosis. J. Gen. Microbiol. 130:1471-1480.
27. Hinchlifle, S. J., K. E. Isherwood, R. A. Stabler, M. B. Prentice, A. Rakin, R. A. Nichols, P. C. Oyston, J. Hinds, R. W. Titball, and B. W. Wren. 2003. Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res. 13:2018-2029.
28. Holmes, E. C., R. Urwin, and M. C. Maiden. 1999. The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol. Biol. Evol. 16:741-749.
29. Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:366-376.
30. Huson, D. H. 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14:68-73.
31. Ibrahim, A. 1995. Genetic diversity among Yersinia enterocolitica strains as revealed by sequence analysis of the 16S rRNA gene. Contrib. Microbiol. Immunol. 13:277-280.
32. Ibrahim, A., B. M. Goebel, W. Liesack, M. Griffiths, and E. Stackebrandt. 1993. The phylogeny of the genus Yersinia based on 16S rDNA sequences. FEMS Microbiol. Lett. 114:173-177.
33. Ibrahim, A., W. Liesack, A. G. Steigerwalt, D. J. Brenner, E. Stackebrandt, and R. M. Robins-Browne. 1997. A cluster of atypical Yersinia strains with a distinctive 16S rRNA signature. FEMS Microbiol. Lett. 146:73-78.
34. Iteman, I., A. Guiyoule, and E. Carniel. 1996. Comparison of three molecular methods for typing and subtyping pathogenic Yersinia enterocolitica strains. J. Med. Microbiol. 45:48-56.
35. Jeanmougin, F., J. D. Thompson, M. Gouy, D. G. Higgins, and T. J. Gibson. 1998. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23:403-405.
36. Jolley, K. A., E. J. Feil, M. S. Chan, and M. C. Maiden. 2001. Sequence type analysis and recombinational tests (START). Bioinformatics 17:1230-1231.
37. Kotetishvili, M., O. C. Stine, A. Kreger, J. G. Morris, Jr., and A. Sulakvelidze. 2002. Multilocus sequence typing for characterization of clinical and environmental Salmonella strains. J. Clin. Microbiol. 40:1626-1635.
38. Kwaga, J., J. O. Iversen, and V. Misra. 1992. Detection of pathogenic Yersinia enterocolitica by polymerase chain reaction and digoxigenin-labeled polynucleotide probes. J. Clin. Microbiol. 30:2668-2673.
39. Lan, R., and P. R. Reeves. 2001. When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol. 9:419-424.
40. Lobato, M. J., E. Landeras, M. A. Gonzalez-Hevia, and M. C. Mendoza. 1998. Genetic heterogeneity of clinical strains of Yersinia enterocolitica traced by ribotyping and relationships between ribotypes, serotypes, and biotypes. J. Clin. Microbiol. 36:3297-3302.
41. Maiden, M. C., J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell, R. Urwin, Q. Zhang, J. Zhou, K. Zurth, D. A. Caugant, I. M. Feavers, M. Achtman, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95:3140-3145.
42. Mendoza, M. C., R. Alzugaray, E. Landeras, and M. A. Gonzalez-Hevia. 1996. Discriminatory power and application of ribotyping of Yersinia enterocolitica O:3 in an epidemiological study. Eur. J. Clin. Microbiol. Infect. Dis. 15:220-226.
43. Najdenski, H., I. Iteman, and E. Carniel. 1994. Efficient subtyping of pathogenic Yersinia enterocolitica strains by pulsed-field gel electrophoresis. J. Clin. Microbiol. 32:2913-2920.
44. Nilehn, B. 1971. Some aspects on phage typing of Yersinia enterocolitica. Acta Pathol. Microbiol. Scand. B 79:446-447.
45. Parkhill, J., B. W. Wren, N. R. Thomson, R. W. Titball, M. T. Holden, M. B. Prentice, M. Sebaihia, K. D. James, C. Churcher, K. L. Mungall, S. Baker, D. Basham, S. D. Bentley, K. Brooks, A. M. Cerdeno-Tarraga, T. Chillingworth, A. Cronin, R. M. Davies, P. Davis, G. Dougan, T. Feltwell, N. Hamlin, S. Holroyd, K. Jagels, A. V. Karlyshev, S. Leather, S. Moule, P. C. Oyston, M. Quail, K. Rutherford, M. Simmonds, J. Skelton, K. Stevens, S. Whitehead, and B. G. Barrell. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413:523-527.
46. Perry, R. D., and J. D. Fetherston. 1997. Yersinia pestis-etiologic agent of plague. Clin. Microbiol. Rev. 10:35-66.
47. Revazishvili, T., M. Kotetishvili, O. C. Stine, A. S. Kreger, J. G. Morris, Jr., and A. Sulakvelidze. 2004. Comparative analysis of multilocus sequence typing and pulsed-field gel electrophoresis for characterizing Listeria monocytogenes strains isolated from environmental and clinical sources. J. Clin. Microbiol. 42:276-285.
48. Schill, W. B., S. R. Phelps, and S. W. Pyle. 1984. Multilocus electrophoretic assessment of the genetic structure and diversity of Yersinia ruckeri. Appl. Environ. Microbiol. 48:975-979.
49. Selander, R. K., D. A. Caugant, H. Ochman, J. M. Musser, M. N. Gilmour, and T. S. Whittam. 1986. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51:873-884.
50. Shubin, F. N., A. L. Gintsburg, V. M. Kitaev, N. V. Ianishevskii, and Z. G. Zenkova. 1989. Analysis of the plasmid composition of Yersinia pseudotuberculosis strains and its use for typing pseudotuberculosis pathogens. Mol. Gen. Mikrobiol. Virusol. 6:20-25.
51. Skurnik, M., and P. Toivanen. 1993. Yersinia enterocolitica lipopolysaccharide: genetics and virulence. Trends Microbiol. 1:148-152.
52. Smith, J. M., E. J. Feil, and N. H. Smith. 2000. Population structure and evolutionary dynamics of pathogenic bacteria. Bioessays 22:1115-1122.
53. Stackebrandt, E., W. Frederiksen, G. M. Garrity, P. A. Grimont, P. Kampfer, M. C. Maiden, X. Nesme, R. Rossello-Mora, J. Swings, H. G. Truper, L. Vauterin, A. C. Ward, and W. B. Whitman. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52:1043-1047.
54. Stroeher, U. H., and P. A. Manning. 1997. Vibrio cholerae serotype O139: swapping genes for surface polysaccharide biosynthesis. Trends Microbiol. 5:178-180.
55. Sulakvelidze, A. 2000. Yersiniae other than Y. enterocolitica, Y. pseudotuberculosis, and Y. pestis: the ignored species. Microbes Infect. 2:497-513.
56. Trebesius, K., D. Harmsen, A. Rakin, J. Schmelz, and J. Heesemann. 1998. Development of rRNA-targeted PCR and in situ hybridization with fluorescently labelled oligonucleotides for detection of Yersinia species. J. Clin. Microbiol. 36:2557-2564.
57. Ursing, J., and S. Aleksic. 1995. Yersinia frederiksenii, a genotypically heterogeneous species with few differential characteristics. Contrib. Microbiol. Immunol. 13:112-116.
58. Wauters, G., S. Aleksic, J. Charlier, and G. Schulze. 1991. Somatic and flagellar antigens of Yersinia enterocolitica and related species. Contrib. Microbiol. Immunol. 12:239-243.
59. Weinstock, G. M. 2000. Genomics and bacterial pathogenesis. Emerg. Infect. Dis. 6:496-504.
60. Woese, C. R., and G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74:5088-5090.
61. Zhang, L., J. Radziejewska-Lebrecht, D. Krajewska-Pietrasik, P. Toivanen, and M. Skurnik. 1997. Molecular and chemical characterization of the lipopolysaccharide O-antigen and its role in the virulence of Yersinia enterocolitica serotype O:8. Mol. Microbiol. 23:63-76.
62. Zhou, S., W. Deng, T. S. Anantharaman, A. Lim, E. T. Dimalanta, J. Wang, T. Wu, T. Chunhong, R. Creighton, A. Kile, E. Kvikstad, M. Bechner, G. Yen, A. Garic-Stankovic, J. Severin, D. Forrest, R. Runnheim, C. Churas, C. Lamers, N. T. Perna, V. Burland, F. R. Blattner, B. Mishra, and D. C. Schwartz. 2002. A whole-genome shotgun optical map of Yersinia pestis strain KIM. Appl. Environ. Microbiol. 68:6321-6331.