Selection and validation of a multilocus variable-number tandem-repeat analysis panel for typing Shigella spp.

Journal of Clinical Microbiology

Volumn 46, Issue 3, 2008, Pages 1026-1036

  Gorgé, Olivier ^a   Lopez, Stéphanie ^a   Hilaire, Valérie ^a   Lisanti, Olivier ^a   Ramisse, Vincent ^a   Vergnaud, Gilles ^a,b  

^a CENTRE D ETUDES DU BOUCHET   (France)

^b UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; ESCHERICHIA COLI; GENE SEQUENCE; GENOTYPE; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SHIGELLA; SHIGELLA BOYDII; SHIGELLA DYSENTERIAE; SHIGELLA FLEXNERI; SHIGELLA SONNEI; VARIABLE NUMBER OF TANDEM REPEAT;

BACTERIAL TYPING TECHNIQUES; DNA, BACTERIAL; DYSENTERY, BACILLARY; GENOME, BACTERIAL; HUMANS; MINISATELLITE REPEATS; SEQUENCE ANALYSIS, DNA; SHIGELLA;

BACTERIA (MICROORGANISMS); ESCHERICHIA; ESCHERICHIA COLI; SHIGELLA;

EID: 40749101543     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.02027-07     Document Type: Article

References (52)

1. Al Dahouk, S., P. Le Flèche, K. Nockler, I. Jacques, M. Grayon, H. C. Scholz, H. Tomaso, G. Vergnaud, and H. Neubauer. 2007. Evaluation of Brucella MLVA typing for human brucellosis. J. Microbiol. Methods 69:137-145.
2. Chaignat, C. 2004. Shigellosis, p. 527-531. In D. L. Heyman (ed.), Control of communicable diseases manual, 18th ed. American Public Health Association, Washington, DC.
3. Denoeud, F., and G. Vergnaud. 2004. Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains: a web-based resource. BMC Bioinformatics 5:4.
4. Escobar-Paramo, P., C. Giudicelli, C. Parsot, and E. Denamur. 2003. The evolutionary history of Shigella and enteroinvasive Escherichia coli revised. J. Mol. Evol. 57:140-148.
5. Faruque, S. M., K. Haider, M. M. Rahman, A. R. Abdul Alim, Q. S. Ahmad, M. J. Albert, and R. B. Sack. 1992. Differentiation of Shigella flexneri strains by rRNA gene restriction patterns. J. Clin. Microbiol. 30:2996-2999.
6. Grissa, I., P. Bouchon, C. Pourcel, and G. Vergnaud. On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing. Biochimie, in press.
7. Hunter, P. R., and M. A. Gaston. 1988. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J. Clin. Microbiol. 26:2465-2466.
8. Hyma, K. E., D. W. Lacher, A. M. Nelson, A. C. Bumbaugh, J. M. Janda, N. A. Strockbine, V. B. Young, and T. S. Whittam. 2005. Evolutionary genetics of a new pathogenic Escherichia species: Escherichia albertii and related Shigella boydii strains. J. Bacteriol. 187:619-628.
9. Hyytia-Trees, E., S. C. Smole, P. A. Fields, B. Swaminathan, and E. M. Ribot. 2006. Second generation subtyping: a proposed PulseNet protocol for multiple-locus variable-number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 (STEC O157). Foodborne Pathog. Dis. 3:118-131.
10. Jin, Q., Z. Yuan, J. Xu, Y. Wang, Y. Shen, W. Lu, J. Wang, H. Liu, J. Yang, F. Yang, X. Zhang, J. Zhang, G. Yang, H. Wu, D. Qu, J. Dong, L. Sun, Y. Xue, A. Zhao, Y. Gao, J. Zhu, B. Kan, K. Ding, S. Chen, H. Cheng, Z. Yao, B. He, R. Chen, D. Ma, B. Qiang, Y. Wen, Y. Hou, and J. Yu. 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30:4432-4441.
11. Johansson, A., J. Farlow, P. Larsson, M. Dukerich, E. Chambers, M. Bystrom, J. Fox, M. Chu, M. Forsman, A. Sjostedt, and P. Keim. 2004. Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis. J. Bacteriol. 186:5808-5818.
12. Keys, C., S. Kemper, and P. Keim. 2005. Highly diverse variable number tandem repeat loci in the E. coli O157:H7 and O55:H7 genomes for high-resolution molecular typing. J. Appl. Microbiol. 98:928-940.
13. Koeck, J. L., B. M. Njanpop-Lafourcade, S. Cade, E. Varon, L. Sangare, S. Valjevac, G. Vergnaud, and C. Pourcel. 2005. Evaluation and selection of tandem repeat loci for Streptococcus pneumoniae MLVA strain typing. BMC Microbiol. 5:66.
14. Kuhnert, P., J. Nicolet, and J. Frey. 1995. Rapid and accurate identification of Escherichia coli K-12 strains. Appl. Environ. Microbiol. 61:4135-4139.
15. Lan, R., M. C. Alles, K. Donohoe, M. B. Martinez, and P. R. Reeves. 2004. Molecular evolutionary relationships of enteroinvasive Escherichia coli and Shigella spp. Infect. Immun. 72:5080-5088.
16. Lan, R., and P. R. Reeves. 2002. Escherichia coli in disguise: molecular origins of Shigella. Microbes Infect. 4:1125-1132.
17. Le Flèche, P., M. Fabre, F. Denoeud, J. L. Koeck, and G. Vergnaud. 2002. High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing. BMC Microbiol. 2:37.
18. Le Flèche, P., Y. Hauck, L. Onteniente, A. Prieur, F. Denoeud, V. Remisse, P. Sylvestre, G. Benson, F. Remisse, and G. Vergnaud. 2001. A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiol. 1:2.
19. Le Flèche, P., I. Jacques, M. Grayon, S. Al Dahouk, P. Bouchon, F. Denoeud, K. Nockler, H. Neubauer, L. A. Guilloteau, and G. Vergnaud. 2006. Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay. BMC Microbiol. 6:9.
20. Liang, S. Y., H. Watanabe, J. Terajima, C. C. Li, J. C. Liao, S. K. Tung, and C. S. Chiou. 2007. Multilocus variable-number tandem repeat analysis for molecular typing of Shigella sonnei. J. Clin. Microbiol. 45:3574-3580.
21. Lindstedt, B. A. 2005. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 26:2567-2582.
22. Lindstedt, B. A., L. T. Brandal, L. Aas, T. Vardund, and G. Kapperud. 2007. Study of polymorphic variable-number of tandem repeats loci in the ECOR collection and in a set of pathogenic Escherichia coli and Shigella isolates for use in a genotyping assay. J. Microbiol. Methods 69:197-205.
23. Lindstedt, B. A., E. Heir, E. Gjernes, T. Vardund, and G. Kapperud. 2003. DNA fingerprinting of Shiga-toxin producing Escherichia coli O157 based on multiple-locus variable-number tandem-repeats analysis (MLVA). Ann. Clin. Microbiol. Antimicrob. 2:12.
24. Lista, F., G. Faggioni, S. Valjevac, A. Ciammaruconi, J. Vaissaire, C. le Doujet, O. Gorgé, R. De Santis, A. Carattoli, A. Ciervo, A. Fasanella, F. Orsini, R. D'Amelio, C. Pourcel, A. Cassone, and G. Vergnaud. 2006. Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis. BMC Microbiol. 6:33.
25. Litwin, C. M., A. L. Storm, S. Chipowsky, and K. J. Ryan. 1991. Molecular epidemiology of Shigella infections: plasmid profiles, serotype correlation, and restriction endonuclease analysis. J. Clin. Microbiol. 29:104-108.
26. Liu, P. Y., Y. J. Lau, B. S. Hu, J. M. Shyr, Z. Y. Shi, W. S. Tsai, Y. H. Lin, and C. Y. Tseng. 1995. Analysis of clonal relationships among isolates of Shigella sonnei by different molecular typing methods. J. Clin. Microbiol. 33:1779-1783.
27. Matsutani, S., H. Ohtsubo, Y. Maeda, and E. Ohtsubo. 1987. Isolation and characterization of IS elements repeated in the bacterial chromosome. J. Mol. Biol. 196:445-455.
28. Melito, P. L., D. L. Woodward, J. Munro, J. Walsh, R. Foster, P. Tilley, A. Paccagnella, J. Isaac-Renton, J. Ismail, and L. K. Ng. 2005. A novel Shigella dysenteriae serovar isolated in Canada. J. Clin. Microbiol. 43:740-744.
29. Noller, A. C., M. C. McEllistrem, A. G. Pacheco, D. J. Boxrud, and L. H. Harrison. 2003. Multilocus variable-number tandem repeat analysis distinguishes outbreak and sporadic Escherichia coli O157:H7 isolates. J. Clin. Microbiol. 41:5389-5397.
30. Onteniente, L., S. Brisse, P. T. Tassios, and G. Vergnaud. 2003. Evaluation of the polymorphisms associated with tandem repeats for Pseudomonas aeruginosa strain typing. J. Clin. Microbiol. 41:4991-4997.
31. Pourcel, C., F. Andre-Mazeaud, H. Neubauer, F. Ramisse, and G. Vergnaud. 2004. Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis. BMC Microbiol. 4:22.
32. Pourcel, C., Y. Vidgop, F. Ramisse, G. Vergnaud, and C. Tram. 2003. Characterization of a tandem repeat polymorphism in Legionella pneumophila and its use for genotyping. J. Clin. Microbiol. 41:1819-1826.
33. Pourcel, C., P. Visca, B. Afshar, S. D'Arezzo, G. Vergnaud, and N. K. Fry. 2007. Identification of variable-number tandem repeat sequences in Legionella pneumophila and development of an optimized MLVA typing scheme. J. Clin. Microbiol. 45:1190-1199.
34. Pupo, G. M., D. K. Karaolis, R. Lan, and P. R. Reeves. 1997. Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies. Infect. Immun. 65:2685-2692.
35. Pupo, G. M., R. Lan, and P. R. Reeves. 2000. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc. Natl. Acad. Sci. USA 97:10567-10572.
36. Ramisse, V., P. Houssu, E. Hernandez, F. Denoeud, V. Hilaire, O. Lisanti, F. Ramisse, J. D. Cavallo, and G. Vergnaud. 2004. Variable number of tandem repeats in Salmonella enterica subsp. enterica for typing purposes. J. Clin. Microbiol. 42:5722-5730.
37. Ribot, E. M., M. A. Fair, R. Gautom, D. N. Cameron, S. B. Hunter, B. Swaminathan, and T. J. Barrett. 2006. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog. Dis. 3:59-67.
38. Rotz, L. D., A. S. Khan, S. R. Lillibridge, S. M. Ostroff, and J. M. Hughes. 2002. Public health assessment of potential biological terrorism agents. Emerg. Infect. Dis. 8:225-230.
39. Rozen, S., and H. Skaletsky. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132:365-386.
40. Sabat, A., J. Krzyszton-Russjan, W. Strzalka, R. Filipek, K. Kosowska, W. Hryniewicz, J. Travis, and J. Potempa. 2003. New method for typing Staphylococcus aureus strains: multiple-locus variable-number tandem repeat analysis of polymorphism and genetic relationships of clinical isolates. J. Clin. Microbiol. 41:1801-1804.
41. Sambrook, J., and D. Russell. 2001. Molecular cloning, a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
42. Swaminathan, B., T. J. Barrett, S. B. Hunter, and R. V. Tauxe. 2001. PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg. Infect. Dis. 7:382-389.
43. U'Ren, J. M., J. M. Schupp, T. Pearson, H. Hornstra, C. L. Friedman, K. L. Smith, R. R. Daugherty, S. D. Rhoton, B. Leadem, S. Georgia, M. Cardon, L. Y. Huynh, D. DeShazer, S. P. Harvey, R. Robison, D. Gal, M. J. Mayo, D. Wagner, B. J. Currie, and P. Keim. 2007. Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping. BMC Microbiol. 7:23.
44. van Belkum, A. 2007. Tracing isolates of bacterial species by multilocus variable number of tandem repeat analysis (MLVA). FEMS Immunol. Med. Microbiol. 49:22-27.
45. Vergnaud, G., and C. Pourcel. 2006. Multiple locus VNTR (variable number of tandem repeat) analysis (MLVA), p. 83-104. In E. Stackebrandt (ed.), Molecular identification, systematics and population structure of prokaryotes, 1st ed. Springer-Verlag, New York, NY.
46. von Seidlein, L., D. R. Kim, M. Ali, H. Lee, X. Wang, V. D. Thiem, G. Canh do, W. Chaicumpa, M. D. Agtini, A. Hossain, Z. A. Bhutta, C. Mason, O. Sethabutr, K. Talukder, G. B. Nair, J. L. Deen, K. Kotloff, and J. Clemens. 2006. A multicentre study of Shigella diarrhoea in six Asian countries: disease burden, clinical manifestations, and microbiology. PLoS Med. 3:e353.
47. Vu-Thien, H., G. Corbineau, K. Hormigos, B. Fauroux, H. Corvol, A. Clement, G. Vergnaud, and C. Pourcel. 2007. Multiple-locus variable-number tandem-repeat analysis for longitudinal survey of sources of Pseudomonas aeruginosa infection in cystic fibrosis patients. J. Clin. Microbiol. 45:3175-3183.
48. Wei, J., M. B. Goldberg, V. Burland, M. M. Venkatesan, W. Deng, G. Fournier, G. F. Mayhew, G. Plunkett III, D. J. Rose, A. Darling, B. Mau, N. T. Perna, S. M. Payne, L. J. Runyen-Janecky, S. Zhou, D. C. Schwartz, and F. R. Blattner. 2003. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71:2775-2786.
49. Woodward, D. L., C. G. Clark, R. A. Caldeira, R. Ahmed, G. Soule, L. Bryden, H. Tabor, P. Melito, R. Foster, J. Walsh, L. K. Ng, G. B. Malcolm, N. Strockbine, and F. G. Rodgers. 2005. Identification and characterization of Shigella boydii 20 serovar nov., a new and emerging Shigella serotype. J. Med. Microbiol. 54:741-748.
50. Yang, F., J. Yang, X. Zhang, L. Chen, Y. Jiang, Y. Yan, X. Tang, J. Wang, Z. Xiong, J. Dong, Y. Xue, Y. Zhu, X. Xu, L. Sun, S. Chen, H. Nie, J. Peng, J. Xu, Y. Wang, Z. Yuan, Y. Wen, Z. Yao, Y. Shen, B. Qiang, Y. Hou, J. Yu, and Q. Jin. 2005. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 33:6445-6458.
51. Yang, J., L. Chen, J. Yu, L. Sun, and Q. Jin. 2006. ShiBASE: an integrated database for comparative genomics of Shigella. Nucleic Acids Res. 34:D398-D401.
52. Yang, J., H. Nie, L. Chen, X. Zhang, F. Yang, X. Xu, Y. Zhu, J. Yu, and Q. Jin. 2007. Revisiting the molecular evolutionary history of Shigella spp. J. Mol. Evol 64:71-79.