Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains

Microbiology

Volumn 153, Issue 5, 2007, Pages 1488-1498

  Labbate, M ^a   Boucher, Y ^a   Joss, M J ^a   Michael, C A ^a   Gillings, M R ^a   Stokes, H W ^a  

^a MACQUARIE UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARGENTINA; ARTICLE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CHOLERA; CHROMOSOMAL LOCALIZATION; CONTROLLED STUDY; DNA MICROARRAY; ENDEMIC DISEASE; GENE CASSETTE; GENE DELETION; GENE INSERTION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC RECOMBINATION; HORIZONTAL GENE TRANSFER; HYPOTHESIS; INTEGRON; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PANDEMIC; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; STRAIN DIFFERENCE; UNINDEXED SEQUENCE; VIBRIO CHOLERAE;

BACTERIAL TYPING TECHNIQUES; CHOLERA; CHROMOSOMES, BACTERIAL; CLUSTER ANALYSIS; DISEASE OUTBREAKS; DNA, BACTERIAL; EPIDEMIOLOGY, MOLECULAR; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; HUMANS; INTEGRONS; INTERSPERSED REPETITIVE SEQUENCES; MOLECULAR SEQUENCE DATA; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; VIBRIO CHOLERAE;

VIBRIO CHOLERAE;

EID: 34249103696     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.2006/001065-0     Document Type: Article

References (36)

1. Arakawa, E., Murase, T., Matsushita, S., Shimada, T., Yamai, S., Ito, T. & Watanabe, H. (2000). Pulsed-field gel electrophoresis-based molecular comparison of Vibrio cholerae O1 isolates from domestic and imported cases of cholera in Japan. J Clin Microbiol 38, 424-426.
2. Ausubel, F. A., Brent R., Kingston, R. F., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. (1998). Current Protocols in Molecular Biology. New York: Wiley.
3. Barker, A., Clark, C. A. & Manning, P. A. (1994). Identification of VCR, a repeated sequence associated with a locus encoding a hemagglutinin in Vibrio cholerae O1. J Bacteriol 176, 5450-5458.
4. Boucher, Y., Nesbo, C., Joss, M., Robinson, A., Mabbutt, B., Gillings, M., Doolittle, W. F. & Stokes, H. W. (2006). Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio. BMC Evol Biol 6, 3.
5. Byun, R., Elbourne, L. D. H., Lan, R. & Reeves, P. R. (1999). Evolutionary relationships of pathogenic clones of Vibrio cholerae by sequence analysis of four housekeeping genes. Infect Immun 67, 1116-1124.
6. Castañeda, N. C., Pichel, M., Orman, B., Binsztein, N., Roy, P. H. & Centrón, D. (2005). Genetic characterization of Vibrio cholerae isolates from Argentina by V. cholerae repeated sequences-polymerase chain reaction. Diagn Microbiol Infect Dis 53, 175-183.
7. Clark, C. A., Purins, L., Kaewrakon, P., Focareta, T. & Manning, P. A. (2000). The Vibrio cholerae O1 chromosomal integron. Microbiology 146, 2605-2612.
8. Collis, C. & Hall, R. (1995). Expression of antibiotic resistance genes in the integrated cassettes of integrons. Antimicrob Agents Chemother 39, 155-162.
9. Dziejman, M., Serruto, D., Tam, V. C., Sturtevant, D., Diraphat, P., Faruque, S. M., Rahman, M. H., Heidelberg, J. F., Decker, J. & other authors (2005). Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system. Proc Natl Acad Sci U S A 102, 3465-3470.
10. Faruque, S. M. & Mekalanos, J. J. (2003). Pathogenicity islands and phages in Vibrio cholerae evolution. Trends Microbiol 11, 505-510.
11. Faruque, S. M., Albert, M. J. & Mekalanos, J. J. (1998). Epidemiology, genetics, and ecology of toxigenic Vibrio cholerae. Microbiol Mol Biol Rev 62, 1301-1314.
12. Franzon, V. L., Barker, A. & Manning, P. A. (1993). Nucleotide sequence encoding the mannose-fucose-resistant hemagglutinin of Vibrio cholerae O1 and construction of a mutant. Infect Immun 61, 3032-3037.
13. Gillings, M. R., Holley, M. P., Stokes, H. W. & Holmes, A. J. (2005). Integrons in Xanthomonas: a source of species genome diversity. Proc Natl Acad Sci U S A 102, 4419-4424.
14. Hall, R. M., Collis, C. M., Kim, M.-J., Partridge, S. R., Recchia, G. D. & Stokes, H. W. (1999). Mobile gene cassettes and integrons in evolution. Ann N Y Acad Sci 870, 68-80.
15. Holmes, A. J., Gillings, M. R., Nield, B. S., Mabbutt, B. C., Nevalainen, K. M. H. & Stokes, H. W. (2003). The gene cassette metagenome is a basic resource for bacterial genome evolution. Environ Microbiol 5, 383-394.
16. Kaper, J., Morris, J., Jr & Levine, M. (1995). Cholera. Clin Microbiol Rev 8, 48-86.
17. Kim, Y. R., Lee, S. E., Kim, C. M., Kim, S. Y., Shin, E. K., Shin, D. H., Chung, S. S., Choy, H. E., Progulske-Fox, A. & other authors (2003). Characterization and pathogenic significance of Vibrio vulnificus antigens preferentially expressed in septicemic patients. Infect Immun 71, 5461-5471.
18. Kotetishvili, M., Stine, O. C., Chen, Y., Kreger, A., Sulakvelidze, A., Sozhamannan, S. & Morris, J. G., Jr (2003). 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, 2191-2196.
19. Lan, R. & Reeves, P. R. (2002). Pandemic spread of cholera: genetic diversity and relationships within the seventh pandemic clone of Vibrio cholerae determined by amplified fragment length polymorphism. J Clin Microbiol 40, 172-181.
20. Lee, J. H., Yang, S.-T., Rho, S.-H., Im, Y. J., Kim, S. Y., Kim, Y. R., Kim, M.-K., Kang, G. B., Kim, J. I. & other authors (2006). Crystal structure and functional studies reveal that PAS factor from Vibrio vulnificus is a novel member of the saposin-fold family. J Mol Biol 355, 491-500.
21. Mazel, D., Dychinco, B., Webb, V. A. & Davies, J. (1998). A distinctive class of integron in the Vibrio cholerae genome. Science 280, 605-608.
22. Michael, C. A., Gillings, M. R., Holmes, A. J., Hughes, L., Andrew, N. R., Holley, M. P. & Stokes, H. W. (2004). Mobile gene cassettes: a fundamental resource for bacterial evolution. Am Nat 164, 1-12.
23. O'Shea, Y. A., Reen, F. J., Quirke, A. M. & Boyd, E. F. (2004). Evolutionary genetic analysis of the emergence of epidemic Vibrio cholerae isolates on the basis of comparative nucleotide sequence analysis and multilocus virulence gene profiles. J Clin Microbiol 42, 4657-4671.
24. Posada, D. & Crandall, K. A. (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818.
25. Ramamurthy, T., Yamasaki, S., Takeda, Y. & Nair, G. B. (2003). Vibrio cholerae O139 Bengal: odyssey of a fortuitous variant. Microbes Infect 5, 329-344.
26. Rowe-Magnus, D. A., Guerout, A.-M., Biskri, L., Bouige, P. & Mazel, D. (2003). Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res 13, 428-442.
27. Salim, A., Lan, R. & Reeves, P. R. (2005). Vibrio cholerae pathogenic clones. Emerg Infect Dis 11, 1758-1760.
28. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
29. Shimada, T., Balakrish Nair, G., Deb, B. C., Albert, M. J., Sack, R. B. & Takeda, Y. (1993). Outbreak of Vibrio cholerae non-O1 in India and Bangladesh. Lancet 341, 1346-1347.
30. Stine, O. C., Sozhamannan, S., Gou, O., Zheng, S., Morris, J. G., Jr & Johnson, J. A. (2000). Phylogeny of Vibrio cholerae based on recA sequence. Infect Immun 68, 7180-7185.
31. Stokes, H. W., O'Gorman, D. B., Recchia, G. D., Parsekhian, M. & Hall, R. M. (1997). Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol Microbiol 26, 731-745.
32. Stroeher, U. H., Jedani, K. E., Dredge, B. K., Morona, R., Brown, M. H., Karageorgos, L. E., Albert, M. J. & Manning, P. A. (1995). Genetic rearrangements in the rfb regions of Vibrio cholerae O1 and O139. Proc Natl Acad Sci U S A 92, 10374-10378.
33. Stroeher, U. H., Parasivam, G., Dredge, B. K. & Manning, P. A. (1997). Novel Vibrio cholerae O139 genes involved in lipopolysac-charide biosynthesis. J Bacteriol 179, 2740-2747.
34. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
35. Tillett, D. & Neilan, B. A. (2000). Xanthogenate nucleic acid isolation from cultured and environmental cyanobacteria. J Phycol 36, 251-258.
36. van Dongen, W. M. A. M. & DeGraaf, F. K. (1986). Molecular cloning of a gene coding for a Vibrio cholerae haemagglutinin. J Gen Microbiol 132, 2225-2234.