1887

Abstract

Variable-number tandem repeats (VNTRs) have been shown to be a powerful tool in the determination of evolutionary relationships and population genetics of bacteria. The sequencing of a number of genomes has allowed the identification of novel VNTR sequences in , which are similar to those used in the study of the evolution of clades. Seven VNTRs, termed staphylococcal interspersed repeat units (SIRUs), distributed around the genome are described, occurring in both unique and multiple sites, and varying in length from 48 to 159 bp. Variations in copy numbers were observed in all loci, within both the sequenced genomes and the UK epidemic methicillin-resistant (EMRSA) isolates. Clonally related UK EMRSA isolates were clustered using SIRUs, which provided a greater degree of discrimination than multi-locus sequence typing, indicating that VNTRs may be a more appropriate evolutionary marker for studying transmission events and the geographical spread of clades.

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2004-12-01
2019-10-13
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References

  1. Baba, T., Takeuchi, F., Kuroda, M. & 11 other authors ( 2002; ). Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 359, 1819–1827.[CrossRef]
    [Google Scholar]
  2. Bennett, S. T., Lucassen, A. M., Gough, S. C. & 7 other authors ( 1995; ). Susceptibility to human type 1 diabetes at IDDM2 is determined by tandem repeat variation at the insulin gene minisatellite locus. Nat Genet 9, 284–292.[CrossRef]
    [Google Scholar]
  3. Blanc, D. S., Francioli, P. & Hauser, P. M. ( 2002; ). Poor value of pulsed-field gel electrophoresis to investigate long-term scale epidemiology of methicillin-resistant Staphylococcus aureus. Infect Genet Evol 2, 145–148.[CrossRef]
    [Google Scholar]
  4. Enright, M. C., Day, N. P., Davies, C. E., Peacock, S. J. & Spratt, B. G. ( 2000; ). Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J Clin Microbiol 38, 1008–1015.
    [Google Scholar]
  5. Enright, M. C., Robinson, D. A., Randle, G., Feil, E. J., Grundmann, H. & Spratt, B. G. ( 2002; ). The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proc Natl Acad Sci U S A 99, 7687–7692.[CrossRef]
    [Google Scholar]
  6. Frothingham, R. & Meeker-O'Connell, W. A. ( 1998; ). Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 144, 1189–1196.[CrossRef]
    [Google Scholar]
  7. Hawkey, P. M., Smith, E. G., Evans, J. T., Monk, G., Bryan, H., Mohamed, H. & Bardhan M.& Pugh, R. N. ( 2003; ). Mycobacterial interspersed repetitive unit typing of Mycobacterium tuberculosis compared to IS6110-based restriction fragement length polymorphism analysis for investigation of apparently clustered cases of tuberculosis. J. Clin. Microbiol 41, 3514–3520.[CrossRef]
    [Google Scholar]
  8. Holden, M. T., Feil, E. J., Lindsay, J. A. & 42 other authors ( 2004; ). Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A 101, 9786–9791.[CrossRef]
    [Google Scholar]
  9. Jeffreys, A. J., Wilson, V. & Thein, S. L. ( 1985; ). Individual-specific ‘finger-prints' of human DNA. Nature 316, 76–79.[CrossRef]
    [Google Scholar]
  10. Jeffreys, A. J., Wilson, V. & Thein, S. L. ( 1992; ). Hypervariable ‘minisatellite’ regions in human DNA. Biotechnology 24, 467–472.
    [Google Scholar]
  11. Keim, P., Price, L. B., Klevytska, A. M., Smith, K. L., Schupp, J. M., Okinaka, R., Jackson, P. J. & Hugh-Jones, M. E. ( 2000; ). Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J Bacteriol 182, 2928–2936.[CrossRef]
    [Google Scholar]
  12. Kerr, S., Kerr, G. E., Makintosh, C. A. & Marples, R. R. ( 1990; ). A survey of methicillin-resistant Staphylococcus aureus affecting patients in England and Wales. J Hosp Infect 16, 35–48.[CrossRef]
    [Google Scholar]
  13. Koreen, L., Ramaswamy, S. V., Graviss, E. A., Naidich, S., Musser, J. M. & Kreiswirth, B. N. ( 2004; ). spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation. J Clin Microbiol 42, 792–799.[CrossRef]
    [Google Scholar]
  14. Krontiris, T. G., Devlin, B., Karp, D. D., Robert, N. J. & Risch, N. ( 1993; ). An association between the risk of cancer and mutations in the HRAS1 minisatellite locus. N Engl J Med 329, 517–523.[CrossRef]
    [Google Scholar]
  15. Kumari, D. N., Keer, V., Hawkey, P. M., Parnell, P., Joseph, N., Richardson, J. F. & Cookson, B. ( 1997; ). Comparison and application of ribosome spacer DNA amplicon polymorphisms and pulsed-field gel electrophoresis for differentiation of methicillin-resistant Staphylococcus aureus strains. J Clin Microbiol 35, 881–885.
    [Google Scholar]
  16. Kuroda, M., Ohta, T., Uchiyama, I. & 34 other authors ( 2001; ). Whole genome sequencing of methicillin-resistant Staphylococcus aureus. Lancet 357, 1225–1240.[CrossRef]
    [Google Scholar]
  17. Le Fleche, P., Hauck, Y., Onteniente, L. & 7 other authors ( 2001; ). A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiol 1, 2.[CrossRef]
    [Google Scholar]
  18. Liu, Y., Lee, M. A., Ooi, E. E., Mavis, Y., Tan, A. L. & Quek, H. H. ( 2003; ). Molecular typing of Salmonella enterica serovar typhi isolates from various countries in Asia by a multiplex PCR assay on variable-number tandem repeats. J Clin Microbiol 41, 4388–4394.[CrossRef]
    [Google Scholar]
  19. Lovett, S. T. ( 2004; ). Encoded errors: mutations and rearrangements mediated by misalignment at repetitive DNA sequences. Mol Microbiol 52, 1243–1253.[CrossRef]
    [Google Scholar]
  20. Mazars, E., Lesjean, S., Banuls, A. L., Gilbert, M., Vincent, V., Gicquel, B., Tibayrenc, M., Locht, C. & Supply, P. ( 2001; ). High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc Natl Acad Sci U S A 98, 1901–1906.[CrossRef]
    [Google Scholar]
  21. Moore, P. C. L. & Lindsay, J. A. ( 2002; ). Molecular characterisation of the dominant UK methicillin-resistant Staphylococcus aureus strains, EMRSA-15 and EMRSA-16. J Med Microbiol 51, 516–521.
    [Google Scholar]
  22. Murchan, S., Kaufmann, M. E., Deplano, A. & 21 other authors ( 2003; ). Harmonization of pulsed-field gel electrophoresis protocols for epidemiological typing of strains of methicillin-resistant Staphylococcus aureus: a single approach developed by consensus in 10 European laboratories and its application for tracing the spread of related strains. J Clin Microbiol 41, 1574–1585.[CrossRef]
    [Google Scholar]
  23. Noller, A. C., McEllistrem, M. C., Pacheco, A. G., Boxrud, D. J. & Harrison, L. H. ( 2003; ). Multilocus variable-number tandem repeat analysis distinguishes outbreak and sporadic Escherichia coli O157 : H7 isolates. J Clin Microbiol 41, 5389–5397.[CrossRef]
    [Google Scholar]
  24. Onteniente, L., Brisse, S., Tassios, P. T. & Vergnaud, G. ( 2003; ). Evaluation of the polymorphisms associated with tandem repeats for Pseudomonas aeruginosa strain typing. J Clin Microbiol 41, 4991–4997.[CrossRef]
    [Google Scholar]
  25. Owerbach, D. & Aagaard, L. ( 1984; ). Analysis of a 1963-bp polymorphic region flanking the human insulin gene. Gene 32, 475–479.[CrossRef]
    [Google Scholar]
  26. Paques, F., Leung, W. Y. & Haber, J. E. ( 1998; ). Expansions and contractions in a tandem repeat induced by double-strand break repair. Mol Cell Biol 18, 2045–2054.
    [Google Scholar]
  27. Pourcel, C., Vidgop, Y., Ramisse, F., Vergnaud, G. & Tram, C. ( 2003; ). Characterization of a tandem repeat polymorphism in Legionella pneumophila and its use for genotyping. J Clin Microbiol 41, 1819–1826.[CrossRef]
    [Google Scholar]
  28. Rocha, E. P. ( 2003; ). DNA repeats lead to the accelerated loss of gene order in bacteria. Trends Genet 19, 600–603.[CrossRef]
    [Google Scholar]
  29. Sabat, A., Krzyszton-Russjan, J., Strzalka, W., Filipek, R., Kosowska, K., Hryniewicz, W., Travis, J. & Potempa, J. ( 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.[CrossRef]
    [Google Scholar]
  30. Sola, C., Filliol, I., Legrand, E., Lesjean, S., Locht, C., Supply, P. & Rastogi, N. ( 2003; ). Genotyping of the Mycobacterium tuberculosis complex using MIRUs: association with VNTR and spoligotyping for molecular epidemiology and evolutionary genetics. Infect Genet Evol 3, 125–133.[CrossRef]
    [Google Scholar]
  31. Supply, P., Magdalena, J., Himpens, S. & Locht, C. ( 1997; ). Identification of novel intergenic repetitive units in a mycobacterial two-component system operon. Mol Microbiol 26, 991–1003.[CrossRef]
    [Google Scholar]
  32. Supply, P., Mazars, E., Lesjean, S., Vincent, V., Gicquel, B. & Locht, C. ( 2000; ). Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome. Mol Microbiol 36, 762–771.
    [Google Scholar]
  33. Tautz, D. & Schlotterer, C. ( 1994; ). Simple sequences. Curr Opin Genet Dev 4, 832–837.[CrossRef]
    [Google Scholar]
  34. Van Belkum, A., Scherer, S., van Leeuwen, W., Willemse, D., van Alphen, L. & Verbrugh, H. ( 1997; ). Variable number of tandem repeats in clinical strains of Haemophilus influenzae. Infect Immun 65, 5017–5027.
    [Google Scholar]
  35. Wolff, R. K., Nakamura, Y. & White, R. ( 1988; ). Molecular characterization of a spontaneously generated new allele at a VNTR locus: no exchange of flanking DNA sequence. Genomics 3, 347–351.[CrossRef]
    [Google Scholar]
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