1887

Abstract

In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies of species. In an effort to identify a more reliable approach, a gene sequence-based database was created. In this study, an approximately 883 bp portion of the gene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (, and ) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcal gene showed higher discrimination (mean similarity 77.6 %) than the 16S rRNA (mean similarity 97.4 %), (mean similarity 86 %), (mean similarity 82 %) and (mean similarity 81.5 %) genes. Analysis of the gene sequence from 20 isolates representing two clinically important species showed <1 % sequence divergence. Phylogenetic data obtained from the gene sequence were in general agreement with those of 16S rRNA gene sequence analysis and DNA–DNA reassociation studies. In conclusion, the gene sequence-based assay is an effective alternative to currently used methods, including 16S rRNA gene sequencing, for identification and taxonomical analysis of species.

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2007-01-01
2024-12-14
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References

  1. Ang D., Liberek K., Skowyra D., Zylicz M., Georgopoulos C. 1991; Biological role and regulation of the universally conserved heat shock proteins. J Biol Chem 266:24233–24236
    [Google Scholar]
  2. Becker K., Harmsen D., Mellmann A., Meier C., Schumann P., Peters G., von Eiff C. 2004; Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species. J Clin Microbiol 42:4988–4995 [CrossRef]
    [Google Scholar]
  3. Drancourt M., Raoult D. 2002; rpoB gene sequence-based identification of Staphylococcus species. J Clin Microbiol 40:1333–1338 [CrossRef]
    [Google Scholar]
  4. Euzéby J. P. 1997; List of bacterial names with standing nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47:590–592 [CrossRef]
    [Google Scholar]
  5. Ezaki T., Saidi S. M., Liu S. L., Hashimoto Y., Yamamoto H., Yabuuchi E. 1990; Rapid procedure to determine the DNA base composition from small amounts of Gram-positive bacteria. FEMS Microbiol Lett 67:127–130 [CrossRef]
    [Google Scholar]
  6. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  7. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [CrossRef]
    [Google Scholar]
  8. Gribaldo S., Cookson B., Saunders N., Marples R., Stanley J. 1997; Rapid identification by specific PCR of coagulase-negative staphylococcal species important in hospital infection. J Med Microbiol 46:45–53 [CrossRef]
    [Google Scholar]
  9. Itoh Y., Kawamura Y., Kasai H., Shah M. M., Nhung P. H., Yamada M., Sun X., Koyana T., Hayashi M. other authors 2006; dnaJ and gyrB gene sequence relationship among species and strains of genus Streptococcus . Syst Appl Microbiol 29:368–374 [CrossRef]
    [Google Scholar]
  10. Kimura M. 1983 The Natural Theory of Molecular Evolution pp  41–46 Cambridge: Cambridge University Press;
    [Google Scholar]
  11. Kloos W. E., Schleifer K.-H. 1986; Genus IV Staphylococcus . In Bergey's Manual of Systematic Bacteriology vol 2 pp  1013–1035 Edited by Sneath P. H. A., Mair N. S., Sharpe M. E., Holt J. G. Baltimore, MD: Williams & Wilkins;
    [Google Scholar]
  12. Kloos W. E., Schleifer K.-H., Götz F. 1991; The genus Staphylococcus . In The Prokaryotes , 2nd edn. pp  1369–1420 Edited by Balows A., Truper H. G., Dworkin M., Harder W., Schleifer K. H. New York: Springer;
    [Google Scholar]
  13. Kloos W. E., Ballard D. N., George C. G., Webster J. A., Hubner R. J., Ludwig W., Schleifer K. H., Fiedler F., Schubert K. 1998; Delimiting the genus Staphylococcus through description of Macrococcus caseolyticus gen.nov., comb. nov. and Macrococcus equipercicus sp. nov., and Macrococcus bovicus sp. nov. and Macrococcus carouselicus sp. nov.. Int J Syst Bacteriol 48:859–877 [CrossRef]
    [Google Scholar]
  14. Kumar S., Tamura K., Nei M. 2004; mega3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163 [CrossRef]
    [Google Scholar]
  15. Kwok A. Y., Chow A. W. 2003; Phylogenetic study of Staphylococcus and Macrococcus species based on partial hsp60 gene sequences. Int J Syst Evol Microbiol 53:87–92 [CrossRef]
    [Google Scholar]
  16. Kwok A. Y., Su S. C., Reynolds R. P., Bay S. J., Av-Gay Y., Dovichi N. J., Chow A. W. 1999; Species identification and phylogenetic relationships based on partial HSP60 gene sequences within the genus Staphylococcus . Int J Syst Bacteriol 49:1181–1192 [CrossRef]
    [Google Scholar]
  17. Liu H., Li Y., Huang X., Kawamura Y., Ezaki T. 2003; Use of the dnaJ gene for the detection and identification of all Legionella pneumophila serogroups and description of the primers used to detect 16S rDNA gene sequences of major members of the genus Legionella . Microbiol Immunol 47:859–869 [CrossRef]
    [Google Scholar]
  18. Macario A. J., Dugan C. B., Clarens M., Conway de Macario E. 1993; dnaJ in Archaea. Nucleic Acids Res 21:2773 [CrossRef]
    [Google Scholar]
  19. Mellmann A., Becker K., von Eiff C., Keckevoet U., Schumann P., Harmsen D. 2006; Sequencing and staphylococci identification. Emerg Infect Dis 12:333–336 [CrossRef]
    [Google Scholar]
  20. Page R. D. 1996; treeview: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358
    [Google Scholar]
  21. Peake S. L., Peter J. V., Chan L., Wise R. P., Butcher A. R., Grove D. I. 2006; First report of septicemia caused by an obligately anaerobic Staphylococcus aureus infection in a human. J Clin Microbiol 44:2311–2313 [CrossRef]
    [Google Scholar]
  22. Poyart C., Quesne G., Boumaila C., Trieu-Cuot P. 2001; Rapid and accurate species-level identification of coagulase-negative staphylococci by using the sodA gene as a target. J Clin Microbiol 39:4296–4301 [CrossRef]
    [Google Scholar]
  23. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  24. Skow A., Mangold K. A., Tajuddin M., Huntington A., Fritz B., Thomson R. B. Jr, Kaul K. L. 2005; Species-level identification of staphylococcal isolates by real-time PCR and melt curve analysis. J Clin Microbiol 43:2876–2880 [CrossRef]
    [Google Scholar]
  25. Švec P., Vancanneyt M., Sedláček I., Engelbeen K., Štětina V., Swings J., Petráš P. 2004; Reclassification of Staphylococcus pulvereri Zakrzewska-Czerwińska et al . 1995 as a later synonym of Staphylococcus vitulinus Webster et al . 1994. Int J Syst Evol Microbiol 54:2213–2215 [CrossRef]
    [Google Scholar]
  26. Takahashi T., Satoh I., Kikuchi N. 1999; Phylogenetic relationships of 38 taxa of the genus Staphylococcus based on 16S rRNA gene sequence analysis. Int J Syst Bacteriol 49:725–728 [CrossRef]
    [Google Scholar]
  27. Takewaki S., Okuzumi K., Ishiko H., Nakahara K., Ohkubo A., Nagai R. 1993; Genus-specific polymerase chain reaction for the mycobacterial dnaJ gene and species-specific oligonucleotide probes. J Clin Microbiol 31:446–450
    [Google Scholar]
  28. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
  29. Victor T. C., Jordaan A. M., Van Schalkwyk E. J., Coetzee G. J., Van Helden P. D. 1996; Strain-specific variation in the dnaJ gene of mycobacteria. J Med Microbiol 44:332–339 [CrossRef]
    [Google Scholar]
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