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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 60, Issue 9

Partial gene sequencing: a new tool for identification and phylogeny within the genus Free

Abstract

Partial sequences of the gene (1249 bp), which encodes a recombination and repair protein, were analysed to determine the phylogenetic relationship and identification of streptococci. The partial sequences presented interspecies nucleotide similarity of 56.4–98.2 % and intersubspecies similarity of 89.8–98 %. The mean DNA sequence similarity of gene sequences (66.6 %) was found to be lower than those of the 16S rRNA gene (94.1 %), (84.6 %), (74.8 %), (78.1 %) and (73.2 %). Phylogenetically derived trees revealed six statistically supported groups: , , //, , and . The ‘mitis’ group was not supported by a significant bootstrap value, but three statistically supported subgroups were noted: //, (the ‘anginosus’ subgroup) and //////. The partial gene sequence comparison highlighted a high percentage of divergence between subsp. and subsp. . This observation is confirmed by other gene sequence comparisons (, , and ). A high percentage of similarity was found between and after sequence comparison of the gene. To study the genetic diversity among the ‘anginosus’ subgroup, , , , and sequences were determined for 36 clinical isolates. The results that were obtained confirmed the high genetic diversity within this group of streptococci.

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Keyword(s): ILD, incongruence length difference
SGM
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2010-09-01
2024-04-19
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References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410 [CrossRef]
     [Google Scholar]
  2. Chen C. C., Teng L. J., Chang T. C. 2004; Identification of clinically relevant viridans group streptococci by sequence analysis of the 16S–23S ribosomal DNA spacer region. J Clin Microbiol 42:2651–2657 [CrossRef]
     [Google Scholar]
  3. Coykendall A. L., Wesbecher P. M., Gustafson K. B. 1987; “ Streptococcus milleri ”, Streptococcus constellatus , and Streptococcus intermedius are later synonyms of Streptococcus anginosus . Int J Syst Bacteriol 37:222–228 [CrossRef]
     [Google Scholar]
  4. Euzéby J. P. 2010; Streptococcus Rosenbach 1884, genus . In List of Bacterial Names with Standing in Nomenclature http://www.bacterio.cict.fr/s/streptococcus.html
     [Google Scholar]
  5. Facklam R. 2002; What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 15:613–630 [CrossRef]
     [Google Scholar]
  6. Farris J. S. 1970; Methods for computing Wagner trees. Syst Zool 19:83–92 [CrossRef]
     [Google Scholar]
  7. Farris J. S., Kallersjo M., Kluge A. G., Bult C. 1994; Testing significance of incongruence. Cladistics 10:315–319 [CrossRef]
     [Google Scholar]
  8. Farrow J. A. E., Collins M. D. 1984; Taxonomic studies on streptococci of serological groups C, G and L and possibly related taxa. Syst Appl Microbiol 5:483–493 [CrossRef]
     [Google Scholar]
  9. Felsenstein J. 1989; phylip – phylogeny inference package (version 3.2). Cladistics 5:164–166
     [Google Scholar]
  10. Garnier F., Gerbaud G., Courvalin P., Galimand M. 1997; Identification of clinically relevant viridans group streptococci to the species level by PCR. J Clin Microbiol 35:2337–2341
     [Google Scholar]
  11. Garvie E. I., Farrow J. A. E., Bramley A. J. 1983; Streptococcus dysgalactiae (Diernhofer) nom. rev. Int J Syst Bacteriol 33:404–405 [CrossRef]
     [Google Scholar]
  12. Glazunova O. O., Raoult D., Roux V. 2006; Streptococcus massiliensis sp. nov., isolated from a patient blood culture. Int J Syst Evol Microbiol 56:1127–1131 [CrossRef]
     [Google Scholar]
  13. Glazunova O. O., Raoult D., Roux V. 2009; Partial sequence comparison of the rpoB , sodA , groEL , and gyrB genes within the genus Streptococcus . Int J Syst Evol Microbiol 59:2317–2322 [CrossRef]
     [Google Scholar]
  14. Hoshino T., Fujiwara T., Kilian M. 2005; Use of phylogenetic and phenotypic analyses to identify nonhemolytic streptococci isolated from bacteremic patients. J Clin Microbiol 43:6073–6085 [CrossRef]
     [Google Scholar]
  15. Hung W. C., Tsai J. C., Hsueh P. R., Chia J. S., Teng L. J. 2005; Species identification of mutans streptococci by groESL gene sequence. J Med Microbiol 54:857–862 [CrossRef]
     [Google Scholar]
  16. Igarashi T., Ichikawa K., Yamamoto A., Goto N. 2001; Identification of mutans streptococcal species by the PCR products of the dex genes. J Microbiol Methods 46:99–105 [CrossRef]
     [Google Scholar]
  17. Kawamura Y., Whiley R. A., Shu S. E., Ezaki T., Hardie J. M. 1999; Genetic approaches to the identification of the mitis group within the genus Streptococcus . Microbiology 145:2605–2613
     [Google Scholar]
  18. Kawamura Y., Itoh Y., Mishima N., Ohkusu K., Kasai H., Ezaki T. 2005 High genetic similarity of Streptococcus agalactiae and Streptococcus difficilis : S. difficilis Eldar et al. 1995 is a later synonym of S. agalactiae Lehmann and Neumann 1896 (Approved Lists 1980). Int J Syst Evol Microbiol 55, 961–965. [CrossRef]
  19. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [CrossRef]
     [Google Scholar]
  20. Kuhnert P., Korczak B. M. 2006; Prediction of whole-genome DNA–DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA). Microbiology 152:2537–2548 [CrossRef]
     [Google Scholar]
  21. Milinovich G. J., Burrell P. C., Pollitt C. C., Bouvet A., Trott D. J. 2008; Streptococcus henryi sp. nov. and Streptococcus caballi sp. nov., isolated from the hindgut of horses with oligofructose-induced laminitis. Int J Syst Evol Microbiol 58:262–266 [CrossRef]
     [Google Scholar]
  22. Nielsen X. C., Justesen U. S., Dargis R., Kemp M., Christensen J. J. 2009; Identification of clinically relevant nonhemolytic streptococci on the basis of sequence analysis of 16S–23S intergenic spacer region and partial gdh gene. J Clin Microbiol 47:932–939 [CrossRef]
     [Google Scholar]
  23. Picard F. J., Ke D., Boudreau D. K., Boissinot M., Huletsky A., Richard D., Ouellette M., Roy P. H., Bergeron M. G. 2004; Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species. J Clin Microbiol 42:3686–3695 [CrossRef]
     [Google Scholar]
  24. Planet P. J. 2006; Tree disagreement: measuring and testing incongruence in phylogenies. J Biomed Inform 39:86–102 [CrossRef]
     [Google Scholar]
  25. Saitou N., Nei M. 1987; The neighbor-joining method, a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
     [Google Scholar]
  26. Shewmaker P. L., Camus A. C., Bailiff T., Steigerwalt A. G., Morey R. E., Carvalho M. G. S. 2007; Streptococcus ictaluri sp. nov., isolated from Channel catfish Ictalurus punctatus broodstock. Int J Syst Evol Microbiol 57:1603–1606 [CrossRef]
     [Google Scholar]
  27. Slabbinck B., Dawyndt P., Martens M., De Vos P., De Baets B. 2008; TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers. Bioinformatics 24:866–867 [CrossRef]
     [Google Scholar]
  28. Swofford D. L. 1998 Phylogenetic analysis using parsimony (paup), version 4 Sunderland, MA: Sinauer Associates;
     [Google Scholar]
  29. Takada K., Hirasawa M. 2008; Streptococcus dentirousetti sp. nov., isolated from the oral cavities of bats. Int J Syst Evol Microbiol 58:160–163 [CrossRef]
     [Google Scholar]
  30. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [CrossRef]
     [Google Scholar]
  31. Tapp J., Thollesson M., Herrmann B. 2003; Phylogenetic relationships and genotyping of the genus Streptococcus by sequence determination of the RNase P RNA gene, rnpB . Int J Syst Evol Microbiol 53:1861–1871 [CrossRef]
     [Google Scholar]
  32. Teng L. J., Hsueh P. R., Tsai J. C., Chen P. W., Hsu J. C., Lai H. C., Lee C. N., Ho S. W. 2002; groESL sequence determination, phylogenetic analysis, and species differentiation for viridans group streptococci. J Clin Microbiol 40:3172–3178 [CrossRef]
     [Google Scholar]
  33. 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 [CrossRef]
     [Google Scholar]
  34. Vandamme P., Pot B., Falsen E., Kersters K., Devriese L. A. 1996 Taxonomic study of Lancefield streptococcal groups C, G, and L ( Streptococcus dysgalactiae ) and proposal of S.dysgalactiae subsp. equisimilis subsp. nov. Int J Syst Bacteriol 46, 774–781 [CrossRef]
  35. Vela A. I., Casamayor A., Sánchez del Rey V., Dominguez L., Fernández-Garayzábal J. F. 2009; Streptococcus plurextorum sp. nov., isolated from pigs. Int J Syst Evol Microbiol 59:504–508 [CrossRef]
     [Google Scholar]
  36. Vieira V. V., Teixeira L. M., Zahner V., Momen H., Facklam R. R., Steigerwalt A. G., Brenner D. J., Castro A. C. 1998; Genetic relationships among the different phenotypes of Streptococcus dysgalactiae strains. Int J Syst Bacteriol 48:1231–1243 [CrossRef]
     [Google Scholar]
  37. Whiley R. A., Beighton D. 1991; Emended descriptions and recognition of Streptococcus constellatus , Streptococcus intermedius , and Streptococcus anginosus as distinct species. Int J Syst Bacteriol 41:1–5 [CrossRef]
     [Google Scholar]
  38. Zeigler D. R. 2003; Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1900 [CrossRef]
     [Google Scholar]
  39. Zeigler D. R. 2005; Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus . Int J Syst Evol Microbiol 55:1171–1179 [CrossRef]
     [Google Scholar]
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Partial recN gene sequencing: a new tool for identification and phylogeny within the genus Streptococcus
Int J Syst Evol Microbiol 60, 2140 (2010); https://doi.org/10.1099/ijs.0.018176-0
/content/journal/ijsem/10.1099/ijs.0.018176-0
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