1887

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.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.018176-0
2010-09-01
2019-12-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/9/2140.html?itemId=/content/journal/ijsem/10.1099/ijs.0.018176-0&mimeType=html&fmt=ahah

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.
  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]
    [Google Scholar]
  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.
  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]
    [Google Scholar]
  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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.018176-0
Loading
/content/journal/ijsem/10.1099/ijs.0.018176-0
Loading

Data & Media loading...

Supplements

vol. , part 9, pp. 2140 - 2148

Studied strains and partial gene sequence accession numbers.

Primers used for PCR and sequencing of gene.

Accession numbers of nucleotide sequences for clinical strains of the 'anginosus'subgroup.

Inter- and intraspecies nucleotide divergence within the 'anginosus' subgroup.

Phylogenetic trees of isolates belonging to the 'anginosus' group of the genus inferred from comparison of sequences of , , , and using the neighbour-joining method.

[PDF file of Supplementary Tables and Figure](139 KB)



PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error