1887

Abstract

is a member of the normal human oral microbiota, capable of opportunistic pathogenicity; like related oral streptococci, it exhibits appreciable phenotypic and genetic variation. A multilocus sequence typing (MLST) scheme for was developed and the resultant data analysed to examine the population structure of the species. Analysis of 113 isolates, confirmed as belonging to the group by 16S rRNA gene sequencing, characterized the population as highly diverse and undergoing inter- and intra-species recombination with a probable clonal complex structure. ClonalFrame analysis of these isolates along with examples of , and grouped the named species into distinct, coherent populations and did not support the clustering of with as reported previously using distance-based methods. Analysis of the individual loci suggested that this discrepancy was due to the possible hybrid nature of . The data are available on the public MLST website (http://pubmlst.org/soralis/).

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.027284-0
2009-08-01
2019-12-15
Loading full text...

Full text loading...

/deliver/fulltext/micro/155/8/2593.html?itemId=/content/journal/micro/10.1099/mic.0.027284-0&mimeType=html&fmt=ahah

References

  1. Alam, S., Brailsford, S. R., Whiley, R. A. & Beighton, D. ( 1999; ). PCR-based methods for genotyping viridans group streptococci. J Clin Microbiol 37, 2772–2776.
    [Google Scholar]
  2. Alam, S., Brailsford, S. R., Adams, S., Allison, C., Sheehy, E., Zoitopoulos, L., Kidd, E. A. & Beighton, D. ( 2000; ). Genotypic heterogeneity of Streptococcus oralis and distinct aciduric subpopulations in human dental plaque. Appl Environ Microbiol 66, 3330–3336.[CrossRef]
    [Google Scholar]
  3. Arbique, J. C., Poyart, C., Trieu-Cuot, P., Quesne, G., Carvalho Mda, G., Steigerwalt, A. G., Morey, R. E., Jackson, D., Davidson, R. J. & Facklam, R. R. ( 2004; ). Accuracy of phenotypic and genotypic testing for identification of Streptococcus pneumoniae and description of Streptococcus pseudopneumoniae sp. nov. J Clin Microbiol 42, 4686–4696.[CrossRef]
    [Google Scholar]
  4. Bek-Thomsen, M., Tettelin, H., Hance, I., Nelson, K. E. & Kilian, M. ( 2008; ). Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy. Infect Immun 76, 1889–1896.[CrossRef]
    [Google Scholar]
  5. Bishop, C. J., Aanensen, D. M., Jordan, G. E., Kilian, M., Hanage, W. P. & Spratt, B. G. ( 2009; ). Assigning strains to bacterial species via the internet. BMC Biol 7, 3 [CrossRef]
    [Google Scholar]
  6. Bruen, T. C., Philippe, H. & Bryant, D. ( 2006; ). A quick and robust statistical test to detect the presence of recombination. Genetics 172, 2665–2681.
    [Google Scholar]
  7. Chi, F., Nolte, O., Bergmann, C., Ip, M. & Hakenbeck, R. ( 2007; ). Crossing the barrier: evolution and spread of a major class of mosaic pbp2x in Streptococcus pneumoniae, S. mitis and S. oralis. Int J Med Microbiol 297, 503–512.[CrossRef]
    [Google Scholar]
  8. Coffey, T. J., Pullinger, G. D., Urwin, R., Jolley, K. A., Wilson, S. M., Maiden, M. C. & Leigh, J. A. ( 2006; ). First insights into the evolution of Streptococcus uberis: a multilocus sequence typing scheme that enables investigation of its population biology. Appl Environ Microbiol 72, 1420–1428.[CrossRef]
    [Google Scholar]
  9. Didelot, X. & Falush, D. ( 2007; ). Inference of bacterial microevolution using multilocus sequence data. Genetics 175, 1251–1266.
    [Google Scholar]
  10. Drancourt, M., Roux, V., Fournier, P.-E. & Raoult, D. ( 2004; ). rpoB gene sequence-based identification of aerobic gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J Clin Microbiol 42, 497–504.[CrossRef]
    [Google Scholar]
  11. Enersen, M., Olsen, I., van Winkelhoff, A. J. & Caugant, D. A. ( 2006; ). Multilocus sequence typing of Porphyromonas gingivalis strains from different geographic origins. J Clin Microbiol 44, 35–41.[CrossRef]
    [Google Scholar]
  12. Enright, M. C. & Spratt, B. G. ( 1998; ). A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144, 3049–3060.[CrossRef]
    [Google Scholar]
  13. Falush, D., Kraft, C., Taylor, N. S., Correa, P., Fox, J. G., Achtman, M. & Suerbaum, S. ( 2001; ). Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc Natl Acad Sci U S A 98, 15056–15061.[CrossRef]
    [Google Scholar]
  14. Feil, E. J. & Spratt, B. G. ( 2001; ). Recombination and the population structures of bacterial pathogens. Annu Rev Microbiol 55, 561–590.[CrossRef]
    [Google Scholar]
  15. Feil, E. J., Li, B. C., Aanensen, D. M., Hanage, W. P. & Spratt, B. G. ( 2004; ). eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 186, 1518–1530.[CrossRef]
    [Google Scholar]
  16. Fraser, C., Hanage, W. P. & Spratt, B. G. ( 2007; ). Recombination and the nature of bacterial speciation. Science 315, 476–480.[CrossRef]
    [Google Scholar]
  17. 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]
  18. Haraldsson, G., Holbrook, W. P. & Könönen, E. ( 2004; ). Clonal persistence of oral Fusobacterium nucleatum in infancy. J Dent Res 83, 500–504.[CrossRef]
    [Google Scholar]
  19. Hohwy, J., Reinholdt, J. & Kilian, M. ( 2001; ). Population dynamics of Streptococcus mitis in its natural habitat. Infect Immun 69, 6055–6063.[CrossRef]
    [Google Scholar]
  20. Holmes, E. C., Urwin, R. & Maiden, M. C. ( 1999; ). The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol Biol Evol 16, 741–749.[CrossRef]
    [Google Scholar]
  21. 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]
  22. 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]
  23. Kilian, M., Poulsen, K., Blomqvist, T., Havarstein, L. S., Bek-Thomsen, M., Tettelin, H. & Sorensen, U. B. S. ( 2008; ). Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS One 3, e2683 [CrossRef]
    [Google Scholar]
  24. Lane, D. J. ( 1991; ). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–148. Edited by E. Stackebrandt & M. Goodfellow. Chichester, UK: Wiley.
  25. Nakano, K., Lapirattanakul, J., Nomura, R., Nemoto, H., Alaluusua, S., Grönroos, L., Vaara, M., Hamada, S., Ooshima, T. & Nakagawa, I. ( 2007; ). Streptococcus mutans clonal variation revealed by multilocus sequence typing. J Clin Microbiol 45, 2616–2625.[CrossRef]
    [Google Scholar]
  26. Nyvad, B. & Kilian, M. ( 1990; ). Microflora associated with experimental root surface caries in humans. Infect Immun 58, 1628–1633.
    [Google Scholar]
  27. Okwumabua, O., O'Connor, M. & Shull, E. ( 2003; ). A polymerase chain reaction (PCR) assay specific for Streptococcus suis based on the gene encoding the glutamate dehydrogenase. FEMS Microbiol Lett 218, 79–84.[CrossRef]
    [Google Scholar]
  28. O'Neill, A. M., Gillespie, S. H. & Whiting, G. C. ( 1999; ). Detection of penicillin susceptibility in Streptococcus pneumoniae by pbp2b PCR-restriction fragment length polymorphism analysis. J Clin Microbiol 37, 157–160.
    [Google Scholar]
  29. Paddick, J. S., Brailsford, S. R., Kidd, E. A., Gilbert, S. C., Clark, D. T., Alam, S., Killick, Z. J. & Beighton, D. ( 2003; ). Effect of the environment on genotypic diversity of Actinomyces naeslundii and Streptococcus oralis in the oral biofilm. Appl Environ Microbiol 69, 6475–6480.[CrossRef]
    [Google Scholar]
  30. Poyart, C., Quesne, G., Coulon, S., Berche, P. & Trieu-Cuot, P. ( 1998; ). Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J Clin Microbiol 36, 41–47.
    [Google Scholar]
  31. Poyart, C., Quesne, G. & Trieu-Cuot, P. ( 2002; ). Taxonomic dissection of the Streptococcus bovis group by analysis of manganese-dependent superoxide dismutase gene (sodA) sequences: reclassification of ‘Streptococcus infantarius subsp. coli’ as Streptococcus lutetiensis sp. nov. and of Streptococcus bovis biotype II.2 as Streptococcus pasteurianus sp. nov. Int J Syst Evol Microbiol 52, 1247–1255.[CrossRef]
    [Google Scholar]
  32. Sheppard, S. K., McCarthy, N. D., Falush, D. & Maiden, M. C. J. ( 2008; ). Convergence of Campylobacter species: implications for bacterial evolution. Science 320, 237–239.[CrossRef]
    [Google Scholar]
  33. Staden, R. ( 1996; ). The Staden sequence analysis package. Mol Biotechnol 5, 233–241.[CrossRef]
    [Google Scholar]
  34. Swofford, D. L. ( 2003; ). paup*. Phylogenetic Analysis Using Parsimony (*and other methods), version 4 beta 10. Sunderland, MA: Sinauer Associates.
  35. 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]
  36. 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]
  37. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. ( 2007; ). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73, 5261–5267.[CrossRef]
    [Google Scholar]
  38. Whatmore, A. M., Efstratiou, A., Pickerill, A. P., Broughton, K., Woodard, G., Sturgeon, D., George, R. & Dowson, C. G. ( 2000; ). Genetic relationships between clinical isolates of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus mitis: characterization of “atypical” pneumococci and organisms allied to S. mitis harboring S. pneumoniae virulence factor-encoding genes. Infect Immun 68, 1374–1382.[CrossRef]
    [Google Scholar]
  39. Whiley, R. A. & Beighton, D. ( 1998; ). Current classification of the oral streptococci. Oral Microbiol Immunol 13, 195–216.[CrossRef]
    [Google Scholar]
  40. Wisplinghoff, H., Reinert, R. R., Cornely, O. & Seifert, H. ( 1999; ). Molecular relationships and antimicrobial susceptibilities of viridans group streptococci isolated from blood of neutropenic cancer patients. J Clin Microbiol 37, 1876–1880.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.027284-0
Loading
/content/journal/micro/10.1099/mic.0.027284-0
Loading

Data & Media loading...

Supplements

List of strains used in this study: subject number, year of isolation, source, ST and allelic profile [ PDF] (21 kb) Tests for congruence among (A) ML gene trees and random trees and (B) ML gene trees from selected STs (34, 26, 47, 75, 7, 59, 5, 3, 32, 70, 40, 72, 65, 33, 38, 6, 63, 30, 57, 73, 37, 18, 74, 42, 53, 8, 64, 19, 66, 71, 49, 60, 41, 54, 12, 11) as representatives of clusters and discrete lineages in Fig. 1(a) ( <0.05 for all -ln values) [ PDF] (41 kb) NeighborNet graphs of and for , , , and loci, constructed in SplitsTree v4.0. The black-labelled STs are loci, the blue label denotes , the red labels denote the loci. [ PDF] (46 kb)

PDF

List of strains used in this study: subject number, year of isolation, source, ST and allelic profile [ PDF] (21 kb) Tests for congruence among (A) ML gene trees and random trees and (B) ML gene trees from selected STs (34, 26, 47, 75, 7, 59, 5, 3, 32, 70, 40, 72, 65, 33, 38, 6, 63, 30, 57, 73, 37, 18, 74, 42, 53, 8, 64, 19, 66, 71, 49, 60, 41, 54, 12, 11) as representatives of clusters and discrete lineages in Fig. 1(a) ( <0.05 for all -ln values) [ PDF] (41 kb) NeighborNet graphs of and for , , , and loci, constructed in SplitsTree v4.0. The black-labelled STs are loci, the blue label denotes , the red labels denote the loci. [ PDF] (46 kb)

PDF

List of strains used in this study: subject number, year of isolation, source, ST and allelic profile [ PDF] (21 kb) Tests for congruence among (A) ML gene trees and random trees and (B) ML gene trees from selected STs (34, 26, 47, 75, 7, 59, 5, 3, 32, 70, 40, 72, 65, 33, 38, 6, 63, 30, 57, 73, 37, 18, 74, 42, 53, 8, 64, 19, 66, 71, 49, 60, 41, 54, 12, 11) as representatives of clusters and discrete lineages in Fig. 1(a) ( <0.05 for all -ln values) [ PDF] (41 kb) NeighborNet graphs of and for , , , and loci, constructed in SplitsTree v4.0. The black-labelled STs are loci, the blue label denotes , the red labels denote the loci. [ PDF] (46 kb)

PDF
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