1887

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Volume 56, Issue 4

Identification of species of , , and by sequence analysis of the ribosomal 16S–23S intergenic spacer region Free

Abstract

The feasibility of sequence analysis of the ribosomal 16S–23S intergenic spacer region (ITS) was evaluated for identification of 24 species of , one species of , 18 species of and three species of . As GenBank currently lacks ITS sequence entries for many species of these four genera, the ITS sequences of 38 type strains were first sequenced and submitted to GenBank to facilitate species identification of these genera. Subsequently, the ITS sequences of 217 strains (84 reference strains and 133 clinical isolates) were determined and species identification was made by search for homologous sequences in public databases. Species other than contained multiple ITS fragments and only the shortest fragment was analysed. A total of 25 isolates (11.5 %) produced discrepant identification by ITS sequencing. The 25 discordant strains were analysed further by sequencing of the 16S rRNA gene for species clarification, and 21 were found to be identified correctly by ITS sequence analysis. The correct identification rate by ITS sequencing was 98.2 % (213/217). Several closely related enterococcal and streptococcal species/subspecies contained specific ITS signature sequences that were useful for differentiating these bacteria. In conclusion, ITS sequencing provides a useful approach towards identifying this group of pathogens on a molecular platform alongside 16S rRNA gene sequencing.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ITS, intergenic spacer region and NVS, nutritionally variant streptococci
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2007-04-01
2024-04-18
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References

  1. 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]
  2. Baele M., Baele P., Vaneechoutte M., Storms V., Butaye P., Devriese L. A., Gillis M., Haesebrouck F. 2000; Application of tRNA intergenic spacer PCR for identification of Enterococcus species. J Clin Microbiol 38:4201–4207
     [Google Scholar]
  3. Baele M., Storms V., Haesebrouck F., Devriese L. A., Gillis M., Verschraegen G., de Baere T., Vaneechoutte M. 2001; Application and evaluation of the interlaboratory reproducibility of tRNA intergenic length polymorphism analysis (tDNA-PCR) for identification of Streptococcus species. J Clin Microbiol 39:1436–1442 [CrossRef]
     [Google Scholar]
  4. Bentley R. W., Leigh J. A., Collins M. D. 1991; Intrageneric structure of Streptococcus based on comparative analysis of small-subunit rRNA sequences. Int J Syst Bacteriol 41:487–494 [CrossRef]
     [Google Scholar]
  5. Bosshard P. P., Abels S., Altwegg M., Bottger E. C., Zbinden R. 2004; Comparison of conventional and molecular methods for identification of aerobic catalase-negative Gram-positive cocci in the clinical laboratory. J Clin Microbiol 42:2065–2073 [CrossRef]
     [Google Scholar]
  6. Chang H. C., Wei Y. F., Dijkshoorn L., Vaneechoutte M., Tang C. T., Chang T. C. 2005; Species-level identification of isolates of the A. calcoaceticus – A. baumannii complex by sequence analysis of the 16S–23S rRNA gene spacer region. J Clin Microbiol 42:1632–1639
     [Google Scholar]
  7. 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]
  8. Clarridge J. E. III 2004; Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17:840–862 [CrossRef]
     [Google Scholar]
  9. Clarridge J. E. III, Attorri S. M., Zhang Q., Bartell J. 2001; 16S ribosomal DNA sequence analysis distinguishes biotypes of Streptococcus bovis : Streptococcus bovis biotype II/2 is a separate genospecies and the predominant clinical isolate in adult males. J Clin Microbiol 39:1549–1552 [CrossRef]
     [Google Scholar]
  10. D’Auria G., Pushker R., Rodriguez-Valera F. 2006; IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships. Bioinformatics 22:527–531 [CrossRef]
     [Google Scholar]
  11. Descheemaeker P., Lammens C., Pot B., Vandamme P., Goossens H. 1997; Evaluation of arbitrarily primed PCR analysis and pulsed-field gel electrophoresis of large genomic DNA fragments for identification of enterococci important in human medicine. Int J Syst Bacteriol 47:555–561 [CrossRef]
     [Google Scholar]
  12. 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]
  13. Facklam R. 2002; What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 15:613–630 [CrossRef]
     [Google Scholar]
  14. 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]
  15. Gürtler V., Stanisich V. A. 1996; New approaches to typing and identification of bacteria using the 16S–23S rDNA spacer region. Microbiology 142:3–16 [CrossRef]
     [Google Scholar]
  16. Hassan A. A., Khan I. U., Abdulmawjood A., Lammler C. 2003; Inter- and intraspecies variations of the 16S–23S rDNA intergenic spacer region of various streptococcal species. Syst Appl Microbiol 26:97–103 [CrossRef]
     [Google Scholar]
  17. 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]
  18. Kawamura Y., Hou X. G., Sultana F., Miura H., Ezaki T. 1995; Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus . Int J Syst Bacteriol 45:406–408 [CrossRef]
     [Google Scholar]
  19. 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]
  20. Li Y. J., Tsoi S. C. 2002; Phylogenetic analysis of vertebrate lactate dehydrogenase (LDH) multigene families. J Mol Evol 54:614–624 [CrossRef]
     [Google Scholar]
  21. Millar B. C., Jiru X., Moore J. E., Earle J. A. 2000; A simple and sensitive method to extract bacterial, yeast and fungal DNA from blood culture material. J Microbiol Methods 42:139–147 [CrossRef]
     [Google Scholar]
  22. 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]
  23. 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]
  24. Poyart C., Quesnes G., Trieu-Cuot P. 2000; Sequencing the gene encoding manganese-dependent superoxide dismutase for rapid species identification of enterococci. J Clin Microbiol 38:415–418
     [Google Scholar]
  25. 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 11.2 as Streptococcus pasteurianus sp. nov. Int J Syst Evol Microbiol 52:1247–1255 [CrossRef]
     [Google Scholar]
  26. Relman D. A. 1993; Universal bacterial 16S rDNA amplification and sequencing. In Diagnostic Molecular Microbiology pp 489–495 Edited by Persing D. H., Smith T. F., Tenover F. C., White T. J. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  27. Roth A., Fischer M., Hamid M. E., Michalke S., Ludwig W., Mauch H. 1998; Differentiation of phylogenetically related slowly growing mycobacteria based on 16S–23S rRNA gene internal transcribed spacer sequences. J Clin Microbiol 36:139–147
     [Google Scholar]
  28. Ruoff K. L. 2003; Aerococcus, Abiotrophia , and other infrequently isolated aerobic catalase-negative, Gram-positive cocci. In Manual of Clinical Microbiology , 8th edn. pp 434–444 Edited by Murray P. R., Baron E. J., Jorgensen J. H., Pfaller M. A., Yolken R. H. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  29. Ruoff K. L., Miller S. I., Garner C. V., Ferraro M. J., Calderwood S. B. 1989; Bacteremia with Streptococcus bovis and Streptococcus salivarius : clinical correlates of more accurate identification of isolates. J Clin Microbiol 27:305–308
     [Google Scholar]
  30. Schlegel L., Grimont F., Collins M. D., Regnault B., Grimont P. A., Bouvet A. 2000; Streptococcus infantarius sp. nov., Streptococcus infantarius subsp.infantarius subsp. nov. and Streptococcusinfantarius subsp. coli subsp. nov., isolated from humans and food. Int J Syst Evol Microbiol 50:1425–1434 [CrossRef]
     [Google Scholar]
  31. Schlegel L., Grimont F., Ageron E., Grimont P. A., Bouvet A. 2003; Reappraisal of the taxonomy of the Streptococcus bovis / Streptococcus equinu s complex and related species: description of Streptococcus gallolyticus subsp. gallolyticus subsp. nov., S. gallolyticus subsp. macedonicus subsp.nov. and S.gallolyticus subsp. pasteurianus subsp. nov. Int J Syst Evol Microbiol 53:631–645 [CrossRef]
     [Google Scholar]
  32. Teixeira L. M., Facklam R. R. 2003; Enterococcus . In Manual of Clinical Microbiology , 8th edn. pp 422–433 Edited by Murray P. R., Baron E. J., Jorgensen J. H., Pfaller M. A., Yolken R. H. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  33. Teixeira L. M., Carvalho M. G., Merquior V. L., Steigerwalt A. G., Teixeira M. G., Brenner D. J., Facklam R. R. 1997; Recent approaches on the taxonomy of the enterococci and some related microorganisms. Adv Exp Med Biol 418:397–400
     [Google Scholar]
  34. Teng L. J., Hsueh P. R., Tsai J. C., Chen P. W., Hsu J. C., Lai H. C., Lee 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]
  35. Tripodi M. F., Adinolfi L. E., Ragone E., Durante Mangoni E., Fortunato R., Iarussi D., Ruggiero G., Utili R. 2004; Streptococcus bovis endocarditis and its association with chronic liver disease: an underestimated risk factor. Clin Infect Dis 38:1394–1400 [CrossRef]
     [Google Scholar]
  36. Whiley R. A., Duke B., Hardie J. M., Hall L. M. 1995; Heterogeneity among 16S–23S rRNA intergenic spacers of species within the ‘ Streptococcus milleri group’. Microbiology 141:1461–1467 [CrossRef]
     [Google Scholar]
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Identification of species of Abiotrophia, Enterococcus, Granulicatella and Streptococcus by sequence analysis of the ribosomal 16S–23S intergenic spacer region
J. Med. Microbiol. 56, 504 (2007); https://doi.org/10.1099/jmm.0.47027-0
/content/journal/jmm/10.1099/jmm.0.47027-0
/content/journal/jmm/10.1099/jmm.0.47027-0
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