1887

Abstract

The aim of this study was to evaluate the use of RNA polymerase subunit () and phenylalanyl-tRNA synthase () gene sequences as species identification tools for enterococci. Ninety-six representative strains comprising all currently recognized species were examined. gene sequences generated a robust classification into species groups similar to the one based on 16S rRNA gene sequence analysis. On the other hand, the gene is a fast-evolving clock even better suited for species delineation than the gene, but not for recognition of species groups within as determined by both and 16S rRNA genes. All enterococcal species were clearly differentiated on the basis of their and sequences. Evaluation of intraspecies variation showed that both and genes have a high degree of homogeneity among strains of the same species. Strains of the same enterococcal species have at least 99 % and 97 % gene sequence similarity, whereas, different enterococcal species have at maximum 97 % and 86 % gene sequence similarity. It was concluded that both genes can be used as reliable tools for identification of clinical and environmental species of and are efficient screening methods for the detection of novel species. The sequence data obtained in this study were compared to the available and 16S rRNA gene sequences. The MLSA approach to taxonomy provides portable, highly reproducible data with lower costs for rapid identification of all enterococcal species.

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2005-07-01
2024-03-28
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References

  1. Angeletti S., Lorino G., Gherardi G., Battistoni F., De Cesaris M., Dicuonzo G. 2001; Routine molecular identification of enterococci by gene-specific PCR and 16S ribosomal DNA sequencing. J Clin Microbiol 39:794–797 [CrossRef]
    [Google Scholar]
  2. Baele M., Baele P., Vaneechoutte M., Storms V., Butaye P., Devriese L. A., Verschraegen G., 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. Carvalho G., Steigerwalt G., Morey E., Shewmaker L., Teixeira M., Facklam R. 2004; Characterization of three new enterococcal species, Enterococcus sp. nov. CDC PNS-E1, Enterococcus sp. nov. CDC PNS-E2, and Enterococcus sp. nov. CDCPNS-E3, isolated from human clinical specimens. J Clin Microbiol 42:1192–1198 [CrossRef]
    [Google Scholar]
  4. Christensen H., Kuhnert P., Olsen J. E., Bisgaard M. 2004; Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae. Int J Syst Evol Microbiol 54:1601–1609 [CrossRef]
    [Google Scholar]
  5. Collins M., Jones D., Farrow J., Kilpper-Balz R., Schleifer K. 1984; Enterococcus avium nom.rev., comb. nov.; E. casseliflavus nom. rev., comb. nov.; E. durans nom. rev., comb. nov.;E. gallinarum comb. nov.; and E. malodoratus sp. nov. Int J Syst Bacteriol 34:220–223 [CrossRef]
    [Google Scholar]
  6. 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]
  7. Devriese L. A., Vancanneyt M., Descheemaeker P., Baele M., Van Landuyt H. W., Gordts B., Butaye P., Swings J., Haesebrouck F. 2002; Differentiation and identification of Enterococcus durans,E. hirae and E. villorum . J Appl Microbiol 92:821–827 [CrossRef]
    [Google Scholar]
  8. Domig K. J., Mayer H. K., Kneifel W. 2003; Methods used for the isolation, enumeration, characterisation and identification of Enterococcus spp. 2. Pheno- and genotypic criteria. Int J Food Microbiol 88:165–188 [CrossRef]
    [Google Scholar]
  9. Drancourt M., Roux V., Fournier P. E., Raoult D. 2004; rpoB gene sequence-based identification of aerobic Gram-positive cocci of the generaStreptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J Clin Microbiol 42:497–504 [CrossRef]
    [Google Scholar]
  10. Dutka-Malen S., Evers S., Courvalin P. 1995; Detection of glycopeptide resistance genotypes and identification to the species level of clinically relevant enterococci by PCR. J Clin Microbiol 33:24–27 erratum 1434
    [Google Scholar]
  11. Dzidic S., Bedekovic V. 2003; Horizontal gene transfer – emerging multidrug resistance in hospital bacteria. Acta Pharmacol Sin 24:519–526
    [Google Scholar]
  12. Fernandez-Guerrero M. L., Herrero L., Bellver M., Gadea I., Roblas R. F, de Gorgolas M. 2002; Nosocomial enterococcal endocarditis: a serious hazard for hospitalized patients with enterococcal bacteraemia. J Intern Med 252:510–515 [CrossRef]
    [Google Scholar]
  13. Fortina M. G., Ricci G., Mora D., Manachini P. L. 2004; Molecular analysis of artisanal Italian cheeses reveals Enterococcus italicus sp. nov. Int J Syst Evol Microbiol 54:1717–1721 [CrossRef]
    [Google Scholar]
  14. Franz C. M., Holzapfel W. H., Stiles M. E. 1999; Enterococci at the crossroads of food safety?. Int J Food Microbiol 47:1–24 [CrossRef]
    [Google Scholar]
  15. Franz C. M., Stiles M. E., Schleifer K. H., Holzapfel W. H. 2003; Enterococci in foods – a conundrum for food safety. Int J Food Microbiol 88:105–122 [CrossRef]
    [Google Scholar]
  16. Gelsomino R., Vancanneyt M., Cogan T. M., Condon S., Swings J. 2002; Source of enterococci in a farmhouse raw-milk cheese. Appl Environ Microbiol 68:3560–3565 [CrossRef]
    [Google Scholar]
  17. Gevers D., Huys G., Swings J. 2001; Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 205:31–36 [CrossRef]
    [Google Scholar]
  18. Godfree A. F., Kay D., Wyer M. D. 1997; Faecal streptococci as indicators of faecal contamination in water. Soc Appl Bacteriol Symp Ser 26:110S–119S
    [Google Scholar]
  19. Homan W. L., Tribe D., Poznanski S., Li M., Hogg G., Spalburg E., Van Embden J. D., Willems R. J. 2002; Multilocus sequence typing scheme for Enterococcus faecium . J Clin Microbiol 40:1963–1971 [CrossRef]
    [Google Scholar]
  20. Huson D. H. 1998; SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14:68–73 [CrossRef]
    [Google Scholar]
  21. Jackson C. R., Fedorka-Cray P. J., Barrett J. B. 2004; Use of a genus- and species-specific multiplex PCR for identification of enterococci. J Clin Microbiol 42:3558–3565 [CrossRef]
    [Google Scholar]
  22. Jett B. D., Huycke M. M., Gilmore M. S. 1994; Virulence of enterococci. Clin Microbiol Rev 7:462–478
    [Google Scholar]
  23. Jolley K. A., Feil E. J., Chan M. S., Maiden M. C. 2001; Sequence type analysis and recombinational tests (start). Bioinformatics 17:1230–1231 [CrossRef]
    [Google Scholar]
  24. Kirschner C., Maquelin K., Pina P. 11 other authors 2001; Classification and identification of enterococci: a comparative phenotypic, genotypic, and vibrational spectroscopic study. J Clin Microbiol 39:1763–1770 [CrossRef]
    [Google Scholar]
  25. Klein G. 2003; Taxonomy, ecology and antibiotic resistance of enterococci from food and the gastro-intestinal tract. Int J Food Microbiol 88:123–131 [CrossRef]
    [Google Scholar]
  26. Knijff E., Dellaglio F., Lombardi A., Andrighetto C., Torriani S. 2001; Rapid identification of Enterococcus durans and Enterococcus hirae by PCR with primers targeted to the ddl genes. J Microbiol Methods 47:35–40 [CrossRef]
    [Google Scholar]
  27. Lerat E., Daubin V., Moran N. A. 2003; From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria. PLoS Biol 1:101–109
    [Google Scholar]
  28. Michel M., Gutmann L. 1997; Methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci: therapeutic realities and possibilities. Lancet 349:1901–1906 [CrossRef]
    [Google Scholar]
  29. Morrison D., Woodford N., Cookson B. 1997; Enterococci as emerging pathogens of humans. Soc Appl Bacteriol Symp Ser 26:89S–99S
    [Google Scholar]
  30. Murray B. E. 1990; The life and times of the Enterococcus. Clin Microbiol Rev 3:46–65
    [Google Scholar]
  31. Naser S., Thompson F. L., Hoste B., Gevers D., Vandemeulebroecke K., Cleenwerck I., Thompson C. C., Vancanneyt M., Swings J. 2005; Phylogeny and identification of enterococci using atpA gene sequence analysis. J Clin Microbiol 43:2224–2230 [CrossRef]
    [Google Scholar]
  32. Navarro F., Courvalin P. 1994; Analysis of genes encoding d-alanine-d-alanine ligase-related enzymes in Enterococcus casseliflavus and Enterococcus flavescens . Antimicrob Agents Chemother 38:1788–1793 [CrossRef]
    [Google Scholar]
  33. Niemi R. M., Niemela S. I., Bamford D. H., Hantula J., Hyvarinen T., Forsten T., Raateland A. 1993; Presumptive fecal streptococci in environmental samples characterized by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Appl Environ Microbiol 59:2190–2196
    [Google Scholar]
  34. Palys T., Nakamura L. K., Cohan F. M. 1997; Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int J Syst Bacteriol 47:1145–1156 [CrossRef]
    [Google Scholar]
  35. Patel R., Piper K. E., Rouse M. S., Steckelberg J. M., Uhl J. R., Kohner P., Hopkins M. K., Cockerill F. R. 3rd, Kline B. C. 1998; Determination of 16S rRNA sequences of enterococci and application to species identification of nonmotile Enterococcus gallinarum isolates. J Clin Microbiol 36:3399–3407
    [Google Scholar]
  36. Pompei R., Berlutti F., Thaller M., Ingianni A., Cortis G., Dainelli B. 1992; Enterococcus flavescens sp. nov., a new species of enterococci of clinical origin. Int J Syst Bacteriol 42:365–369 [CrossRef]
    [Google Scholar]
  37. 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]
  38. Ratanasuwan W., Iwen P. C., Hinrichs S. H., Rupp M. E. 1999; Bacteremia due to motile Enterococcus species: clinical features and outcomes. Clin Infect Dis 28:1175–1177 [CrossRef]
    [Google Scholar]
  39. Rybak M. J., Coyle E. A. 1999; Vancomycin-resistant Enterococcus: infectious endocarditis treatment. Curr Infect Dis Rep 1:148–152 [CrossRef]
    [Google Scholar]
  40. Saitou N., Nei M. 1987; The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  41. Santos S. R., Ochman H. 2004; Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6:754–759 [CrossRef]
    [Google Scholar]
  42. Saxena S., Prakash S. K., Malik V. K., Mathur M. D. 2003; Vancomycin resistant Enterococcus in nosocomial urinary tract infections. Ind J Pathol Microbiol 46:256–258
    [Google Scholar]
  43. Sedgley C. M., Lennan S. L., Clewell D. B. 2004; Prevalence, phenotype and genotype of oral enterococci. Oral Microbiol Immunol 19:95–101 [CrossRef]
    [Google Scholar]
  44. Stackebrandt E. 2003; The richness of prokaryotic diversity: there must be a species somewhere. Food Technol Biotechnol 41:17–22
    [Google Scholar]
  45. Stackebrandt E., Frederiksen W., Garrity G. M. 10 other authors 2002; Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047 [CrossRef]
    [Google Scholar]
  46. Svec P., Devriese L. A., Sedlacek I., Baele M., Vancanneyt M., Haesebrouck F., Swings J., Doskar J. 2001; Enterococcus haemoperoxidus sp. nov. and Enterococcus moraviensis sp. nov., isolated from water. Int J Syst Evol Microbiol 51:1567–1574
    [Google Scholar]
  47. 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]
  48. Vancanneyt M., Snauwaert C., Cleenwerck I. 8 other authors 2001; Enterococcus villorum sp. nov., an enteroadherent bacterium associated with diarrhoea in piglets. Int J Syst Evol Microbiol 51:393–400
    [Google Scholar]
  49. Vancanneyt M., Lombardi A., Andrighetto C. 11 other authors 2002; Intraspecies genomic groups in Enterococcus faecium and their correlation with origin and pathogenicity. Appl Environ Microbiol 68:1381–1391 [CrossRef]
    [Google Scholar]
  50. Vancanneyt M., Zamfir M., Devriese L. A. 7 other authors 2004; Enterococcus saccharominimus sp. nov., from dairy products. Int J Syst Evol Microbiol 54:2175–2179 [CrossRef]
    [Google Scholar]
  51. Ventura M., Canchaya C., van Sinderen D., Fitzgerald G. F., Zink R. 2004; Bifidobacterium lactis DSM 10140: identification of the atp (atpBEFHAGDC) operon and analysis of its genetic structure, characteristics, and phylogeny. Appl Environ Microbiol 70:3110–3121 [CrossRef]
    [Google Scholar]
  52. Willey B. M., Jones R. N., McGeer A., Witte W., French G., Roberts R. B., Jenkins S. G., Nadler H., Low D. E. 1999; Practical approach to the identification of clinically relevant Enterococcus species. Diagn Microbiol Infect Dis 34:165–171 [CrossRef]
    [Google Scholar]
  53. 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]
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