1887

Abstract

The nucleotide sequences (604 bp) of partial heat-shock protein genes () from 161 strains containing 56 reference species and 105 clinical isolates were determined and compared. sequence analysis showed a higher degree of divergence between species than did 16S rRNA gene analysis. Generally, the topology of the phylogenetic tree based on the DNA sequences was similar to that of the 16S rRNA gene, thus revealing natural relationships among species. When a direct sequencing protocol targeting 422 bp sequences was applied to 70 non-tuberculous mycobacterium (NTM) clinical isolates, all NTMs were clearly identified. In addition, an I PCR restriction fragment length polymorphism analysis method for the differentiation of complex from NTM strains was developed during this study. The results obtained suggest that 604 bp sequences are useful for the phylogenetic analysis and species identification of mycobacteria.

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2005-07-01
2024-03-29
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References

  1. Chang Y. H., Shangkuan Y. H., Lin H. C., Liu H. W. 2003; PCR assay of the groEL gene for detection and differentiation of Bacillus cereus group cells. Appl Environ Microbiol 69:4502–4510 [CrossRef]
    [Google Scholar]
  2. Clayton R. A., Sutton G., Hinkle P. S. Jr, Bult C., Fields C. 1995; Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45:595–599 [CrossRef]
    [Google Scholar]
  3. Devallois A., Goh K. S., Rastogi N. 1997; Rapid identification of mycobacteria to species level by PCR-restriction fragment length polymorphism analysis of the hsp65 gene and proposition of an algorithm to differentiate 34 mycobacterial species. J Clin Microbiol 35:2969–2973
    [Google Scholar]
  4. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  5. Felsenstein J. 1993 phylip – Phylogeny Inference Package, version 3.5. Distributed by the author. Department of Genome Sciences University of Washington; Seattle, USA:
    [Google Scholar]
  6. Fitch W. M. 1972; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416
    [Google Scholar]
  7. Fox G. E., Wisotzkey J. D., Jurtshuk P. Jr 1992; How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170 [CrossRef]
    [Google Scholar]
  8. Goodfellow M., Magee J. G. 1998; Taxonomy of mycobacteria. In Mycobacteria , vol. 2, Basic Aspects pp  1–71 Edited by Gangadharam P. R. J., Jenkins P. A. New York & London: Chapman & Hall;
    [Google Scholar]
  9. Hafner B., Haag H., Geiss H. K., Nolte O. 2004; Different molecular methods for the identification of rarely isolated non-tuberculous mycobacteria and description of new hsp65 restriction fragment length polymorphism patterns. Mol Cell Probes 18:59–65 [CrossRef]
    [Google Scholar]
  10. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism pp  21–132 Edited by Munro H. N. New York: Academic Press;
    [Google Scholar]
  11. Kim B. J., Lee S. H., Lyu M. A., Kim S. J., Bai G. H., Chae G. T., Kim E. C., Cha C. Y., Kook Y. H. 1999; Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene ( rpoB . J Clin Microbiol 37:1714–1720
    [Google Scholar]
  12. Kim B. J., Lee K. H., Park B. N., Kim S. J., Bai G. H., Kim S. J., Kook Y. H. 2001; Differentiation of mycobacterial species by PCR-restriction analysis of DNA (342 base pairs) of the RNA polymerase gene ( rpoB ). J Clin Microbiol 39:2102–2109 [CrossRef]
    [Google Scholar]
  13. Kirschner P., Springer B., Vogel U., Meier A., Wrede A., Kiekenbeck M., Bange F. C., Bottger E. C. 1993; Genotypic identification of mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory. J Clin Microbiol 31:2882–2889
    [Google Scholar]
  14. Kumar S., Tamura K., Jakobsen I. B., Nei M. 2001 mega2: Molecular Evolutionary Genetics Analysis software Arizona State University; Tempe, AZ, USA:
    [Google Scholar]
  15. Kwok A. Y., Su S. C., Reynolds R. P., Bay S. J., Av-Gay Y., Dovichi N. J., Chow A. W. 1999; Species identification and phylogenetic relationships based on partial HSP60 gene sequences within the genus Staphylococcus . Int J Syst Bacteriol 49:1181–1192 [CrossRef]
    [Google Scholar]
  16. Lee J. H., Park H. S., Jang W. J. 9 other authors 2003; Differentiation of rickettsiae by groEL gene analysis. J Clin Microbiol 41:2952–2960 [CrossRef]
    [Google Scholar]
  17. Ninet B., Monod M., Emler S., Pawlowski J., Metral C., Rohner P., Auckenthaler R., Hirschel B. 1996; Two different 16S rRNA genes in a mycobacterial strain. J Clin Microbiol 34:2531–2536
    [Google Scholar]
  18. 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]
  19. Pitulle C., Dorsch M., Kazda J., Wolters J., Stackebrandt E. 1992; Phylogeny of rapidly growing members of the genus Mycobacterium . Int J Syst Bacteriol 42:337–343 [CrossRef]
    [Google Scholar]
  20. Reischl U., Feldmann K., Naumann L., Gaugler B. J. M., Ninet B., Hirschel B., Emler S. 1998; 16S rRNA sequence diversity in Mycobacterium celatum strains caused by presence of two different copies of 16S rRNA gene. J Clin Microbiol 36:1761–1764
    [Google Scholar]
  21. Ringuet H., Akoua-Koffi C., Honore S., Varnerot A., Vincent V., Berche P., Gaillard J. L., Pierre-Audigier C. 1999; hsp65 sequencing for identification of rapidly growing mycobacteria. J Clin Microbiol 37:852–857
    [Google Scholar]
  22. Rogall T., Wolters J., Flohr T., Böttger E. C. 1990; Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium . Int J Syst Bacteriol 40:323–330 [CrossRef]
    [Google Scholar]
  23. 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]
  24. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  25. Segal G., Ron E. Z. 1996; Regulation and organization of the groE and dnaK operons in Eubacteria . FEMS Microbiol Lett 138:1–10 [CrossRef]
    [Google Scholar]
  26. Smole S. C., McAleese F., Ngampasutadol J., Von Reyn C. F., Arbeit R. D. 2002; Clinical and epidemiological correlates of genotypes within the Mycobacterium avium complex defined by restriction and sequence analysis of hsp65 . J Clin Microbiol 40:3374–3380 [CrossRef]
    [Google Scholar]
  27. Stahl D. A., Urbance J. W. 1990; The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria. J Bacteriol 172:116–124
    [Google Scholar]
  28. Stone B. B., Nietupski R. M., Breton G. L., Weisburg W. G. 1995; Comparison of Mycobacterium 23S rRNA sequences by high-temperature reverse transcription and PCR. Int J Syst Bacteriol 45:811–819 [CrossRef]
    [Google Scholar]
  29. Swanson D. S., Pan X., Musser J. M. 1996; Identification and subspecific differentiation of Mycobacterium scrofulaceum by automated sequencing of a region of the gene ( hsp65 ) encoding a 65-kilodalton heat shock protein. J Clin Microbiol 34:3151–3159
    [Google Scholar]
  30. Takewaki S. I., Okuzumi K., Manabe I., Tanimura M., Miyamura K., Nakahara K. I., Yazaki Y., Ohkubo A., Nagai R. 1994; Nucleotide sequence comparison of the mycobacterial dnaJ gene and PCR-restriction fragment length polymorphism analysis for identification of mycobacterial species. Int J Syst Bacteriol 44:159–166 [CrossRef]
    [Google Scholar]
  31. Telenti A., Marchesi F., Balz M., Bally F., Bottger E. C., Bodmer T. 1993; Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol 31:175–178
    [Google Scholar]
  32. Turenne C. Y., Tschetter L., Wolfe J., Kabani A. 2001; Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species. J Clin Microbiol 39:3637–3648 [CrossRef]
    [Google Scholar]
  33. Viale A. M., Arakaki A. K., Soncini F. C., Ferreyra R. G. 1994; Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons. Int J Syst Bacteriol 44:527–533 [CrossRef]
    [Google Scholar]
  34. Wayne L. G., Kubica G. P. 1986; The mycobacteria. In Bergey's Manual of Determinative Bacteriology , 9th edn. pp  1435–1457 Edited by Buchanan R. E., Gibbons N. E. Baltimore: Williams & Wilkins;
    [Google Scholar]
  35. Williams D. L., Gillis T. P., Booth R. J., Looker D., Watson J. D. 1990; The use of a specific DNA probe and polymerase chain reaction for the detection of Mycobacterium leprae . J Infect Dis 162:193–200 [CrossRef]
    [Google Scholar]
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