Skip to main content
NCBI home page
Journal of Clinical Microbiology logoLink to Journal of Clinical Microbiology
. 1996 Apr;34(4):866–869. doi: 10.1128/jcm.34.4.866-869.1996

Rapid identification of mycobacterial species by PCR amplification of hypervariable 16S rRNA gene promoter region.

P Dobner 1, K Feldmann 1, M Rifai 1, T Löscher 1, H Rinder 1
PMCID: PMC228907  PMID: 8815098

Abstract

A total of 0.3 to 0.4 kb of the promoter region of the 16S rRNA genes from Mycobacterium tuberculosis, M. gordonae, M. xenopi, and M. leprae was PCR amplified, cloned, and sequenced. The observed number of substitutions, insertions, and deletions exceeded those found in previously used target sequences, including the entire 16S coding region. A simple and generally applicable restriction fragment length polymorphism method that can be used to distinguish between mycobacterial species is described.

Full Text

The Full Text of this article is available as a PDF (250.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Böddinghaus B., Rogall T., Flohr T., Blöcker H., Böttger E. C. Detection and identification of mycobacteria by amplification of rRNA. J Clin Microbiol. 1990 Aug;28(8):1751–1759. doi: 10.1128/jcm.28.8.1751-1759.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Böttger E. C., Hirschel B., Coyle M. B. Mycobacterium genavense sp. nov. Int J Syst Bacteriol. 1993 Oct;43(4):841–843. doi: 10.1099/00207713-43-4-841. [DOI] [PubMed] [Google Scholar]
  3. Compton J. Nucleic acid sequence-based amplification. Nature. 1991 Mar 7;350(6313):91–92. doi: 10.1038/350091a0. [DOI] [PubMed] [Google Scholar]
  4. Dams E., Yamada T., De Baere R., Huysmans E., Vandenberghe A., De Wachter R. Structure of 5S rRNA in actinomycetes and relatives and evolution of eubacteria. J Mol Evol. 1987;25(3):255–260. doi: 10.1007/BF02100019. [DOI] [PubMed] [Google Scholar]
  5. Haas W. H., Kirschner P., Ziesing S., Bremer H. J., Böttger E. C. Cervical lymphadenitis in a child caused by a previously unknown mycobacterium. J Infect Dis. 1993 Jan;167(1):237–240. doi: 10.1093/infdis/167.1.237. [DOI] [PubMed] [Google Scholar]
  6. Higgins D. G., Sharp P. M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 1988 Dec 15;73(1):237–244. doi: 10.1016/0378-1119(88)90330-7. [DOI] [PubMed] [Google Scholar]
  7. Ji Y. E., Colston M. J., Cox R. A. Nucleotide sequence and secondary structures of precursor 16S rRNA of slow-growing mycobacteria. Microbiology. 1994 Jan;140(Pt 1):123–132. doi: 10.1099/13500872-140-1-123. [DOI] [PubMed] [Google Scholar]
  8. Kapur V., Li L. L., Hamrick M. R., Plikaytis B. B., Shinnick T. M., Telenti A., Jacobs W. R., Jr, Banerjee A., Cole S., Yuen K. Y. Rapid Mycobacterium species assignment and unambiguous identification of mutations associated with antimicrobial resistance in Mycobacterium tuberculosis by automated DNA sequencing. Arch Pathol Lab Med. 1995 Feb;119(2):131–138. [PubMed] [Google Scholar]
  9. Kempsell K. E., Ji Y. E., Estrada I. C., Colston M. J., Cox R. A. The nucleotide sequence of the promoter, 16S rRNA and spacer region of the ribosomal RNA operon of Mycobacterium tuberculosis and comparison with Mycobacterium leprae precursor rRNA. J Gen Microbiol. 1992 Aug;138(Pt 8):1717–1727. doi: 10.1099/00221287-138-8-1717. [DOI] [PubMed] [Google Scholar]
  10. Kirschner P., Teske A., Schröder K. H., Kroppenstedt R. M., Wolters J., Böttger E. C. Mycobacterium confluentis sp. nov. Int J Syst Bacteriol. 1992 Apr;42(2):257–262. doi: 10.1099/00207713-42-2-257. [DOI] [PubMed] [Google Scholar]
  11. Liesack W., Pitulle C., Sela S., Stackebrandt E. Nucleotide sequence of the 16S rRNA from Mycobacterium leprae. Nucleic Acids Res. 1990 Sep 25;18(18):5558–5558. doi: 10.1093/nar/18.18.5558. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Mehra V., Sweetser D., Young R. A. Efficient mapping of protein antigenic determinants. Proc Natl Acad Sci U S A. 1986 Sep;83(18):7013–7017. doi: 10.1073/pnas.83.18.7013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Meier A., Kirschner P., Schröder K. H., Wolters J., Kroppenstedt R. M., Böttger E. C. Mycobacterium intermedium sp. nov. Int J Syst Bacteriol. 1993 Apr;43(2):204–209. doi: 10.1099/00207713-43-2-204. [DOI] [PubMed] [Google Scholar]
  14. Pitulle C., Dorsch M., Kazda J., Wolters J., Stackebrandt E. Phylogeny of rapidly growing members of the genus Mycobacterium. Int J Syst Bacteriol. 1992 Jul;42(3):337–343. doi: 10.1099/00207713-42-3-337. [DOI] [PubMed] [Google Scholar]
  15. Rogall T., Wolters J., Flohr T., Böttger E. C. Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium. Int J Syst Bacteriol. 1990 Oct;40(4):323–330. doi: 10.1099/00207713-40-4-323. [DOI] [PubMed] [Google Scholar]
  16. Ross B. C., Jackson K., Yang M., Sievers A., Dwyer B. Identification of a genetically distinct subspecies of Mycobacterium kansasii. J Clin Microbiol. 1992 Nov;30(11):2930–2933. doi: 10.1128/jcm.30.11.2930-2933.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  18. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sela S., Clark-Curtiss J. E. Cloning and characterization of the Mycobacterium leprae putative ribosomal RNA promoter in Escherichia coli. Gene. 1991 Feb 1;98(1):123–127. doi: 10.1016/0378-1119(91)90114-q. [DOI] [PubMed] [Google Scholar]
  20. Smida J., Kazda J., Stackebrandt E. Molecular-genetic evidence for the relationship of Mycobacterium leprae to slow-growing pathogenic mycobacteria. Int J Lepr Other Mycobact Dis. 1988 Sep;56(3):449–454. [PubMed] [Google Scholar]
  21. Springer B., Kirschner P., Rost-Meyer G., Schröder K. H., Kroppenstedt R. M., Böttger E. C. Mycobacterium interjectum, a new species isolated from a patient with chronic lymphadenitis. J Clin Microbiol. 1993 Dec;31(12):3083–3089. doi: 10.1128/jcm.31.12.3083-3089.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Stahl D. A., Urbance J. W. The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria. J Bacteriol. 1990 Jan;172(1):116–124. doi: 10.1128/jb.172.1.116-124.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Telenti A., Marchesi F., Balz M., Bally F., Böttger E. C., Bodmer T. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol. 1993 Feb;31(2):175–178. doi: 10.1128/jcm.31.2.175-178.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. van der Vliet G. M., Schukkink R. A., van Gemen B., Schepers P., Klatser P. R. Nucleic acid sequence-based amplification (NASBA) for the identification of mycobacteria. J Gen Microbiol. 1993 Oct;139(10):2423–2429. doi: 10.1099/00221287-139-10-2423. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Clinical Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES