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. 1997 Nov;35(11):2969–2973. doi: 10.1128/jcm.35.11.2969-2973.1997

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.

A Devallois 1, K S Goh 1, N Rastogi 1
PMCID: PMC230098  PMID: 9350770

Abstract

PCR-restriction fragment length polymorphism analysis (PRA) of the hsp65 gene (A. Telenti, F. Marchesi, M. Balz, F. Bally, E. C. Böttger, and T. Bodmer, J. Clin. Microbiol. 31:175-178, 1993) was applied to 108 mycobacterial isolates representing 34 species to evaluate its potential as a rapid reference method. A total of 49 distinct patterns were obtained; 25 species were characterized by a single PRA pattern, while 9 species gave more than one specific pattern. An algorithm describing these 34 species (which includes five additional species and new subgroups of Mycobacterium kansasii, M. abscessus, and M. peregrinum) is proposed. A relatively simple and inexpensive method, PRA may be particularly helpful in routine clinical microbiology laboratories.

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Selected References

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  1. Abed Y., Bollet C., De Micco P. Demonstration of Mycobacterium kansasii species heterogeneity by the amplification of the 16S-23S spacer region. J Med Microbiol. 1995 Aug;43(2):156–158. doi: 10.1099/00222615-43-2-156. [DOI] [PubMed] [Google Scholar]
  2. Avaniss-Aghajani E., Jones K., Holtzman A., Aronson T., Glover N., Boian M., Froman S., Brunk C. F. Molecular technique for rapid identification of mycobacteria. J Clin Microbiol. 1996 Jan;34(1):98–102. doi: 10.1128/jcm.34.1.98-102.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bosne S., Lévy-Frébault V. V. Mycobactin analysis as an aid for the identification of Mycobacterium fortuitum and Mycobacterium chelonae subspecies. J Clin Microbiol. 1992 May;30(5):1225–1231. doi: 10.1128/jcm.30.5.1225-1231.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Butler W. R., Jost K. C., Jr, Kilburn J. O. Identification of mycobacteria by high-performance liquid chromatography. J Clin Microbiol. 1991 Nov;29(11):2468–2472. doi: 10.1128/jcm.29.11.2468-2472.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. Devallois A., Legrand E., Rastogi N. Evaluation of Amplicor MTB test as adjunct to smears and culture for direct detection of Mycobacterium tuberculosis in the French Caribbean. J Clin Microbiol. 1996 May;34(5):1065–1068. doi: 10.1128/jcm.34.5.1065-1068.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Devallois A., Picardeau M., Goh K. S., Sola C., Vincent V., Rastogi N. Comparative evaluation of PCR and commercial DNA probes for detection and identification to species level of Mycobacterium avium and Mycobacterium intracellulare. J Clin Microbiol. 1996 Nov;34(11):2756–2759. doi: 10.1128/jcm.34.11.2756-2759.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Falkinham J. O., 3rd Epidemiology of infection by nontuberculous mycobacteria. Clin Microbiol Rev. 1996 Apr;9(2):177–215. doi: 10.1128/cmr.9.2.177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hance A. J., Grandchamp B., Lévy-Frébault V., Lecossier D., Rauzier J., Bocart D., Gicquel B. Detection and identification of mycobacteria by amplification of mycobacterial DNA. Mol Microbiol. 1989 Jul;3(7):843–849. doi: 10.1111/j.1365-2958.1989.tb00233.x. [DOI] [PubMed] [Google Scholar]
  10. Hughes M. S., Skuce R. A., Beck L. A., Neill S. D. Identification of mycobacteria from animals by restriction enzyme analysis and direct DNA cycle sequencing of polymerase chain reaction-amplified 16S rRNA gene sequences. J Clin Microbiol. 1993 Dec;31(12):3216–3222. doi: 10.1128/jcm.31.12.3216-3222.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. Kirschner P., Springer B., Vogel U., Meier A., Wrede A., Kiekenbeck M., Bange F. C., Böttger E. C. Genotypic identification of mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory. J Clin Microbiol. 1993 Nov;31(11):2882–2889. doi: 10.1128/jcm.31.11.2882-2889.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lebrun L., Espinasse F., Poveda J. D., Vincent-Levy-Frebault V. Evaluation of nonradioactive DNA probes for identification of mycobacteria. J Clin Microbiol. 1992 Sep;30(9):2476–2478. doi: 10.1128/jcm.30.9.2476-2478.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lévy-Frébault V. V., Thorel M. F., Varnerot A., Gicquel B. DNA polymorphism in Mycobacterium paratuberculosis, "wood pigeon mycobacteria," and related mycobacteria analyzed by field inversion gel electrophoresis. J Clin Microbiol. 1989 Dec;27(12):2823–2826. doi: 10.1128/jcm.27.12.2823-2826.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lévy-Frébault V., Daffé M., Goh K. S., Lanéelle M. A., Asselineau C., David H. L. Identification of Mycobacterium fortuitum and Mycobacterium chelonei. J Clin Microbiol. 1983 May;17(5):744–752. doi: 10.1128/jcm.17.5.744-752.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Mabilat C., Desvarenne S., Panteix G., Machabert N., Bernillon M. H., Guardiola G., Cros P. Routine identification of Mycobacterium tuberculosis complex isolates by automated hybridization. J Clin Microbiol. 1994 Nov;32(11):2702–2705. doi: 10.1128/jcm.32.11.2702-2705.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Picardeau M., Prod'Hom G., Raskine L., LePennec M. P., Vincent V. Genotypic characterization of five subspecies of Mycobacterium kansasii. J Clin Microbiol. 1997 Jan;35(1):25–32. doi: 10.1128/jcm.35.1.25-32.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Plikaytis B. B., Plikaytis B. D., Yakrus M. A., Butler W. R., Woodley C. L., Silcox V. A., Shinnick T. M. Differentiation of slowly growing Mycobacterium species, including Mycobacterium tuberculosis, by gene amplification and restriction fragment length polymorphism analysis. J Clin Microbiol. 1992 Jul;30(7):1815–1822. doi: 10.1128/jcm.30.7.1815-1822.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Shinnick T. M. The 65-kilodalton antigen of Mycobacterium tuberculosis. J Bacteriol. 1987 Mar;169(3):1080–1088. doi: 10.1128/jb.169.3.1080-1088.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Shinnick T. M., Vodkin M. H., Williams J. C. The Mycobacterium tuberculosis 65-kilodalton antigen is a heat shock protein which corresponds to common antigen and to the Escherichia coli GroEL protein. Infect Immun. 1988 Feb;56(2):446–451. doi: 10.1128/iai.56.2.446-451.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Soini H., Böttger E. C., Viljanen M. K. Identification of mycobacteria by PCR-based sequence determination of the 32-kilodalton protein gene. J Clin Microbiol. 1994 Dec;32(12):2944–2947. doi: 10.1128/jcm.32.12.2944-2947.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Springer B., Stockman L., Teschner K., Roberts G. D., Böttger E. C. Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods. J Clin Microbiol. 1996 Feb;34(2):296–303. doi: 10.1128/jcm.34.2.296-303.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Takewaki S., Okuzumi K., Manabe I., Tanimura M., Miyamura K., Nakahara K., Yazaki Y., Ohkubo A., Nagai R. Nucleotide sequence comparison of the mycobacterial dnaJ gene and PCR-restriction fragment length polymorphism analysis for identification of mycobacterial species. Int J Syst Bacteriol. 1994 Jan;44(1):159–166. doi: 10.1099/00207713-44-1-159. [DOI] [PubMed] [Google Scholar]
  25. Taylor T. B., Patterson C., Hale Y., Safranek W. W. Routine use of PCR-restriction fragment length polymorphism analysis for identification of mycobacteria growing in liquid media. J Clin Microbiol. 1997 Jan;35(1):79–85. doi: 10.1128/jcm.35.1.79-85.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. Thorel M. F., Blom-Potar M. C., Rastogi N. Characterization of Mycobacterium paratuberculosis and "wood-pigeon" mycobacteria by isoenzyme profile and selective staining of immunoprecipitates. Res Microbiol. 1990 Jun;141(5):551–561. doi: 10.1016/0923-2508(90)90019-m. [DOI] [PubMed] [Google Scholar]
  28. Tortoli E., Simonetti M. T., Lacchini C., Penati V., Urbano P. Tentative evidence of AIDS-associated biotype of Mycobacterium kansasii. J Clin Microbiol. 1994 Jul;32(7):1779–1782. doi: 10.1128/jcm.32.7.1779-1782.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Vaneechoutte M., De Beenhouwer H., Claeys G., Verschraegen G., De Rouck A., Paepe N., Elaichouni A., Portaels F. Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis. J Clin Microbiol. 1993 Aug;31(8):2061–2065. doi: 10.1128/jcm.31.8.2061-2065.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]

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