Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis (original) (raw)

Abstract

A rapid procedure for the identification of cultured Mycobacterium isolates, based on the combination of enzymatic amplification and restriction analysis, is described. The 16S rRNA genes (rDNA) of 99 strains belonging to 18 different species of the genus Mycobacterium were enzymatically amplified. Amplified rDNA restriction analysis with the enzymes CfoI, MboI, and RsaI was carried out. The combination of the amplified rDNA restriction analysis patterns obtained after restriction with CfoI and MboI enabled differentiation between Mycobacterium asiaticum (number of strains = 4), M. avium (n = 22), M. chelonae (n = 5), M. flavescens (n = 1), M. fortuitum (n = 6), M. gordonae (n = 6), M. intracellulare (n = 13), M. marinum (n = 7), M. nonchromogenicum (n = 1), M. simiae (n = 5), M. terrae (n = 5), the M. tuberculosis complex (n = 11), and 2 of 4 strains of M. xenopi. Further restriction with RsaI was necessary to differentiate between the species M. kansasii (n = 5), M. scrofulaceum (n = 4), and the 2 other M. xenopi strains. The M. avium-M. intracellulare complex was characterized by a specific MboI pattern, and M. avium and M. intracellulare strains could further be differentiated by restriction with CfoI. The whole procedure, including sample preparation prior to the polymerase chain reaction, can be carried out within 8 h, starting from a pure culture.

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  1. Cousins D. V., Wilton S. D., Francis B. R., Gow B. L. Use of polymerase chain reaction for rapid diagnosis of tuberculosis. J Clin Microbiol. 1992 Jan;30(1):255–258. doi: 10.1128/jcm.30.1.255-258.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Del Portillo P., Murillo L. A., Patarroyo M. E. Amplification of a species-specific DNA fragment of Mycobacterium tuberculosis and its possible use in diagnosis. J Clin Microbiol. 1991 Oct;29(10):2163–2168. doi: 10.1128/jcm.29.10.2163-2168.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Deng S., Hiruki C., Robertson J. A., Stemke G. W. Detection by PCR and differentiation by restriction fragment length polymorphism of Acholeplasma, Spiroplasma, Mycoplasma, and Ureaplasma, based upon 16S rRNA genes. PCR Methods Appl. 1992 Feb;1(3):202–204. doi: 10.1101/gr.1.3.202. [DOI] [PubMed] [Google Scholar]
  4. Edwards U., Rogall T., Blöcker H., Emde M., Böttger E. C. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 1989 Oct 11;17(19):7843–7853. doi: 10.1093/nar/17.19.7843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fiss E. H., Chehab F. F., Brooks G. F. DNA amplification and reverse dot blot hybridization for detection and identification of mycobacteria to the species level in the clinical laboratory. J Clin Microbiol. 1992 May;30(5):1220–1224. doi: 10.1128/jcm.30.5.1220-1224.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Grimont F., Grimont P. A. Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. Ann Inst Pasteur Microbiol. 1986 Sep-Oct;137B(2):165–175. doi: 10.1016/s0769-2609(86)80105-3. [DOI] [PubMed] [Google Scholar]
  7. Gurtler V., Wilson V. A., Mayall B. C. Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. J Gen Microbiol. 1991 Nov;137(11):2673–2679. doi: 10.1099/00221287-137-11-2673. [DOI] [PubMed] [Google Scholar]
  8. Hermans P. W., Schuitema A. R., Van Soolingen D., Verstynen C. P., Bik E. M., Thole J. E., Kolk A. H., van Embden J. D. Specific detection of Mycobacterium tuberculosis complex strains by polymerase chain reaction. J Clin Microbiol. 1990 Jun;28(6):1204–1213. doi: 10.1128/jcm.28.6.1204-1213.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Jayarao B. M., Doré J. J., Jr, Oliver S. P. Restriction fragment length polymorphism analysis of 16S ribosomal DNA of Streptococcus and Enterococcus species of bovine origin. J Clin Microbiol. 1992 Sep;30(9):2235–2240. doi: 10.1128/jcm.30.9.2235-2240.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kirschner P., Kiekenbeck M., Meissner D., Wolters J., Böttger E. C. Genetic heterogeneity within Mycobacterium fortuitum complex species: genotypic criteria for identification. J Clin Microbiol. 1992 Nov;30(11):2772–2775. doi: 10.1128/jcm.30.11.2772-2775.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kolk A. H., Evers R., Groothuis D. G., Gilis H., Kuijper S. Production and characterization of monoclonal antibodies against specific serotypes of Mycobacterium avium and the Mycobacterium avium-Mycobacterium intracellulare-Mycobacterium scrofulaceum complex. Infect Immun. 1989 Aug;57(8):2514–2521. doi: 10.1128/iai.57.8.2514-2521.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kunze Z. M., Portaels F., McFadden J. J. Biologically distinct subtypes of Mycobacterium avium differ in possession of insertion sequence IS901. J Clin Microbiol. 1992 Sep;30(9):2366–2372. doi: 10.1128/jcm.30.9.2366-2372.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kusunoki S., Ezaki T. Proposal of Mycobacterium peregrinum sp. nov., nom. rev., and elevation of Mycobacterium chelonae subsp. abscessus (Kubica et al.) to species status: Mycobacterium abscessus comb. nov. Int J Syst Bacteriol. 1992 Apr;42(2):240–245. doi: 10.1099/00207713-42-2-240. [DOI] [PubMed] [Google Scholar]
  14. Pao C. C., Yen T. S., You J. B., Maa J. S., Fiss E. H., Chang C. H. Detection and identification of Mycobacterium tuberculosis by DNA amplification. J Clin Microbiol. 1990 Sep;28(9):1877–1880. doi: 10.1128/jcm.28.9.1877-1880.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Peneau A., Moinard D., Berard I., Pascal O., Moisan J. P. Detection of mycobacteria using the polymerase chain reaction. Eur J Clin Microbiol Infect Dis. 1992 Mar;11(3):270–271. doi: 10.1007/BF02098099. [DOI] [PubMed] [Google Scholar]
  16. Peterson E. M., Lu R., Floyd C., Nakasone A., Friedly G., de la Maza L. M. Direct identification of Mycobacterium tuberculosis, Mycobacterium avium, and Mycobacterium intracellulare from amplified primary cultures in BACTEC media using DNA probes. J Clin Microbiol. 1989 Jul;27(7):1543–1547. doi: 10.1128/jcm.27.7.1543-1547.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. Rodrigo G., Källenius G., Hoffmann E., Svenson S. B. Diagnosis of mycobacterial infections by PCR and restriction enzyme digestion. Lett Appl Microbiol. 1992 Aug;15(2):41–44. doi: 10.1111/j.1472-765x.1992.tb00720.x. [DOI] [PubMed] [Google Scholar]
  19. Rossau R., Duhamel M., Jannes G., Decourt J. L., Van Heuverswyn H. The development of specific rRNA-derived oligonucleotide probes for Haemophilus ducreyi, the causative agent of chancroid. J Gen Microbiol. 1991 Feb;137(2):277–285. doi: 10.1099/00221287-137-2-277. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Wilton S., Cousins D. Detection and identification of multiple mycobacterial pathogens by DNA amplification in a single tube. PCR Methods Appl. 1992 May;1(4):269–273. doi: 10.1101/gr.1.4.269. [DOI] [PubMed] [Google Scholar]
  22. Wolinsky E. Mycobacterial diseases other than tuberculosis. Clin Infect Dis. 1992 Jul;15(1):1–10. doi: 10.1093/clinids/15.1.1. [DOI] [PubMed] [Google Scholar]