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Volume 154, Issue 12

sequence-based identification of complex species Free

Abstract

The complex (MAC) comprises slowly growing mycobacteria responsible for opportunistic infections and zoonoses. The ability to speciate MAC isolates in the clinical microbiology laboratory is critical for determining the organism implicated in clinical disease and for epidemiological investigation of the source of infection. Investigation of a 711 bp variable fragment of flanked by the Myco-F/Myco-R primers found a 0.7–5.1 % divergence among MAC reference strains, with and being the most closely related. Using a 0.7 % divergence cut-off, 83 % of 100 clinical isolates, which had been previously identified by phenotypic characteristics and 16S–23S rDNA intergenic spacer (ITS) probing, were identified as , 8 % as and 2 % as . The uniqueness of seven isolates, exhibiting <99.3 % sequence similarity with MAC reference strains, was confirmed by 16S rDNA, ITS and sequencing and phylogenetic analyses. Partial gene sequencing using the Myco-F/Myco-R primers permits one-step identification of MAC isolates at the species level and the detection of potentially novel MAC species.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): ITS, intergenic spacer , MAC, Mycobacterium avium complex and RGM, rapidly growing mycobacteria
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2008-12-01
2024-04-18
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References

  1. Abed Y., Bollet C., de Micco P. 1995; Identification and strain differentiation of Mycobacterium species on the basis of DNA 16S–23S spacer region polymorphism. Res Microbiol 146:405–413
     [Google Scholar]
  2. Adékambi T., Colson P., Drancourt M. 2003; rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J Clin Microbiol 41:5699–5708
     [Google Scholar]
  3. Barry T., Colleran G., Glennon M., Dunican L. K., Gannon F. 1991; The 16s/23s ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods Appl 1:51–56
     [Google Scholar]
  4. Blackwood K. S., He C., Gunton J., Turenne C. Y., Wolfe J., Kabani A. M. 2000; Evaluation of recA sequences for identification of Mycobacterium species. J Clin Microbiol 38:2846–2852
     [Google Scholar]
  5. Colson P., Tamalet C., Raoult D. 2006; SVARAP and aSVARAP: simple tools for quantitative analysis of nucleotide and amino acid variability and primer selection for clinical microbiology. BMC Microbiol 6:21
     [Google Scholar]
  6. Devallois A., Picardeau M., Goh K. S., Sola C., Vincent V., Rastogi N. 1996; Comparative evaluation of PCR and commercial DNA probes for detection and identification to species level of Mycobacterium avium and Mycobacterium intracellulare . J Clin Microbiol 34:2756–2759
     [Google Scholar]
  7. Devulder G., Pérouse de Montclos M., Flandrois J. P. 2005; A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Int J Syst Evol Microbiol 55:293–302
     [Google Scholar]
  8. Djelouagji Z., Drancourt M. 2006; Inactivation of cultured Mycobacterium tuberculosis organisms prior to DNA extraction. J Clin Microbiol 44:1594–1595
     [Google Scholar]
  9. Esparcia Ó., Navarro F., Quer M., Coll P. 2008; Lymphadenopathy caused by Mycobacterium colombiense . J Clin Microbiol 46:1885–1887
     [Google Scholar]
  10. Frothingham R., Wilson K. H. 1993; Sequence-based differentiation of strains in the Mycobacterium avium complex. J Bacteriol 175:2818–2825
     [Google Scholar]
  11. Gingeras T. R., Ghandour G., Wang E., Berno A., Small P. M., Drobniewski F., Alland D., Desmond E., Holodniy M., Drenkow J. 1998; Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Res 8:435–448
     [Google Scholar]
  12. Glennon M., Smith T., Cormican M., Noone D., Barry T., Maher M., Dawson M., Gilmartin J. J., Gannon F. 1994; The ribosomal intergenic spacer region: a target for the PCR based diagnosis of tuberculosis. Tuber Lung Dis 75:353–360
     [Google Scholar]
  13. Karakousis P. C., Moore R. D., Chaisson R. E. 2004; Mycobacterium avium complex in patients with HIV infection in the era of highly active antiretroviral therapy. Lancet Infect Dis 4:557–565
     [Google Scholar]
  14. Kasai H., Ezaki T., Harayama S. 2000; Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J Clin Microbiol 38:301–308
     [Google Scholar]
  15. 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]
  16. 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
     [Google Scholar]
  17. Kumar S., Tamura K., Nei M. 2004; mega3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5:150–163
     [Google Scholar]
  18. Lauzi S., Pasotto D., Amadori M., Archetti I. L., Poli G., Bonizzi L. 2000; Evaluation of the specificity of the gamma-interferon test in Italian bovine tuberculosis-free herds. Vet J 160:17–24
     [Google Scholar]
  19. Leao S. C., Briones M. R., Sircili M. P., Balian S. C., Mores N., Ferreira-Neto J. S. 1999; Identification of two novel Mycobacterium avium allelic variants in pig and human isolates from Brazil by PCR-restriction enzyme analysis. J Clin Microbiol 37:2592–2597
     [Google Scholar]
  20. Lebrun L., Weill F. X., Lafendi L., Houriez F., Casanova F., Gutierrez M. C., Ingrand D., Lagrange P., Vincent V., Herrmann J. L. 2005; Use of the INNO-LiPA-MYCOBACTERIA assay (version 2) for identification of Mycobacterium avium-- Mycobacterium intracellulare-- Mycobacterium scrofulaceum complex isolates. J Clin Microbiol 43:2567–2574
     [Google Scholar]
  21. Liu X., Feng Z., Harris N. B., Cirillo J. D., Bercovier H., Barletta R. G. 2001; Identification of a secreted superoxide dismutase in Mycobacterium avium ssp. paratuberculosis . FEMS Microbiol Lett 202:233–238
     [Google Scholar]
  22. Mijs W., de Haas P., Rossau R., Van der Laan T., Rigouts L., Portaels F., van Soolingen D. 2002; Molecular evidence to support a proposal to reserve the designation Mycobacterium avium subsp. avium for bird-type isolates and ‘ M.avium subsp. hominissuis’ for the human/porcine type of M. avium . Int J Syst Evol Microbiol 52:1505–1518
     [Google Scholar]
  23. Morita Y., Maruyama S., Kabeya H., Nagai A., Kozawa K., Kato M., Nakajima T., Mikami T., Katsube Y., Kimura H. 2004; Genetic diversity of the dnaJ gene in the Mycobacterium avium complex. J Med Microbiol 53:813–817
     [Google Scholar]
  24. Murcia M. I., Tortoli E., Menendez M. C., Palenque E., Garcia M. J. 2006; Mycobacterium colombiense sp. nov., a novel member of the Mycobacterium avium complex and description of MAC-X as a new ITS genetic variant. Int J Syst Evol Microbiol 56:2049–2054
     [Google Scholar]
  25. 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]
  26. Soini H., Agha S. A., El-Fiky A., Viljanen M. K. 1996; Comparison of amplicor and 32-kilodalton PCR for detection of Mycobacterium tuberculosis from sputum specimens. J Clin Microbiol 34:1829–1830
     [Google Scholar]
  27. Swanson D. S., Kapur V., Stockbauer K., Pan X., Frothingham R., Musser J. M. 1997; Subspecific differentiation of Mycobacterium avium complex strains by automated sequencing of a region of the gene ( hsp65) encoding a 65-kilodalton heat shock protein. Int J Syst Bacteriol 47:414–419
     [Google Scholar]
  28. 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]
  29. Thierry D., Bauge S., Poveda J. D., Vincent V., Guesdon J. L. 1993; Rapid identification of Mycobacterium avium-intracellulare complex strains: clinical practice evaluation of DT6 and DT1 probes.>. J Infect Dis 168:1337–1338
     [Google Scholar]
  30. Thorel M. F., Krichevsky M., Levy-Frebault V. V. 1990; Numerical taxonomy of mycobactin-dependent mycobacteria, emended description of Mycobacterium avium, and description of Mycobacterium avium subsp. avium subsp. nov., Mycobacterium avium subsp. paratuberculosis subsp. nov., and Mycobacterium avium subsp. silvaticum subsp. nov. Int J Syst Bacteriol 40:254–260
     [Google Scholar]
  31. Tortoli E., Cichero P., Piersimoni C., Simonetti M. T., Gesu G., Nista D. 1999; Use of BACTEC MGIT 960 for recovery of mycobacteria from clinical specimens: multicenter study. J Clin Microbiol 37:3578–3582
     [Google Scholar]
  32. Tortoli E., Mariottini A., Mazzarelli G. 2003; Evaluation of INNO-LiPA MYCOBACTERIA v2: improved reverse hybridization multiple DNA probe assay for mycobacterial identification. J Clin Microbiol 41:4418–4420
     [Google Scholar]
  33. Tortoli E., Rindi L., Garcia M. J., Chiaradonna P., Dei R., Garzelli C., Kroppenstedt R. M., Lari N., Mattei R. other authors 2004; Proposal to elevate the genetic variant MAC-A, included in the Mycobacterium avium complex, to species rank as Mycobacterium chimaera sp. nov. Int J Syst Evol Microbiol 54:1277–1285
     [Google Scholar]
  34. Turenne C. Y., Semret M., Cousins D. V., Collins D. M., Behr M. A. 2006; Sequencing of hsp65 distinguishes among subsets of the Mycobacterium avium complex. J Clin Microbiol 44:433–440
     [Google Scholar]
  35. Turenne C. Y., Wallace R. Jr, Behr M. A. 2007; Mycobacterium avium in the postgenomic era. Clin Microbiol Rev 20:205–229
     [Google Scholar]
  36. Woese C. R. 1987; Bacterial evolution. Microbiol Rev 51:221–271
     [Google Scholar]
  37. Yajko D. M., Chin D. P., Gonzalez P. C., Nassos P. S., Hopewell P. C., Reingold A. L., Horsburgh C. R. Jr, Yakrus M. A., Ostroff S. M., Hadley W. K. 1995; Mycobacterium avium complex in water, food, and soil samples collected from the environment of HIV-infected individuals. J Acquir Immune Defic Syndr Hum Retrovirol 9:176–182
     [Google Scholar]
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rpoB sequence-based identification of Mycobacterium avium complex species
Microbiology 154, 3715 (2008); https://doi.org/10.1099/mic.0.2008/020164-0
/content/journal/micro/10.1099/mic.0.2008/020164-0
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