1887

Abstract

Six strains of a rapidly growing scotochromogenic mycobacterium were isolated from pulmonary specimens of independent patients. Biochemical and cultural tests were not suitable for their identification. The mycolic acid pattern analysed by HPLC was different from that of any other mycobacterium. Genotypic characterization, targeting seven housekeeping genes, revealed the presence of microheterogeneity in all of them. Different species were more closely related to the test strains in various regions: the type strain of showed 99.0 % 16S rRNA gene sequence similarity, and 91.5–96.5 % similarity for the remaining six regions. The whole genome sequences of the proposed type strain and that of presented an average nucleotide identity (ANI) of 82.9 %. Phylogenetic analysis produced poorly robust trees in most genes with the exception of and where and were the closest species. This phylogenetic relatedness was confirmed by the tree inferred from five concatenated genes, which was very robust. The polyphasic characterization of the test strains, supported by the ANI value, demonstrates that they belong to a previously unreported species, for which the name sp. nov. is proposed. The type strain is AFPC-000207 ( = DSM 46765 = JCM 18439).

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2015-02-01
2019-10-19
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References

  1. Adékambi T., Colson P., Drancourt M.. ( 2003;). rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. . J Clin Microbiol 41:, 5699–5708. [CrossRef][PubMed]
    [Google Scholar]
  2. Bolger A. M., Lohse M., Usadel B.. ( 2014;). Trimmomatic: a flexible trimmer for Illumina sequence data. . Bioinformatics 30:, 2114–2120. [CrossRef][PubMed]
    [Google Scholar]
  3. Cavuşoğlu C., Tortoli E.. ( 2006;). [Characterization of two new pigmented mycobacteria isolates]. . Mikrobiyol Bul 40:, 185–194. [in Turkish] Medline[PubMed]
    [Google Scholar]
  4. CLSI (2011). Susceptibility Testing of Mycobacteria, Nocardiae and other Aerobic Actinomycetes; Approved Standard, 2nd edn, M24-A2. Wayne, PA: CLSI.
  5. Dai J., Chen Y., Dean S., Morris J. G., Salfinger M., Johnson J. A.. ( 2011;). Multiple-genome comparison reveals new loci for Mycobacterium species identification. . J Clin Microbiol 49:, 144–153. [CrossRef][PubMed]
    [Google Scholar]
  6. 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. [CrossRef][PubMed]
    [Google Scholar]
  7. Gomila M., Ramirez A., Lalucat J.. ( 2007;). Diversity of environmental Mycobacterium isolates from hemodialysis water as shown by a multigene sequencing approach. . Appl Environ Microbiol 73:, 3787–3797. [CrossRef][PubMed]
    [Google Scholar]
  8. Kent P. T., Kubica G. P.. ( 1985;). Public Health Mycobacteriology. A Guide for the Level III Laboratory. Atlanta:: US Department of Health and Human Services;.
    [Google Scholar]
  9. Kim M., Oh H. S., Park S. C., Chun J.. ( 2014;). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. . Int J Syst Evol Microbiol 64:, 346–351. [CrossRef][PubMed]
    [Google Scholar]
  10. Kirschner P., Springer B., Vogel U., Meier A., Wrede A., Kiekenbeck M., Bange F. C., Böttger 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.[PubMed]
    [Google Scholar]
  11. Konstantinidis K. T., Tiedje J. M.. ( 2005;). Genomic insights that advance the species definition for prokaryotes. . Proc Natl Acad Sci U S A 102:, 2567–2572. [CrossRef][PubMed]
    [Google Scholar]
  12. McNabb A., Eisler D., Adie K., Amos M., Rodrigues M., Stephens G., Black W. A., Isaac-Renton J.. ( 2004;). Assessment of partial sequencing of the 65-kilodalton heat shock protein gene (hsp65) for routine identification of Mycobacterium species isolated from clinical sources. . J Clin Microbiol 42:, 3000–3011. [CrossRef][PubMed]
    [Google Scholar]
  13. Mignard S., Flandrois J. P.. ( 2008;). A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees. . Int J Syst Evol Microbiol 58:, 1432–1441. [CrossRef][PubMed]
    [Google Scholar]
  14. Saitou N., Nei M.. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  15. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A., Kämpfer P., Maiden M. C., Nesme X., Rosselló-Mora R., Swings J.. & other authors ( 2002;). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. . Int J Syst Evol Microbiol 52:, 1043–1047. [CrossRef][PubMed]
    [Google Scholar]
  16. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30:, 2725–2729. [CrossRef][PubMed]
    [Google Scholar]
  17. Telenti A., Marchesi F., Balz M., Bally F., Böttger 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.[PubMed]
    [Google Scholar]
  18. Thompson J. D., Higgins D. G., Gibson T. J.. ( 1994;). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22:, 4673–4680. [CrossRef][PubMed]
    [Google Scholar]
  19. Tortoli E.. ( 2003;). Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. . Clin Microbiol Rev 16:, 319–354. [CrossRef][PubMed]
    [Google Scholar]
  20. Tortoli E.. ( 2009;). Clinical manifestations of nontuberculous mycobacteria infections. . Clin Microbiol Infect 15:, 906–910. [CrossRef][PubMed]
    [Google Scholar]
  21. Zerbino D. R., Birney E.. ( 2008;). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. . Genome Res 18:, 821–829. [CrossRef][PubMed]
    [Google Scholar]
  22. Zolg J. W., Philippi-Schulz S.. ( 1994;). The superoxide dismutase gene, a target for detection and identification of mycobacteria by PCR. . J Clin Microbiol 32:, 2801–2812.[PubMed]
    [Google Scholar]
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