Mycobacterium celeriflavum sp. nov., a rapidly growing scotochromogenic bacterium isolated from clinical specimens

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. [View Article] [PubMed]
   [Google Scholar]
2. Bolger A. M., Lohse M., Usadel B. ( 2014 ). Trimmomatic: a flexible trimmer for Illumina sequence data. . Bioinformatics 30, 2114–2120. [View Article] [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. [View Article] [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. [View Article] [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. [View Article] [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. [View Article] [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. [View Article] [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. [View Article] [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. [View Article] [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. [View Article] [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. [View Article] [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. [View Article] [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. [View Article] [PubMed]
    [Google Scholar]
20. Tortoli E. ( 2009 ). Clinical manifestations of nontuberculous mycobacteria infections. . Clin Microbiol Infect 15, 906–910. [View Article] [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. [View Article] [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]