1887

Abstract

Bacterial whole-genome sequences contain informative features of their evolutionary pathways. Comparison of whole-genome sequences have become the method of choice for classification of prokaryotes, thus allowing the identification of bacteria from an evolutionary perspective, and providing data to resolve some current controversies. Currently, controversy exists about the assignment of members of the complex, as is for the cases of and ‘’. These two mycobacteria, closely related to on the basis of standard phenotypic and single gene-sequences comparisons, were not considered a member of such species on the basis on some particular differences displayed by a single strain. Whole-genome sequence comparison procedures, namely the average nucleotide identity and the genome distance, showed that those two mycobacteria should be considered members of the species . The results were confirmed with other whole-genome comparison supplementary methods. According to the data provided, and ‘’ should be considered and renamed and included as members of . This study highlights the problems caused when a novel species is accepted on the basis of a single strain, as was the case for . Based mainly on whole-genome sequence analysis, we conclude that should be reclassified as a subspecies of as subsp. and classified in the same subspecies as the type strain of and classified as subsp.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002767
2018-06-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/6/1998.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002767&mimeType=html&fmt=ahah

References

  1. Coenye T, Gevers D, Van de Peer Y, Vandamme P, Swings J. Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 2005; 29:147–167 [View Article][PubMed]
    [Google Scholar]
  2. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  3. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea . Syst Appl Microbiol 2015; 38:209–216 [View Article][PubMed]
    [Google Scholar]
  4. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  5. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M et al. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 2014; 64:384–391 [View Article][PubMed]
    [Google Scholar]
  6. Tortoli E. The new species of the genus Mycobacterium, microbiological features and clinical relevance. Clin Microbiol Rev 2014; 27:727–752 [Crossref]
    [Google Scholar]
  7. Shinnick TM, Good RC. Mycobacterial taxonomy. Eur J Clin Microbiol Infect Dis 1994; 13:884–901 [View Article][PubMed]
    [Google Scholar]
  8. Iakhiaeva E, McNulty S, Brown Elliott BA, Falkinham JO, Williams MD et al. Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping of Mycobacterium intracellulare for strain comparison with establishment of a PCR-based database. J Clin Microbiol 2013; 51:409–416 [View Article][PubMed]
    [Google Scholar]
  9. Devallois A, Picardeau M, Goh KS, Sola C, Vincent V et al. 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; 34:2756–2759[PubMed]
    [Google Scholar]
  10. Tortoli E, Rindi L, Garcia MJ, Chiaradonna P, Dei R et al. 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 2004; 54:1277–1285 [View Article][PubMed]
    [Google Scholar]
  11. Falkinham JO. Epidemiology of infection by nontuberculous mycobacteria. Clin Microbiol Rev 1996; 9:177–215[PubMed]
    [Google Scholar]
  12. Inderlied CB, Kemper CA, Bermudez LE. The Mycobacterium avium complex. Clin Microbiol Rev 1993; 6:266–310 [View Article][PubMed]
    [Google Scholar]
  13. Turenne CY, Wallace R, Behr MA. Mycobacterium avium in the postgenomic era. Clin Microbiol Rev 2007; 20:205–229 [View Article][PubMed]
    [Google Scholar]
  14. Kim BJ, Math RK, Jeon CO, Yu HK, Park YG et al. Mycobacterium yongonense sp. nov., a slow-growing non-chromogenic species closely related to Mycobacterium intracellulare . Int J Syst Evol Microbiol 2013; 63:192–199 [View Article][PubMed]
    [Google Scholar]
  15. Saini V, Raghuvanshi S, Talwar GP, Ahmed N, Khurana JP et al. Polyphasic taxonomic analysis establishes Mycobacterium indicus pranii as a distinct species. PLoS One 2009; 4:e6263 [View Article][PubMed]
    [Google Scholar]
  16. Garcia-Betancur JC, Menendez MC, Del Portillo P, Garcia MJ. Alignment of multiple complete genomes suggests that gene rearrangements may contribute towards the speciation of Mycobacteria. Infect Genet Evol 2012; 12:819–826 [View Article][PubMed]
    [Google Scholar]
  17. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  18. Whitman WB. Genome sequences as the type material for taxonomic descriptions of prokaryotes. Syst Appl Microbiol 2015; 38:217–222 [View Article][PubMed]
    [Google Scholar]
  19. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article][PubMed]
    [Google Scholar]
  20. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article][PubMed]
    [Google Scholar]
  21. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  22. Karlin S, Mrázek J, Campbell AM. Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 1997; 179:3899–3913 [View Article][PubMed]
    [Google Scholar]
  23. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394–1403 [View Article][PubMed]
    [Google Scholar]
  24. Tortoli E, Kohl TA, Brown-Elliott BA, Trovato A, Leão SC et al. Emended description of Mycobacterium abscessus, Mycobacterium abscessus subsp. abscessus and Mycobacterium abscessus subsp. bolletii and designation of Mycobacterium abscessus subsp. massiliense comb. nov. Int J Syst Evol Microbiol 2016; 66:4471–4479 [View Article][PubMed]
    [Google Scholar]
  25. Park JH, Shim TS, Lee SA, Lee H, Lee IK et al. Molecular characterization of Mycobacterium intracellulare-related strains based on the sequence analysis of hsp65, internal transcribed spacer and 16S rRNA genes. J Med Microbiol 2010; 59:1037–1043 [View Article][PubMed]
    [Google Scholar]
  26. Tortoli E, Mariottini A, Pierotti P, Simonetti TM, Rossolini GM. Mycobacterium yongonense in pulmonary disease, Italy. Emerg Infect Dis 2013; 19:1902–1904 [View Article][PubMed]
    [Google Scholar]
  27. Hong SK, Kim EC. Possible misidentification of Mycobacterium yongonense . Emerg Infect Dis 2014; 20:1089–1090 [View Article][PubMed]
    [Google Scholar]
  28. Kim BJ, Kim BR, Lee SY, Seok SH, Kook YH et al. Whole-genome sequence of a novel species, Mycobacterium yongonense DSM 45126T. Genome Announc 2013; 1:e00604-13 [View Article][PubMed]
    [Google Scholar]
  29. Kim BJ, Hong SH, Kook YH, Kim BJ. Molecular evidence of lateral gene transfer in rpoB gene of Mycobacterium yongonense strains via multilocus sequence analysis. PLoS One 2013; 8:e51846 [View Article][PubMed]
    [Google Scholar]
  30. Kim BJ, Kim BR, Lee SY, Kim GN, Kook YH et al. Molecular taxonomic evidence for two distinct genotypes of Mycobacterium yongonense via genome-based phylogenetic analysis. PLoS One 2016; 11:e0152703 [View Article][PubMed]
    [Google Scholar]
  31. Tortoli E, Fedrizzi T, Meehan CJ, Trovato A, Grottola A et al. The new phylogeny of the genus Mycobacterium: the old and the news. Infect Genet Evol 2017; 56:19–25 [View Article][PubMed]
    [Google Scholar]
  32. Saini V, Raghuvanshi S, Khurana JP, Ahmed N, Hasnain SE et al. Massive gene acquisitions in Mycobacterium indicus pranii provide a perspective on mycobacterial evolution. Nucleic Acids Res 2012; 40:10832–10850 [View Article][PubMed]
    [Google Scholar]
  33. Alexander DC, Turenne CY. "Mycobacterium indicus pranii" is a strain of Mycobacterium intracellulare . mBIO 2015; 6:e00013-15 [View Article][PubMed]
    [Google Scholar]
  34. Cuttino JT, McCabe AM. Pure granulomatous nocardiosis: a new fungus disease distinguished by intracellular parasitism. Am J Clin Pathol 1949; 25:1–34
    [Google Scholar]
  35. Runyon EH. Pathogenic Mycobacteria. Adv Tuberc Res 1965; 14:235–287
    [Google Scholar]
  36. Meissner G, Schröder KH, Amadio GE, Anz W, Chaparas S et al. A co-operative numerical analysis of nonscoto- and nonphotochromogenic slowly growing mycobacteria. J Gen Microbiol 1974; 83:207–235 [View Article][PubMed]
    [Google Scholar]
  37. Saito H, Tomioka H, Sato K, Tasaka H, Tsukamura M et al. Identification and partial characterization of Mycobacterium avium and Mycobacterium intracellulare by using DNA probes. J Clin Microbiol 1989; 27:994–997[PubMed]
    [Google Scholar]
  38. Tortoli E, Nanetti A, Piersimoni C, Cichero P, Farina C et al. Performance assessment of new multiplex probe assay for identification of mycobacteria. J Clin Microbiol 2001; 39:1079–1084 [View Article][PubMed]
    [Google Scholar]
  39. Tortoli E, Mariottini A, Mazzarelli G. Evaluation of INNO-LiPA MYCOBACTERIA v2: improved reverse hybridization multiple DNA probe assay for mycobacterial identification. J Clin Microbiol 2003; 41:4418–4420 [View Article][PubMed]
    [Google Scholar]
  40. Parker CT, Tindall BJ, George M, Garrity GM. International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2008 Revision). Int J Syst Evol Microbiol 2015 doi:10.1099/ijsem.0.000778
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002767
Loading
/content/journal/ijsem/10.1099/ijsem.0.002767
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error