1887

Abstract

The species within the Complex (MTBC) have undergone numerous taxonomic and nomenclatural changes, leaving the true structure of the MTBC in doubt. We used next-generation sequencing (NGS), digital DNA–DNA hybridization (dDDH), and average nucleotide identity (ANI) to investigate the relationship between these species. The type strains of , , , and were sequenced via NGS. Pairwise dDDH and ANI comparisons between these, previously sequenced MTBC type strain genomes (including ‘’, ‘’ and ‘’) and H37Rv were performed. Further, all available genome sequences in GenBank for species in or putatively in the MTBC were compared to H37Rv. Pairwise results indicated that all of the type strains of the species are extremely closely related to each other (dDDH: 91.2–99.2 %, ANI: 99.21–99.92 %), greatly exceeding the respective species delineation thresholds, thus indicating that they belong to the same species. Results from the GenBank genomes indicate that all the strains examined are within the circumscription of H37Rv (dDDH: 83.5–100 %). We, therefore, formally propose a union of the species of the MTBC as , , , and are reclassified as later heterotypic synonyms of . ‘’, ‘’, and ‘’ are classified as strains of the species . We further recommend use of the infrasubspecific term ‘variant’ (‘var.’) and infrasubspecific designations that generally retain the historical nomenclature associated with the groups or otherwise convey such characteristics, e.g. var. bovis.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002507
2018-01-01
2020-01-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/1/324.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002507&mimeType=html&fmt=ahah

References

  1. Magee JG, Ward AC. Genus I. Mycobacterium Lehmann and Neumann 1896, 363AL. In Goodfellow M, Kampfer P, Busse HJ, Trujillo ME, Suzuki K. et al. (editors) Bergey's Manual of Systematic Bateriology, 2nd ed.vol. 5 The Actinobacteria, Part A New York: Springer; 2012; pp.312–375
    [Google Scholar]
  2. Parte AC. LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014;42:D613–D616 [CrossRef][PubMed]
    [Google Scholar]
  3. Aranaz A, Liébana E, Gómez-Mampaso E, Galán JC, Cousins D et al. Mycobacterium tuberculosis subsp. caprae subsp. nov.: a taxonomic study of a new member of the Mycobacterium tuberculosis complex isolated from goats in Spain. Int J Syst Bacteriol 1999;49:1263–1273 [CrossRef][PubMed]
    [Google Scholar]
  4. Niemann S, Richter E, Rüsch-Gerdes S. Biochemical and genetic evidence for the transfer of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to the species Mycobacterium bovis Karlson and Lessel 1970 (Approved Lists 1980) as Mycobacterium bovis subsp. caprae comb. nov. Int J Syst Evol Microbiol 2002;52:433–436 [CrossRef][PubMed]
    [Google Scholar]
  5. Aranaz A, Cousins D, Mateos A, Domínguez L. Elevation of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to species rank as Mycobacterium caprae comb. nov., sp. nov. Int J Syst Evol Microbiol 2003;53:1785–1789 [CrossRef][PubMed]
    [Google Scholar]
  6. Pfyffer GE, Auckenthaler R, van Embden JD, van Soolingen D. Mycobacterium canettii, the smooth variant of M. tuberculosis, isolated from a Swiss patient exposed in Africa. Emerg Infect Dis 1998;4:631–634 [CrossRef][PubMed]
    [Google Scholar]
  7. Alexander KA, Laver PN, Michel AL, Williams M, van Helden PD et al. Novel Mycobacterium tuberculosis complex pathogen, M. mungi. Emerg Infect Dis 2010;16:1296–1299 [CrossRef][PubMed]
    [Google Scholar]
  8. van Ingen J, Rahim Z, Mulder A, Boeree MJ, Simeone R et al. Characterization of Mycobacterium orygis as M. tuberculosis complex subspecies. Emerg Infect Dis 2012;18:653–655 [CrossRef][PubMed]
    [Google Scholar]
  9. Koch R. Die äetiologie der Tuberkulose. Berl klin Wchschr 1882;19:221–230
    [Google Scholar]
  10. Reed G. Genus Mycobacterium (species affecting warm-blooded animals except those causing leprosy). In Breed RS, Murray EGD, Smith NR. (editors) Bergey's Manual of Determinative Bacteriology, 7th ed. Baltimore: Williams & Wilkins; 1957; pp.703–704
    [Google Scholar]
  11. Castets M, Rist N, Boisvert H. La variété africaine du bacille tuberculeux humain. Médecine d'Afrique Noire 1969;16:321–322
    [Google Scholar]
  12. Karlson AG, Lessel EF. Mycobacterium bovis nom. nov. Int J Syst Bacteriol 1970;20:273–282 [CrossRef]
    [Google Scholar]
  13. Rodriguez-Campos S, Smith NH, Boniotti MB, Aranaz A. Overview and phylogeny of Mycobacterium tuberculosis complex organisms: implications for diagnostics and legislation of bovine tuberculosis. Res Vet Sci 2014;97:S5–S19 [CrossRef][PubMed]
    [Google Scholar]
  14. Ei PW, Aung WW, Lee JS, Choi GE, Chang CL. Molecular strain typing of Mycobacterium tuberculosis: a review of frequently used methods. J Korean Med Sci 2016;31:1673–1683 [CrossRef][PubMed]
    [Google Scholar]
  15. Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C et al. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci USA 2002;99:3684–3689 [CrossRef][PubMed]
    [Google Scholar]
  16. Shabbeer A, Cowan LS, Ozcaglar C, Rastogi N, Vandenberg SL et al. TB-lineage: an online tool for classification and analysis of strains of Mycobacterium tuberculosis complex. Infect Genet Evol 2012;12:789–797 [CrossRef][PubMed]
    [Google Scholar]
  17. Coscolla M, Gagneux S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol 2014;26:431–444 [CrossRef][PubMed]
    [Google Scholar]
  18. Cohan FM, Perry EB. A systematics for discovering the fundamental units of bacterial diversity. Curr Biol 2007;17:R373–R386 [CrossRef][PubMed]
    [Google Scholar]
  19. Smith NH, Kremer K, Inwald J, Dale J, Driscoll JR et al. Ecotypes of the Mycobacterium tuberculosis complex. J Theor Biol 2006;239:220–225 [CrossRef][PubMed]
    [Google Scholar]
  20. Wayne LG. Microbiology of tubercle bacilli. Am Rev Respir Dis 1982;125:31–41 [CrossRef][PubMed]
    [Google Scholar]
  21. 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 [CrossRef][PubMed]
    [Google Scholar]
  22. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [Google Scholar]
  23. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010;2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014;9:2 [CrossRef][PubMed]
    [Google Scholar]
  26. Liu Y, Lai Q, Göker M, Meier-Kolthoff JP, Wang M et al. Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 2015;5:14082 [CrossRef][PubMed]
    [Google Scholar]
  27. Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP et al. Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. MBio 2014;5:e02136 [CrossRef][PubMed]
    [Google Scholar]
  28. Chosewood LC, Wilson DE.Centers for Disease Control and Prevention (U.S.)National Institutes of Health (U.S.) Biosafety in Microbiological and Biomedical Laboratories (BMBL), 5th ed. Washington, DC: U.S. Dept. of Health and Human Services, Public Health Service, Centers for Disease Control and Prevention, National Institutes of Health; 2009; pp.xxii 415
    [Google Scholar]
  29. Lee I, Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  30. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  31. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015;32:2798–2800 [CrossRef][PubMed]
    [Google Scholar]
  32. Xia E, Teo YY, Ong RT. SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Genome Med 2016;8:19 [CrossRef][PubMed]
    [Google Scholar]
  33. Demay C, Liens B, Burguière T, Hill V, Couvin D et al. SITVITWEB-a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology. Infect Genet Evol 2012;12:755–766 [CrossRef][PubMed]
    [Google Scholar]
  34. Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2015; [CrossRef][PubMed]
    [Google Scholar]
  35. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015;38:209–216 [CrossRef][PubMed]
    [Google Scholar]
  36. Skerman VBD, Sneath PHA, Mcgowan V. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980;30:225–420 [CrossRef]
    [Google Scholar]
  37. Le Minor L, Popoff MY. Designation of Salmonella enterica sp. nov., nom. rev., as the type and only species of the genus Salmonella: request for an opinion. Int J Syst Bacteriol 1987;37:465–468 [CrossRef]
    [Google Scholar]
  38. Euzéby JP. Revised Salmonella nomenclature: designation of Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 sp. nov., nom. rev. as the neotype species of the genus Salmonella Lignieres 1900 (Approved Lists 1980), rejection of the name Salmonella choleraesuis (Smith 1894) Weldin 1927 (Approved Lists 1980), and conservation of the name Salmonella typhi (Schroeter 1886) Warren and Scott 1930 (Approved Lists 1980). Request for an opinion. Int J Syst Bacteriol 1999;49:927–930 [CrossRef][PubMed]
    [Google Scholar]
  39. Judicial Commission of the International Committee on Systematics of Prokaryotes The type species of the genus Salmonella Lignieres 1900 is Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987, with the type strain LT2T, and conservation of the epithet enterica in Salmonella enterica over all earlier epithets that may be applied to this species. Opinion 80. Int J Syst Evol Microbiol 2005;55:519–520 [CrossRef][PubMed]
    [Google Scholar]
  40. IATA Dangerous Goods Regulations, 3.6.2.2.2.1 Category A Section 3.6.2.2 Classification of infectious substances 2015;https://www.iata.org/whatwedo/cargo/dgr/Documents/infectious-substance-classification-DGR56-en.pdf
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002507
Loading
/content/journal/ijsem/10.1099/ijsem.0.002507
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited articles

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