1887

Abstract

A polyphasic study was undertaken to determine the taxonomic status of a rapidly growing, scotochromogenic organism that had been received as Mycobacterium vaccae NCTC 11659. The organism was found to have chemotaxonomic and cultural properties in accord with its assignment to the genus Mycobacterium and was distinguished from the type strain of Mycobacterium vaccae and from other closely related reference strains on the basis of concatenated sequences of 16S rRNA, gyrB, hsp65, recA and rpoB genes. It was also distinguished from M. vaccae strain DSM 43292 and from the type strain of Mycobacterium obuense , its nearest phylogenetic neighbour, on the basis of chemotaxonomic and phenotypic data and digital DNA –DNA relatedness values of 22.7 and 68.3 %, respectively. These datasets not only indicate that strain NCTC 11659 had been misclassified as M. vaccae but that it merits recognition as representing a novel species of the genus Mycobacterium . It is proposed that the organism be classified as Mycobacteriumkyogaense sp. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003039
2018-10-09
2024-03-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/12/3726.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003039&mimeType=html&fmt=ahah

References

  1. Lehmann KB, Neumann R. Atlas und Grundriss der Bakteriologie und Lehrbuch der speziellen bakteriologischen Diagnostik. München 1869
    [Google Scholar]
  2. Chester FD. Report of mycologist: bacteriological work. Del Agric Exp Sta Bull 1897; 9:38–145
    [Google Scholar]
  3. Goodfellow M, Jones AL. Order V. Corynebacteriales ord. nov. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 5 The Actinobacteria New York: Springer; 2012 pp. 232–243
    [Google Scholar]
  4. Wayne LG, Kubica GP. The mycobacteria. In Sneath PHA, Mair NS, Sharpe ME, Holt JG. (editors) Bergey's Manual of Systematic Bacteriology vol. 2 Baltimore: Williams & Wilkins; 1986 pp. 1435–1457
    [Google Scholar]
  5. Adékambi T, Colson P, Drancourt M. rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J Clin Microbiol 2003; 41:5699–5708 [View Article][PubMed]
    [Google Scholar]
  6. McNabb A, Eisler D, Adie K, Amos M, Rodrigues M et al. 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 2004; 42:3000–3011 [View Article][PubMed]
    [Google Scholar]
  7. Ramaprasad EV, Rizvi A, Banerjee S, Sasikala C, Ramana CV. Mycobacterium oryzae sp. nov., a scotochromogenic, rapidly growing species is able to infect human macrophage cell line. Int J Syst Evol Microbiol 2016; 66:4530–4536 [View Article][PubMed]
    [Google Scholar]
  8. Nouioui I, Carro L, Teramoto K, Igual JM, Jando M et al. Mycobacterium eburneum sp. nov., a non-chromogenic, fast-growing strain isolated from sputum. Int J Syst Evol Microbiol 2017; 67:3174–3181 [View Article][PubMed]
    [Google Scholar]
  9. Teramoto K, Suga M, Sato T, Wada T, Yamamoto A et al. Characterization of mycolic acids in total fatty acid methyl ester fractions from Mycobacterium species by high resolution MALDI-TOFMS. Mass Spectrom 2015; 4:A0035 [View Article][PubMed]
    [Google Scholar]
  10. Tran PM, Dahl JL. Mycobacterium sarraceniae sp. nov. and Mycobacterium helvum sp. nov., isolated from the pitcher plant Sarracenia purpurea. Int J Syst Evol Microbiol 2016; 66:4480–4485 [View Article][PubMed]
    [Google Scholar]
  11. Shahraki AH, Trovato A, Mirsaeidi M, Borroni E, Heidarieh P et al. Mycobacterium persicum sp. nov., a novel species closely related to Mycobacterium kansasii and Mycobacterium gastri. Int J Syst Evol Microbiol 2017; 67:1766–1770 [View Article][PubMed]
    [Google Scholar]
  12. Stanford JL, Paul RC. A priliminary report on some studies of environmental mycobacteria from Uganda. Ann Soc Belge Med Trop 1973; 53:389–393
    [Google Scholar]
  13. Lorian V. Differentiation of Mycobacterium tuberculosis and Runyon Group 3 "V" strains on direct cord-reading agar. Am Rev Respir Dis 1968; 97:1133–1135 [View Article][PubMed]
    [Google Scholar]
  14. Adékambi T, Berger P, Raoult D, Drancourt M. rpoB gene sequence-based characterization of emerging non-tuberculous mycobacteria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov. and Mycobacterium aubagnense sp. nov. Int J Syst Evol Microbiol 2006; 56:133–143 [View Article][PubMed]
    [Google Scholar]
  15. Tsukamura M, van der Meulen HJ, Grabow WOK. Numerical taxonomy of rapidly growing, scotochromogenic mycobacteria of the Mycobacterium parafortuitum complex: Mycobacterium austroafricanum sp. nov. and Mycobacterium diernhoferi sp. nov., nom. rev. Int J Syst Bacteriol 1983; 33:460–469 [View Article]
    [Google Scholar]
  16. Häggblom MM, Nohynek LJ, Palleroni NJ, Kronqvist K, Nurmiaho-Lassila EL et al. Transfer of polychlorophenol-degrading Rhodococcus chlorophenolicus (Apajalahti et al. 1986) to the genus Mycobacterium as Mycobacterium chlorophenolicum comb. nov. Int J Syst Bacteriol 1994; 44:854–493 [View Article][PubMed]
    [Google Scholar]
  17. Tsukamura M, Mizuno S, Tsukamura S. Numerical analysis of rapidly growing, scotochromogenic mycobacteria, including Mycobacterium obuense sp. nov., nom. rev., Mycobacterium rhodesiae sp. nov., nom. rev., Mycobacterium aichiense sp. nov., nom. rev., Mycobacterium chubuense sp. nov., nom. rev., and Mycobacterium tokaiense sp. nov., nom. rev. Int J Syst Bacteriol 1981; 31:263–275 [View Article]
    [Google Scholar]
  18. Derz K, Klinner U, Schuphan I, Stackebrandt E, Kroppenstedt RM. Mycobacterium pyrenivorans sp. nov., a novel polycyclic-aromatic-hydrocarbon-degrading species. Int J Syst Evol Microbiol 2004; 54:2313–2317 [View Article][PubMed]
    [Google Scholar]
  19. Trujillo ME, Velázquez E, Kroppenstedt RM, Schumann P, Rivas R et al. Mycobacterium psychrotolerans sp. nov., isolated from pond water near a uranium mine. Int J Syst Evol Microbiol 2004; 54:1459–1463 [View Article][PubMed]
    [Google Scholar]
  20. Hennessee CT, Seo JS, Alvarez AM, Li QX. Polycyclic aromatic hydrocarbon-degrading species isolated from Hawaiian soils: Mycobacterium crocinum sp. nov., Mycobacterium pallens sp. nov., Mycobacterium rutilum sp. nov., Mycobacterium rufum sp. nov. and Mycobacterium aromaticivorans sp. nov. Int J Syst Evol Microbiol 2009; 59:378–387 [View Article][PubMed]
    [Google Scholar]
  21. Khan AA, Kim SJ, Paine DD, Cerniglia CE. Classification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Mycobacterium sp. strain PYR-1, as Mycobacterium vanbaalenii sp. nov. Int J Syst Evol Microbiol 2002; 52:1997–2002 [View Article][PubMed]
    [Google Scholar]
  22. Bönicke R, Juhasz SE. Beschreibung der neuen Species Mycobacterium vaccae n. sp. Zentralbl Bakteriol Parasitenkde Infektionskr Hyg Abt Orig 1964; 192:133–135
    [Google Scholar]
  23. Runyon EH, Karlson AG, Kubica GP, Wayne LG. Mycobacterium Washington, DC: American Society for Microbiology; 1980
    [Google Scholar]
  24. Jensen KA. Reinzuechtung und Typenbestimmung von Tuberkelbazillenstämmen. Zentralbl Bakteriol I Orig 1932; 125:222–239
    [Google Scholar]
  25. MacFaddin JF. Media for Isolation–Cultivation–Identification–Maintenance of Medical Bacteria Baltimore: Williams & Wilkins; 1985
    [Google Scholar]
  26. Magee JG, Ward AC. Genus I. Mycobacterium. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI et al. (editors) Bergey's Manual of Systematic Bacteriology, 2nd ed. vol. 5 The Actinobacteria New York: Springer; 2012 pp. 312–375
    [Google Scholar]
  27. Amaro A, Duarte E, Amado A, Ferronha H, Botelho A. Comparison of three DNA extraction methods for Mycobacterium bovis, Mycobacterium tuberculosis and Mycobacterium avium subsp. avium. Lett Appl Microbiol 2008; 47:8–11 [View Article][PubMed]
    [Google Scholar]
  28. Kim SB, Goodfellow M. Streptomyces thermospinisporus sp. nov., a moderately thermophilic carboxydotrophic streptomycete isolated from soil. Int J Syst Evol Microbiol 2002; 52:1225–1228 [View Article][PubMed]
    [Google Scholar]
  29. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  30. 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]
  31. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
    [Google Scholar]
  32. 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 [View Article][PubMed]
    [Google Scholar]
  33. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  34. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  35. Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010; 17:337–354 [View Article][PubMed]
    [Google Scholar]
  36. Goloboff PA, Farris JS, Nixon KC. TNT, a free program for phylogenetic analysis. Cladistics 2008; 24:774–786 [View Article]
    [Google Scholar]
  37. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 Sunderland: Sinauer Associates; 2002
    [Google Scholar]
  38. Sangal V, Jones AL, Goodfellow M, Hoskisson PA, Kämpfer P et al. Genomic analyses confirm close relatedness between Rhodococcus defluvii and Rhodococcus equi (Rhodococcus hoagii). Arch Microbiol 2015; 197:113–116 [View Article][PubMed]
    [Google Scholar]
  39. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  40. 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]
  41. 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 [View Article]
    [Google Scholar]
  42. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article][PubMed]
    [Google Scholar]
  43. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
    [Google Scholar]
  44. Collins MD. Analysis of isoprenoid quinones. Meth Microbiol 1985; 18:329–366
    [Google Scholar]
  45. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 173–199
    [Google Scholar]
  46. Minnikin DE, Goodfellow M. Lipid composition in the classification and identification of nocardiae and related taxa. In Goodfellow M, Brownell GH, Serrano JA. (editors) The Biology of the Nocardiae London: Academic Press; 1976 pp. 160–219
    [Google Scholar]
  47. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  48. Lechavalier MP, Lechevalier HA. Composition of whole-cell hydrolysates as a criterion in the classification of aerobic actinomycetes. In Prauser H. (editor) The Actinomycetales Jena: Gustav Fischer Verlag; 1970 pp. 311–316
    [Google Scholar]
  49. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586[PubMed]
    [Google Scholar]
  50. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  51. Sasser MJ. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101, Microbial ID. Newark, USA: Del Inc; 1990
    [Google Scholar]
  52. Lechevalier MP, de Bievre C, Lechevalier H. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5:249–260 [View Article]
    [Google Scholar]
  53. Trujillo ME, Velázquez E, Kroppenstedt RM, Schumann P, Rivas R et al. Mycobacterium psychrotolerans sp. nov., isolated from pond water near a uranium mine. Int J Syst Evol Microbiol 2004; 54:1459–1463 [View Article][PubMed]
    [Google Scholar]
  54. Vaas LA, Sikorski J, Hofner B, Fiebig A, Buddruhs N et al. opm: an R package for analysing OmniLog(R) phenotype microarray data. Bioinformatics 2013; 29:1823–1824 [View Article][PubMed]
    [Google Scholar]
  55. Tomioka H, Saito H, Sato K, Dawson DJ. Arylsulfatase activity for differentiating Mycobacterium avium and Mycobacterium intracellulare. J Clin Microbiol 1990; 28:2104–2106[PubMed]
    [Google Scholar]
  56. Palomino JC, Leão SC, Ritacco V. Tuberculosis 2007 - From basic science to patient care; 2007 www.Tuberculosistextbook.com
  57. Sequeira de Latini MD, Barrera L. Manual para el Diagnóstico Bacteriológico de la Tuberculosis: Normas y Guía Técnica. Parte I Baciloscopía. Organización Panamericana de la Salud 2008
    [Google Scholar]
  58. Kent PT, Kubica GP. Public Health Mycobacteriology A Guide for the Level III Laboratory Atlanta, GA: Centers for Disease control and Prevention; 1985
    [Google Scholar]
  59. Kilburn JO, Silcox VA, Kubica GP. Differential identification of mycobacteria V. The tellurite reduction test. Am Rev Resp Dis 1969; 99:94–100
    [Google Scholar]
  60. Ribón W. Chemical isolation and identification of mycobacteria. In Jimenez-Lopez JC. (editor) Biochemical testing: InTech 2012
    [Google Scholar]
  61. Gupta RS, Lo B, Son J. Phylogenomics and comparative genomic studies robustly support division of the genus Mycobacterium into an emended genus Mycobacterium and four novel genera. Front Microbiol 2018; 9:67 [View Article][PubMed]
    [Google Scholar]
  62. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003039
Loading
/content/journal/ijsem/10.1099/ijsem.0.003039
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