1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 10

sp. nov., sp. nov., sp. nov., sp. nov., sp. nov. and sp. nov., isolated from humans and animals Open Access

Abstract

Thirty-three strains previously characterized by the French National Reference Laboratory (YNRL) and isolated from humans and animals were suspected to belong to six novel species by a recently described core genome multilocus sequence typing scheme. These strains and five additional strains from the YNRL were characterized using a polyphasic taxonomic approach including a phylogenetic analysis based on 500 core genes, determination of average nucleotide identity (ANI), determination of DNA G+C content and identification of phenotypic features. Phylogenetic analysis confirmed that the 38 studied strains formed six well-demarcated clades. ANI values between these clades and their closest relatives were <94.7 % and ANI values within each putative novel species were >97.5 %. Distinctive biochemical characteristics were identified in five out of the six novel species. All of these data demonstrated that the 38 strains belong to six novel species of the genus : sp. nov., type strain IP42281 (=CIP 111845=DSM 110725); sp. nov., type strain IP37424 (=CIP 111847=DSM 110727); sp. nov., type strain IP38850 (=CIP 111848=DSM 110726); sp. nov., type strain IP38594 (=CIP 111844=DSM 110738); sp. nov., type strain IP34646 (=CIP 111842=DSM 110736); and sp. nov., type strain IP35638 (=CIP 111843=DSM 110739).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): cgMLST , species , Yersinia and Yersiniaceae
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004417
2020-08-27
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/10/5363.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004417&mimeType=html&fmt=ahah

References

  1. Adeolu M, Alnajar S, Naushad S, S Gupta R. Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575–5599 [View Article][PubMed]
     [Google Scholar]
  2. Demeure C, Dussurget O, Fiol GM, Le Guern A-S, Savin C et al. Yersinia pestis and plague: an updated view on evolution, virulence determinants, immune subversion, vaccination and diagnostics. Microbes Infect 2019; 21:202–212 [View Article][PubMed]
     [Google Scholar]
  3. Carniel E, Autenrieth I, Cornelis G, Fukushima H, Guinet F et al. Y. enterocolitica and Y. pseudotuberculosis . In Dworkin MM, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E et al. (editors) The Prokaryotes, a Handbook on the Biology of Bacteria 6, 3rd ed. Springer; 2006 pp 270–398
     [Google Scholar]
  4. Savin C, Martin L, Bouchier C, Filali S, Chenau J et al. The Yersinia pseudotuberculosis complex: characterization and delineation of a new species, Yersinia wautersii . Int J Med Microbiol 2014; 304:452–463 [View Article][PubMed]
     [Google Scholar]
  5. Kumar G, Menanteau-Ledouble S, Saleh M, El-Matbouli M. Yersinia ruckeri, the causative agent of enteric redmouth disease in fish. Vet Res 2015; 46:103 [View Article][PubMed]
     [Google Scholar]
  6. Hurst MRH, Beattie AK, Jones SA, Hsu P-C, Calder J et al. Temperature-dependent Galleria mellonella mortality as a result of Yersinia entomophaga infection. Appl Environ Microbiol 2015; 81:6404–6414 [View Article][PubMed]
     [Google Scholar]
  7. Bercovier H, Steigerwalt AG, Guiyoule A, Huntley-Carter G, Brenner DJ. Yersinia aldovae (formerly Yersinia enterocolitica-like group X2): a new species of Enterobacteriaceae isolated from aquatic ecosystems. Int J Syst Bacteriol 1984; 34:166–172 [View Article]
     [Google Scholar]
  8. Sprague LD, Neubauer H. Yersinia aleksiciae sp. nov. Int J Syst Evol Microbiol 2005; 55:831–835 [View Article][PubMed]
     [Google Scholar]
  9. Wauters G, Janssens M, Steigerwalt AG, Brenner DJ. Yersinia mollaretii sp. nov. and Yersinia bercovieri sp. nov., formerly called Yersinia enterocolitica biogroups 3A and 3B. Int J Syst Bacteriol 1988; 38:424–429 [View Article]
     [Google Scholar]
  10. Ursing J, Don Brennert J, Bercovier H, Richard Fanning G, Steigerwalt AG et al. Yersinia frederiksenii: a new species of Enterobacteriaceae composed of rhamnose-positive strains (formerly called atypical Yersinia enterocolitica or Yersinia enterocolitica-like). Curr Microbiol 1980; 4:213–217 [View Article]
     [Google Scholar]
  11. Brenner DJ, Bercovier H, Ursing J, Alonso JM, Steigerwalt AG et al. Yersinia intermedia: a new species of Enterobacteriaceae composed of rhamnose-positive, melibiose-positive, raffinose-positive strains (formerly called Yersinia enterocolitica or Yersinia enterocolitica-like). Curr Microbiol 1980; 4:207–212 [View Article]
     [Google Scholar]
  12. Bercovier H, Ursing J, Don Brenner J, Steigerwalt AG, Fanning GR et al. Yersinia kristensenii: a new species of Enterobacteriaceae composed of sucrose-negative strains (formerly called atypical Yersinia enterocolitica or Yersinia enterocolitica-like). Curr Microbiol 1980; 4:219–224 [View Article]
     [Google Scholar]
  13. Merhej V, Adékambi T, Pagnier I, Raoult D, Drancourt M. Yersinia massiliensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2008; 58:779–784 [View Article][PubMed]
     [Google Scholar]
  14. Murros-Kontiainen A, Fredriksson-Ahomaa M, Korkeala H, Johansson P, Rahkila R et al. Yersinia nurmii sp. nov. Int J Syst Evol Microbiol 2011; 61:2368–2372 [View Article][PubMed]
     [Google Scholar]
  15. Murros-Kontiainen A, Johansson P, Niskanen T, Fredriksson-Ahomaa M, Korkeala H et al. Yersinia pekkanenii sp. nov. Int J Syst Evol Microbiol 2011; 61:2363–2367 [View Article][PubMed]
     [Google Scholar]
  16. Aleksic S, Steigerwalt AG, Bockemuhl J, Huntleycarter GP, Brenner DJ. Yersinia-rohdei sp. nov., isolated from human and dog feces and Surface-Water. Int J Syst Bacteriol 1987; 37:327–332
     [Google Scholar]
  17. Sprague LD, Scholz HC, Amann S, Busse H-J, Neubauer H. Yersinia similis sp. nov. Int J Syst Evol Microbiol 2008; 58:952–958 [View Article][PubMed]
     [Google Scholar]
  18. Nguyen SV, Muthappa DM, Hurley D, Donoghue O, McCabe E et al. Yersinia hibernica sp. nov., isolated from pig-production environments. Int J Syst Evol Microbiol 2019; 69:2023–2027 [View Article][PubMed]
     [Google Scholar]
  19. Nguyen SV, Greig DR, Hurley D, Donoghue O, Cao Y et al. Yersinia canariae sp. nov., isolated from a human yersiniosis case. Int J Syst Evol Microbiol 2020; 70:2382–2387 [View Article][PubMed]
     [Google Scholar]
  20. Savin C, Criscuolo A, Guglielmini J, Le Guern A-S, Carniel E et al. Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization. Microb Genom 2019; 5: [View Article][PubMed]
     [Google Scholar]
  21. 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]
  22. Roosaare M, Puustusmaa M, Möls M, Vaher M, Remm M. PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads. PeerJ 2018; 6:e4588 [View Article][PubMed]
     [Google Scholar]
  23. 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]
  24. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article][PubMed]
     [Google Scholar]
  25. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 2005; 102:2567–2572 [View Article][PubMed]
     [Google Scholar]
  26. Janvier M, Grimont PA. The genus Methylophaga, a new line of descent within phylogenetic branch gamma of Proteobacteria. Res Microbiol 1995; 146:543–550 [View Article][PubMed]
     [Google Scholar]
  27. Lee WH. Two plating media modified with tween 80 for isolating Yersinia enterocolitica . Appl Environ Microbiol 1977; 33:215–216 [View Article][PubMed]
     [Google Scholar]
  28. Kandolo K, Wauters G. Pyrazinamidase activity in Yersinia enterocolitica and related organisms. J Clin Microbiol 1985; 21:980–982 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004417
Loading
Yersinia artesiana sp. nov., Yersinia proxima sp. nov., Yersinia alsatica sp. nov., Yersina vastinensis sp. nov., Yersinia thracica sp. nov. and Yersinia occitanica sp. nov., isolated from humans and animals
Int J Syst Evol Microbiol 70, 5363 (2020); https://doi.org/10.1099/ijsem.0.004417
/content/journal/ijsem/10.1099/ijsem.0.004417
/content/journal/ijsem/10.1099/ijsem.0.004417
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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