1887

Abstract

Seven strains of an unidentifiable species recovered from blood cultures, urine or cerebrospinal fluid over 26 years, closest to but differentiated from by 16S rRNA gene and partial gene sequencing, were studied. In November 2017, Atasayar described a blood culture isolate as sp. nov., which had >99 % similarity by 16S rRNA gene sequencing to the Canadian strains. In January 2018, Jani described sp. nov., recovered from the Godavari River, India, which also had >99 % similarity by 16S/ sequencing to the Canadian strains and In May 2018, Wei described recovered from hadopelagic water; this too had >99 % similarity by 16S rRNA gene sequencing to , and the Canadian strains. DSM 103494 and LMG 29598 were acquired and whole genome sequencing was performed (not previously done). Results were compared with genomes from (GenBank accession NQMQ01) and the Canadian isolates. We found that these ten genomes formed a single taxon when compared using digital DNA–DNAhybridization, average nucleotide identity using n and average amino acid identity criteria but exhibited some subtle biochemical and chemotaxonomic differences. Heuristically, we propose that and are later heterotypic synonyms of, and the Canadian isolates are identifiable as, . We provide an emended description of Atasayar . 2017; genomes ranged from 2.48 to 2.69 Mb ( DSM 103494, 2.62 Mb) with G+C content of 65.1–65.6 mol% (WGS), recovered from clinical and environmental sites.

Funding
This study was supported by the:
  • Kathy A. Bernard , Public Health Agency of Canada , (Award ABase)
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/content/journal/ijsem/10.1099/ijsem.0.004153
2020-04-24
2020-06-04
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References

  1. Atasayar E, Zimmermann O, Spröer C, Schumann P, Groß U. Corynebacterium gottingense sp. nov., isolated from a clinical patient. Int J Syst Evol Microbiol 2017; 67:4494–4499 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  2. Jani K, Khare K, Senik S, Karodi P, Vemuluri VR et al. Corynebacterium godavarianum sp. nov., isolated from the Godavari river, India. Int J Syst Evol Microbiol 2018; 68:241–247 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  3. Wei Y, Fang J, Xu Y, Zhao W, Cao J. Corynebacterium hadale sp. nov. isolated from hadopelagic water of the New Britain Trench. Int J Syst Evol Microbiol 2018; 68:1474–1478 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  4. Bernard KA, Shuttleworth L, Munro C, Forbes-Faulkner JC, Pitt D et al. Propionibacterium australiense sp. nov. derived from granulomatous bovine lesions. Anaerobe 2002; 8:41–47 [CrossRef]
    [Google Scholar]
  5. Khamis A, Raoult D, La Scola B. rpoB gene sequencing for identification of Corynebacterium species. J Clin Microbiol 2004; 42:3925–3931 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Bernard KA, Pacheco AL, Loomer C, Burdz T, Wiebe D et al. Corynebacterium lowii sp. nov. and Corynebacterium oculi sp. nov., derived from human clinical disease and an emended description of Corynebacterium mastitidis . Int J Syst Evol Microbiol 2016; 66:2803–2812 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Bernier A-M, Peters GA, Bernard K. Whole-Genome Sequences of Four Corynebacterium CDC Group F-1 Strains Isolated from Urine. Genome Announc 2017; 5:5:e01537-16 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  8. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  9. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Ciufo S, Kannan S, Sharma S, Badretdin A, Clark K et al. Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int J Syst Evol Microbiol 2018; 68:2386–2392 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–2105 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  12. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [CrossRef]
    [Google Scholar]
  13. Bernard KA, Bellefeuille M, Ewan EP. Cellular fatty acid composition as an adjunct to the identification of asporogenous, aerobic gram-positive rods. J Clin Microbiol 1991; 29:83–89 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  14. Bernard KA, Funke G et al. Genus Corynebacterium. In Whitman WB, Goodfellow M, Kämpfer P, Busse H, Trujillo ME et al. (editors) Bergey's Manual of Systematic Bacteriology. Volume 5: The Actinobacteria, 2nd ed. New York: Springer; 2012 pp 245–289
    [Google Scholar]
  15. Baek I, Kim M, Lee I, Na S-I, Goodfellow M et al. Phylogeny trumps chemotaxonomy: a case study involving Turicella otitidis . Front Microbiol 2018; 9:834 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  16. Tippelt A, Möllmann S, Albersmeier A, Jaenicke S, Rückert C et al. Mycolic acid biosynthesis genes in the genome sequence of Corynebacterium atypicum DSM 44849. Genome Announc 2014; 2:e00845-14 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. Bernard KA, Munro C, Wiebe D, Ongsansoy E. Characteristics of rare or recently described Corynebacterium species recovered from human clinical material in Canada. J Clin Microbiol 2002; 40:4375–4381 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  18. Bernard KA, Wiebe D, Burdz T, Reimer A, Ng B et al. Assignment of Brevibacterium stationis (ZoBell and Upham 1944) breed 1953 to the genus Corynebacterium, as Corynebacterium stationis comb. nov., and emended description of the genus Corynebacterium to include isolates that can alkalinize citrate. Int J Syst Evol Microbiol 2010; 60:874–879 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  19. Patel JB, Cockerill FRI, Eliopoulos GM, Jenkins SG et al. Clinical Laboratory Standards Institute Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Second Informational Supplement 36 Wayne, PA: CLSI document M100-S26. Wayne PA; 2016 p 249
    [Google Scholar]
  20. Clinical Laboratory Standards Institute M45-2A. Methods for Antimicrobial Dilution and Disk Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria; Approved guideline, Volume 30, Number 18, 2nd ed. Wayne, Pa: Clinical Laboratory Standards Institute; 2010
    [Google Scholar]
  21. Bernard K, Pacheco AL. In vitro activity of 22 antimicrobial agents against Corynebacterium and Microbacterium species referred to the Canadian national microbiology laboratory. Clin Microbiol Newsl 2015; 37:187–198 [CrossRef]
    [Google Scholar]
  22. Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of prokaryotes. Int J Syst Evol Microbiol 2019; 69:S1–S111 [CrossRef][PubMed][PubMed]
    [Google Scholar]
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