sp. nov., isolated from the respiratory tract of diseased Chacoan peccaries () Free

Abstract

Novel catalase-negative, Gram-stain-positive, beta-haemolytic, coccus-shaped organisms were isolated from Chacoan peccaries that died from respiratory disease. The initial API 20 Strep profiles suggested with acceptable identification scores, but the 16S rRNA gene similarity (1548 bp) to available sequences of streptococci was below 98 %. Next taxa of the genus , displaying highest similarities to the strains from this study, were NZ1587 (97.5 %), ATCC 29178 (97.5 %), HKU30 (97.4 %), DSM 6631 (97.1 %), CAIM 1838 (97.1 %), DSM 18513 (97.0 %), DSM 15616 (96.6 %), 707-05 (96.6 %), JCM 5709 (96.5 %) and NCTC 10999 (96.4 %). All other species had sequence similarities of below 96.4 %. A gene as well as whole genome-based core genome phylogeny of three representative strains and 145 available genomes confirmed the unique taxonomic position. Interstrain average nucleotide identity (ANI) and amino acid identity (AAI) values were high (ANI >96 %; AAI 100%), but for other streptococci clearly below the proposed species boundary of 95–96 % (ANI <75 %; AAI <83 %). Results were confirmed by genome-to-genome distance calculations. Pairwise digital DNA–DNA hybridization estimates were high (>90 %) between the novel strains, but well below the species boundary of 70 % for closely related type strains (23.5–19.7 %). Phenotypic properties as obtained from extended biochemical profiles and MALDI-TOF mass spectrometry supported the outstanding rank. Based on the presented molecular and physiological data of the six strains, we propose a novel taxon for which we suggest the name sp. nov. with the type strain 99-1/2017 (=DSM 110457=CCUG 74072) and five reference strains.

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2020-09-17
2024-03-28
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References

  1. Kryściak W, Pluskwa KK, Jurczak A, Kościelniak D. The pathogenicity of the Streptococcus genus. Eur J Clin Microbiol Infect Dis 2013; 32:1361–1376 [View Article][PubMed]
    [Google Scholar]
  2. Whiley RA, Hardie JM. Streptococcus Rosenbach 1884, 22AL. In Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J et al. (editors) Bergey’s Manual of Systematics of Archaea and Bacteria 2015 New York: Springer;
    [Google Scholar]
  3. Agnew W, Barnes AC. Streptococcus iniae: an aquatic pathogen of global veterinary significance and a challenging candidate for reliable vaccination. Vet Microbiol 2007; 122:1–15 [View Article][PubMed]
    [Google Scholar]
  4. de Vries SPW, Hadjirin NF, Lay EM, Zadoks RN, Peacock SJ et al. Streptococcus bovimastitidis sp. nov., isolated from a dairy cow with mastitis. Int J Syst Evol Microbiol 2018; 68:21–27 [View Article][PubMed]
    [Google Scholar]
  5. Morales-Covarrubias MS, Del Carmen Bolan-Mejía M, Vela Alonso AI, Fernandez-Garayzabal JF, Gomez-Gil B. Streptococcus penaeicida sp. nov., isolated from a diseased farmed Pacific white shrimp (Penaeus vannamei). Int J Syst Evol Microbiol 2018; 68:1490–1495 [View Article][PubMed]
    [Google Scholar]
  6. Mühldorfer K, Rau J, Fawzy A, Heydel C, Glaeser SP et al. Streptococcus castoreus, an uncommon group A Streptococcus in beavers. Antonie van Leeuwenhoek 2019; 112:1663–1673 [View Article][PubMed]
    [Google Scholar]
  7. Rurangirwa FR, Teitzel CA, Cui J, French DM, McDonough PL et al. Streptococcus didelphis sp. nov., a streptococcus with marked catalase activity isolated from opossums (Didelphis virginiana) with suppurative dermatitis and liver fibrosis. Int J Syst Evol Microbiol 2000; 50 Pt 2:759–765 [View Article][PubMed]
    [Google Scholar]
  8. Taurisano ND, Butler BP, Stone D, Hariharan H, Fields PJ et al. Streptococcus phocae in marine mammals of northeastern Pacific and Arctic Canada: a retrospective analysis of 85 postmortem investigations. J Wildl Dis 2018; 54:101–111 [View Article][PubMed]
    [Google Scholar]
  9. Bartlett G, Smith W, Dominik C, Batac F, Dodd E et al. Prevalence, pathology, and risk factors associated with Streptococcus phocae infection in southern sea otters (Enhydra lutris nereis), 2004-10. J Wildl Dis 2016; 52:1–9 [View Article][PubMed]
    [Google Scholar]
  10. Eisenberg T, Rau J, Westerhüs U, Knauf-Witzens T, Fawzy A et al. Streptococcus agalactiae in elephants - A comparative study with isolates from human and zoo animal and livestock origin. Vet Microbiol 2017; 204:141–150 [View Article][PubMed]
    [Google Scholar]
  11. Delannoy CMJ, Crumlish M, Fontaine MC, Pollock J, Foster G et al. Human Streptococcus agalactiae strains in aquatic mammals and fish. BMC Microbiol 2013; 13:41 [View Article][PubMed]
    [Google Scholar]
  12. Höner OP, Wachter B, Speck S, Wibbelt G, Ludwig A et al. Severe Streptococcus infection in spotted hyenas in the Ngorongoro crater, Tanzania. Vet Microbiol 2006; 115:223–228 [View Article][PubMed]
    [Google Scholar]
  13. Mioni MdeSR, Castro FFC, Moreno LZ, Apolinário CM, Belaz LD et al. Septicemia due to Streptococcus dysgalactiae subspecies dysgalactiae in vampire bats (Desmodus rotundus). Sci Rep 2018; 8:9772 [View Article][PubMed]
    [Google Scholar]
  14. Pinho MD, Foster G, Pomba C, Machado MP, Baily JL et al. Streptococcus canis are a single population infecting multiple animal hosts despite the diversity of the universally present M-like protein SCM. Front Microbiol 2019; 10:631 [View Article][PubMed]
    [Google Scholar]
  15. Munch-Petersen E, Christie R. On the effect of the interaction of staphylococcal β toxin and group-B streptococcal substance on red blood corpuscles and its use as a test for the identification of Streptococcus agalactiae. J Pathol Bacteriol 1947; 59:367–371 [View Article]
    [Google Scholar]
  16. Facklam R, Elliott JA. Identification, classification, and clinical relevance of catalase-negative, gram-positive cocci, excluding the streptococci and enterococci. Clin Microbiol Rev 1995; 8:479–495 [View Article][PubMed]
    [Google Scholar]
  17. Rau J, Eisenberg T, Männig A, Wind C, Lasch R et al. MALDI-UP – An internet platform for the exchange of mass spectra - User guide for https://maldi-up.ua-bw.de/. Aspects of food control and animal health 01/2016; https://ejournal.cvuas.de/docs/cvuas_ejournal_201601.pdf.
  18. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  19. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article][PubMed]
    [Google Scholar]
  20. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  21. Roehr JT, Dieterich C, Reinert K. Flexbar 3.0 - SIMD and multicore parallelization. Bioinformatics 2017; 33:2941–2942 [View Article][PubMed]
    [Google Scholar]
  22. Nikolenko SI, Korobeynikov AI, Alekseyev MA. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics 2013; 14 Suppl 1:S7 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C et al. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 2016; 44:W22–W28 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  27. 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 [View Article][PubMed]
    [Google Scholar]
  28. Lau SKP, Curreem SOT, Lin CCN, Fung AMY, Yuen K-Y et al. Streptococcus hongkongensis sp. nov., isolated from a patient with an infected puncture wound and from a marine flatfish. Int J Syst Evol Microbiol 2013; 63:2570–2576 [View Article][PubMed]
    [Google Scholar]
  29. Bekal S, Gaudreau C, Laurence RA, Simoneau E, Raynal L. Streptococcus pseudoporcinus sp. nov., a novel species isolated from the genitourinary tract of women. J Clin Microbiol 2006; 44:2584–2586 [View Article][PubMed]
    [Google Scholar]
  30. Fernández E, Blume V, Garrido P, Collins MD, Mateos A et al. Streptococcus equi subsp. ruminatorum subsp. nov., isolated from mastitis in small ruminants. Int J Syst Evol Microbiol 2004; 54:2291–2296 [View Article][PubMed]
    [Google Scholar]
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