1887

Abstract

A description of an outbreak of necrotizing enterocolitis among neonates, linked to the putative novel species Clostridium neonatale and assignable to the genus Clostridium , was previously reported in brief but that name had never been validly published (Alfa et al. Clin Inf Dis 2002;35:S101–S105). Features of this taxon group and its phylogenetic position with respect to contemporary species in the genus Clostridium were recently reviewed and still found to be unique. Therefore, we provide here a description based on biochemical, chemotaxonomic and antimicrobial susceptibility testing (AST), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, 16S rRNA gene sequencing as well as information obtained by whole genome sequencing (WGS) for strains 99A005 and 99A006. Those two C. neonatale strains were essentially identical to each other, with genome sizes of 4 658 596–4 705 520 bp and G+C content of 28.4–28.5 mol% (WGS). AST inferred susceptibility to 14 antibiotics. MALDI-TOF spectra were unique and could potentially be used for identification. The type strain is (NML) LCDC 99A005 [=ATCC BAA-265 =CCUG 46077=St. Boniface Hospital 30686]. While performing this review, we found that the names of 24 validly published species assignable to the genus Clostridium had been omitted from the emended description of the genus (Lawson and Rainey Int J Syst Evol Microbiol 2016;66 :1009–1016). Those species are listed in brief here. Lastly, based on this review, we also propose that Eubacterium budayi , Eubacterium nitritogenes and Eubacterium combesii be transferred to the emended genus Clostridium , as Clostridium budayi comb. nov., Clostridium nitritogenes comb. nov. and Clostridium combesii comb. nov., respectively.

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2018-06-11
2020-05-29
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References

  1. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J et al. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 1994;44:812–826 [CrossRef][PubMed]
    [Google Scholar]
  2. Alfa MJ, Robson D, Davi M, Bernard K, Van Caeseele P et al. An outbreak of necrotizing enterocolitis associated with a novel Clostridium species in a neonatal intensive care unit. Clin Infect Dis 2002;35:S101–S105 [CrossRef][PubMed]
    [Google Scholar]
  3. Bouvet P, Ferraris L, Dauphin B, Popoff MR, Butel MJ et al. 16S rRNA gene sequencing, multilocus sequence analysis, and mass spectrometry identification of the proposed new species "Clostridium neonatale". J Clin Microbiol 2014;52:4129–4136 [CrossRef][PubMed]
    [Google Scholar]
  4. Ferraris L, Schönherr S, Bouvet P, Dauphin B, Popoff M et al. One-step multiplex PCR assay for differentiating proposed new species "Clostridium neonatale" from closely related species. J Clin Microbiol 2015;53:3621–3623 [CrossRef][PubMed]
    [Google Scholar]
  5. Azcarate-Peril MA, Foster DM, Cadenas MB, Stone MR, Jacobi SK et al. Acute necrotizing enterocolitis of preterm piglets is characterized by dysbiosis of ileal mucosa-associated bacteria. Gut Microbes 2011;2:234–243 [CrossRef][PubMed]
    [Google Scholar]
  6. Benamar S, Cassir N, La Scola B. Genome sequence of a Clostridium neonatale strain isolated in a canadian neonatal intensive care unit. Genome Announc 2016;1:
    [Google Scholar]
  7. Lawson PA, Rainey FA. Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species. Int J Syst Evol Microbiol 2016;66:1009–1016 [CrossRef][PubMed]
    [Google Scholar]
  8. 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]
  9. Ghanem FM, Ridpath AC, Moore WE, Moore LV. Identification of Clostridium botulinum, Clostridium argentinense, and related organisms by cellular fatty acid analysis. J Clin Microbiol 1991;29:1114–1124[PubMed]
    [Google Scholar]
  10. 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]
    [Google Scholar]
  11. Patel JB, Weinstein MP, Eliopoulos GM, Jenkins SG. Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Second Informational Supplementvol. 37 CLSI document M100-S27 Wayne, PA: Clinical Laboratory Standards Institute; 2017; pp.250
    [Google Scholar]
  12. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152–155
    [Google Scholar]
  13. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  14. 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]
    [Google Scholar]
  15. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol 2017;34:2115–2122 [CrossRef][PubMed]
    [Google Scholar]
  16. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016;44:W16–W21 [CrossRef][PubMed]
    [Google Scholar]
  17. 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]
  18. Biebl H, Spröer C. Taxonomy of the glycerol fermenting clostridia and description of Clostridium diolis sp. nov. Syst Appl Microbiol 2002;25:491–497 [CrossRef][PubMed]
    [Google Scholar]
  19. Tindall BJ. Priority of the genus name Clostridium Prazmowski 1880 (Approved Lists 1980) vs Sarcina Goodsir 1842 (Approved Lists 1980) and the creation of the illegitimate combinations Clostridium maximum (Lindner 1888) Lawson and Rainey 2016 and Clostridium ventriculi (Goodsir 1842) Lawson and Rainey 2016 that may not be used. Int J Syst Evol Microbiol 2016;66:4890–4894 [CrossRef][PubMed]
    [Google Scholar]
  20. Rainey FA, Hollen BJ, Small A. Genus I. Clostridium Prazmowski 1880, 23AL. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey's Manual of Systematic Bacteriology, 2nd ed. Dordrecht Heidelberg London New York: Springer; 2008; pp.738–828
    [Google Scholar]
  21. Wade WG. Genus I. Eubacterium Prévot 1938. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey's Manual of Systematic Bacteriology, 2nd ed. Dordrecht Heidelberg London New York: Springer; 2008; pp.865–891
    [Google Scholar]
  22. Holdeman LV, Cato EP, Moore WEC. Anaerobe Laboratory Manual, 4th ed. Blacksburg, Virgina: Virginia Polytechic Institute and State University; 1977
    [Google Scholar]
  23. Prévot AR, Laplanche J. Étude d'une bactérie anaerobie nouvelle de Guinée Française Cillobacterium combesi n. sp. Ann Inst Pasteur Microbiol 1947;73:687–688
    [Google Scholar]
  24. Holdeman LV, Moore WEC. Eubacterium. In Cato EP, Cummins CS, Holdeman LV, Johnson JL, Moore WEC et al. (editors) Outline of Clinical Methods in Anaerobic Bacteriology, 2nd rev. ed. Blacksburg, VA: Virginia Polytechnic Institute; 1970; pp.23–30
    [Google Scholar]
  25. Moore WEC, Holdeman LV. New names and combinations in the genera Bacteroides Castellani and Chalmers, Fusobacterium Knorr, Eubacterium Prevot, Propionibacterium Delwich, and Lactobacillus Orla-Jensen. Int J Syst Bacteriol 1973;23:69–74 [CrossRef]
    [Google Scholar]
  26. Dobritsa AP, Kutumbaka KK, Werner K, Wiedmann M, Asmus A et al. Clostridium tepidum sp. nov., a close relative of Clostridium sporogenes and Clostridium botulinum group I. Int J Syst Evol Microbiol 2017;67:2317–2322 [CrossRef][PubMed]
    [Google Scholar]
  27. Jousimies-Somer HR, Summanen P, Citron DM, Baron EJ, Wexler HM et al. Wadsworth-KTL Anaerobic Bacteriology Manual, 6th ed. Belmount CA: Star Publishing; 2002
    [Google Scholar]
  28. Weigand MR, Pena-Gonzalez A, Shirey TB, Broeker RG, Ishaq MK et al. Implications of genome-based discrimination between Clostridium botulinum group i and Clostridium sporogenes strains for bacterial taxonomy. Appl Environ Microbiol 2015;81:5420–5429 [CrossRef][PubMed]
    [Google Scholar]
  29. Williamson CHD, Vazquez AJ, Hill K, Smith TJ, Nottingham R et al. Differentiating botulinum neurotoxin-producing Clostridia with a simple, multiplex PCR assay. Appl Environ Microbiol 2017;83:e00806-17 [CrossRef][PubMed]
    [Google Scholar]
  30. Prévot AR, Turpin A, Kaiser P. Les Bactéries Anaérobies Paris: Dunod; 1967
    [Google Scholar]
  31. Inglett KS, Bae HS, Aldrich HC, Hatfield K, Ogram AV. Clostridium chromiireducens sp. nov., isolated from Cr(VI)-contaminated soil. Int J Syst Evol Microbiol 2011;61:2626–2631 [CrossRef][PubMed]
    [Google Scholar]
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