Core-, pan- and accessory genome analyses of : insights into genetic diversity Open Access

Abstract

is a potential opportunistic pathogen recovered from faecal samples in cases of necrotizing enterocolitis (NEC), a gastrointestinal disease affecting preterm neonates. Although the species description and name validation were published in 2018, comparative genomics are lacking. In the present study, we provide the closed genome assembly of the ATCC BAA-265 (=250.09) reference strain with a manually curated functional annotation of the coding sequences. Pan-, core- and accessory genome analyses were performed using the complete 250.09 genome (4.7 Mb), three new assemblies (4.6–5.6 Mb), and five publicly available draft genome assemblies (4.6–4.7 Mb). The pan-genome contains 6840 genes, while the core-genome has 3387 genes. Pan-genome analysis revealed an ‘open’ state and genomic diversity. The strain-specific gene families ranged from five to 742 genes. Multiple mobile genetic elements were predicted, including a total of 201 genomic islands, 13 insertion sequence families, one CRISPR-Cas type I-B system and 15 predicted intact prophage signatures. Primary virulence classes including offensive, defensive, regulation of virulence-associated genes and non-specific virulence factors were identified. The presence of a (W/N/W) gene encoding a tetracycline resistance ribosomal protection protein and a 23S rRNA methyltransferase gene were identified in two different strains. Together, our results revealed a genetic diversity and plasticity of genomes and provide a comprehensive view of this species genomic features, paving the way for the characterization of its biological capabilities.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000813
2022-05-13
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/mgen/8/5/mgen000813.html?itemId=/content/journal/mgen/10.1099/mgen.0.000813&mimeType=html&fmt=ahah

References

  1. Prazmowski A. Untersuchung über die Entwickelungsgeschichte und Fermentwirking einiger Bacterien-Arten. Inaug Diss Hugo Voigt; Leipzig, Ger; 1880 http://www.marinespecies.org/aphia.php?p=sourcedetails&id=377531
  2. 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 [View Article] [PubMed]
    [Google Scholar]
  3. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  4. Bergey DH, Whitman WB, Vos PD, Garrity GM, Jones D. Bergey’s Manual of Systematic Bacteriology New York: Springer; 2009
    [Google Scholar]
  5. Kuehne SA, Minton NP. ClosTron-mediated engineering of Clostridium. Bioengineered 2012; 3:247–254 [View Article] [PubMed]
    [Google Scholar]
  6. Bazacliu C, Neu J. Pathophysiology of necrotizing enterocolitis: an update. Curr Pediatr Rev 2019; 15:68–87 [View Article] [PubMed]
    [Google Scholar]
  7. 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:S101–5 [View Article] [PubMed]
    [Google Scholar]
  8. Bouvet P, Ferraris L, Dauphin B, Popoff M-R, 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 [View Article] [PubMed]
    [Google Scholar]
  9. Bernard K, Burdz T, Wiebe D, Alfa M, Bernier AM. Clostridium neonatale sp. nov. linked to necrotizing enterocolitis in neonates and a clarification of species assignable to the genus Clostridium (Prazmowski 1880) emend. Lawson and Rainey 2016. Int J Syst Evol Microbiol 2018; 68:2416–2423 [View Article] [PubMed]
    [Google Scholar]
  10. Schönherr-Hellec S, Aires J. Clostridia and necrotizing enterocolitis in preterm neonates. Anaerobe 2019; 58:6–12 [View Article] [PubMed]
    [Google Scholar]
  11. Rozé J-C, Ancel P-Y, Lepage P, Martin-Marchand L, Al Nabhani Z et al. Nutritional strategies and gut microbiota composition as risk factors for necrotizing enterocolitis in very-preterm infants. Am J Clin Nutr 2017; 106:821–830 [View Article] [PubMed]
    [Google Scholar]
  12. Hosny M, Baptiste E, Levasseur A, La Scola B. Molecular epidemiology of Clostridium neonatale and its relationship with the occurrence of necrotizing enterocolitis in preterm neonates. New Microbes New Infect 2019; 32:100612 [View Article] [PubMed]
    [Google Scholar]
  13. Cassir N, Benamar S, Khalil JB, Croce O, Saint-Faust M et al. Clostridium butyricum strains and dysbiosis linked to necrotizing enterocolitis in preterm neonates. Clin Infect Dis 2015; 61:1107–1115 [View Article] [PubMed]
    [Google Scholar]
  14. 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 [View Article] [PubMed]
    [Google Scholar]
  15. Popoff MR, Szylit O, Ravisse P, Dabard J, Ohayon H. Experimental cecitis in gnotoxenic chickens monoassociated with Clostridium butyricum strains isolated from patients with neonatal necrotizing enterocolitis. Infect Immun 1985; 47:697–703 [View Article] [PubMed]
    [Google Scholar]
  16. Bousseboua H, Le Coz Y, Dabard J, Szylit O, Raibaud P et al. Experimental cecitis in gnotobiotic quails monoassociated with Clostridium butyricum strains isolated from patients with neonatal necrotizing enterocolitis and from healthy newborns. Infect Immun 1989; 57:932–936 [View Article] [PubMed]
    [Google Scholar]
  17. Waligora-Dupriet A-J, Dugay A, Auzeil N, Huerre M, Butel M-J. Evidence for clostridial implication in necrotizing enterocolitis through bacterial fermentation in a gnotobiotic quail model. Pediatr Res 2005; 58:629–635 [View Article] [PubMed]
    [Google Scholar]
  18. Waligora-Dupriet AJ, Dugay A, Auzeil N, Nicolis I, Rabot S et al. Short-chain fatty acids and polyamines in the pathogenesis of necrotizing enterocolitis: Kinetics aspects in gnotobiotic quails. Anaerobe 2009; 15:138–144 [View Article] [PubMed]
    [Google Scholar]
  19. 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; 4:5–6 [View Article]
    [Google Scholar]
  20. 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]
  21. Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S et al. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 2006; 34:53–65 [View Article] [PubMed]
    [Google Scholar]
  22. Monot M, Boursaux-Eude C, Thibonnier M, Vallenet D, Moszer I et al. Reannotation of the genome sequence of Clostridium difficile strain 630. J Med Microbiol 2011; 60:1193–1199 [View Article] [PubMed]
    [Google Scholar]
  23. 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 [View Article] [PubMed]
    [Google Scholar]
  24. Kolde R. n.d Pheatmap: pretty heatmaps. R package version 061.
  25. Grant JR, Stothard P. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 2008; 36:W181–4 [View Article] [PubMed]
    [Google Scholar]
  26. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article] [PubMed]
    [Google Scholar]
  27. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460–2461 [View Article] [PubMed]
    [Google Scholar]
  28. Tettelin H, Riley D, Cattuto C, Medini D. Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 2008; 11:472–477 [View Article] [PubMed]
    [Google Scholar]
  29. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article] [PubMed]
    [Google Scholar]
  30. Chen L, Yang J, Yu J, Yao Z, Sun L et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005; 33:D325–8 [View Article] [PubMed]
    [Google Scholar]
  31. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 2013; 57:3348–3357 [View Article] [PubMed]
    [Google Scholar]
  32. Bertelli C, Laird MR, Williams KP. Simon Fraser University Research Computing Group Lau BY et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45:W30–W35 [View Article] [PubMed]
    [Google Scholar]
  33. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–6 [View Article] [PubMed]
    [Google Scholar]
  34. Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 2018; 46:W246–W251 [View Article] [PubMed]
    [Google Scholar]
  35. 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:W16–21 [View Article] [PubMed]
    [Google Scholar]
  36. Pellow D, Mizrahi I, Shamir R. PlasClass improves plasmid sequence classification. PLOS Comput Biol 2020; 16:e1007781 [View Article] [PubMed]
    [Google Scholar]
  37. Société Française de Microbiologie CASFM / EUCAST: Société Française de Microbiologie Ed 2021
    [Google Scholar]
  38. Udaondo Z, Duque E, Ramos JL. The pangenome of the genus Clostridium. Environ Microbiol 2017; 19:2588–2603 [View Article] [PubMed]
    [Google Scholar]
  39. Liberato V, Benevenuti C, Coelho F, Botelho A, Amaral P et al. Clostridium sp. as bio-catalyst for fuels and chemicals production in a biorefinery context. Catalysts 2019; 9:962 [View Article]
    [Google Scholar]
  40. Zhao X, Condruz S, Chen J, Jolicoeur M. A quantitative metabolomics study of high sodium response in Clostridium acetobutylicum ATCC 824 acetone-butanol-ethanol (ABE) fermentation. Sci Rep 2016; 6:28307 [View Article] [PubMed]
    [Google Scholar]
  41. Celińska E, Grajek W. Biotechnological production of 2,3-butanediol--current state and prospects. Biotechnol Adv 2009; 27:715–725 [View Article] [PubMed]
    [Google Scholar]
  42. Silver S. Bacterial resistances to toxic metal ions--a review. Gene 1996; 179:9–19 [View Article] [PubMed]
    [Google Scholar]
  43. Nourdin-Galindo G, Sánchez P, Molina CF, Espinoza-Rojas DA, Oliver C et al. Comparative pan-genome analysis of Piscirickettsia salmonis reveals genomic divergences within genogroups. Front Cell Infect Microbiol 2017; 7:1–16 [View Article] [PubMed]
    [Google Scholar]
  44. Feng Y, Fan X, Zhu L, Yang X, Liu Y et al. Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens. Microb Genom 2020; 6:1–15 [View Article] [PubMed]
    [Google Scholar]
  45. Hampton HG, Watson BNJ, Fineran PC. The arms race between bacteria and their phage foes. Nature 2020; 577:327–336 [View Article] [PubMed]
    [Google Scholar]
  46. Broniewski JM, Meaden S, Paterson S, Buckling A, Westra ER. The effect of phage genetic diversity on bacterial resistance evolution. ISME J 2020; 14:828–836 [View Article] [PubMed]
    [Google Scholar]
  47. Gill EM, Jung K, Qvist N, Ellebæk MB. Antibiotics in the medical and surgical treatment of necrotizing enterocolitis. A systematic review. BMC Pediatr 2022; 22:66 [View Article] [PubMed]
    [Google Scholar]
  48. Hosny M, Bou Khalil JY, Caputo A, Abdallah RA, Levasseur A et al. Multidisciplinary evaluation of Clostridium butyricum clonality isolated from preterm neonates with necrotizing enterocolitis in South France between 2009 and 2017. Sci Rep 2019; 9:1–7 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000813
Loading
/content/journal/mgen/10.1099/mgen.0.000813
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Most cited Most Cited RSS feed