Insights into the acquisition of the island and production of colibactin in the population Open Access

Abstract

The island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine isolates, we identified 109 strains carrying a highly conserved island, mostly from phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios of acquisition were deduced from whole genome sequence and phylogenetic analysis. In the main scenario, was introduced and stabilized into certain sequence types (STs) of the B2 phylogroup, such as ST73 and ST95, at the tRNA locus located in the vicinity of the yersiniabactin-encoding High Pathogenicity Island (HPI). In a few B2 strains, inserted at the or tRNA loci close to the HPI and occasionally was located next to the remnant of an integrative and conjugative element. In a last scenario specific to B1/A strains, was acquired, independently of the HPI, at a non-tRNA locus. All the -positive strains except 18 produced colibactin. Sixteen strains contained mutations in or or a fusion of and and were no longer genotoxic but most of them still produced low amounts of potentially active metabolites associated with the island. One strain was fully metabolically inactive without alteration, but colibactin production was restored by overexpressing the ClbR regulator. In conclusion, the island is not restricted to human pathogenic B2 strains and is more widely distributed in the population, while preserving its functionality.

Funding
This study was supported by the:
  • INSERM
    • Principle Award Recipient: CamilleChagneau
  • Ministère de l'Agriculture
    • Principle Award Recipient: AlexandrePerrat
  • Region Occitanie (Award ALDOCT-000610)
    • Principle Award Recipient: AlexandrePerrat
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2021-05-07
2024-03-28
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References

  1. Denamur E, Clermont O, Bonacorsi S, Gordon D. The population genetics of pathogenic Escherichia coli. Nat Rev Microbiol 2021; 19:37-54 [View Article][PubMed]
    [Google Scholar]
  2. Tenaillon O, Skurnik D, Picard B, Denamur E. The population genetics of commensal Escherichia coli. . Nat Rev Microbiol 2010; 8:207–217 [View Article][PubMed]
    [Google Scholar]
  3. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature 2000; 405:299–304 [View Article][PubMed]
    [Google Scholar]
  4. Kaper JB, Nataro JP, Mobley HL. Pathogenic Escherichia coli. Nat Rev Microbiol 2004; 2:123–140 [View Article][PubMed]
    [Google Scholar]
  5. Nougayrède HS, Homburg S, Taieb F, Boury M, Brzuszkiewicz E, Gottschalk G et al. Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 2006; 313:848–851 [View Article][PubMed]
    [Google Scholar]
  6. Putze J, Hennequin C, Nougayrède JP, Zhang W, Homburg S et al. Genetic structure and distribution of the colibactin genomic island among members of the family Enterobacteriaceae. Infect Immun 2009; 77:4696–4703 [View Article][PubMed]
    [Google Scholar]
  7. Engel P, Vizcaino MI, Crawford JM. Gut symbionts from distinct hosts exhibit genotoxic activity via divergent colibactin biosynthesis pathways. Appl Environ Microbiol 2015; 81:1502–1512 [View Article][PubMed]
    [Google Scholar]
  8. Bondarev V, Richter M, Romano S, Piel J, Schwedt A et al. The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. Environ Microbiol 2013; 15:2095–2113 [View Article][PubMed]
    [Google Scholar]
  9. Marcq I, Martin P, Payros D, Cuevas-Ramos G, Boury M et al. The genotoxin colibactin exacerbates lymphopenia and decreases survival rate in mice infected with septicemic Escherichia coli. . J Infect Dis 2014; 210:285–294 [View Article][PubMed]
    [Google Scholar]
  10. Martin P, Marcq I, Magistro G, Penary M, Garcie C et al. Interplay between siderophores and colibactin genotoxin biosynthetic pathways in Escherichia coli. PLoS Pathog 2013; 9:e1003437 [View Article][PubMed]
    [Google Scholar]
  11. McCarthy AJ, Martin P, Cloup E, Stabler RA, Oswald E et al. The genotoxin colibactin is a determinant of virulence in Escherichia coli K1 experimental neonatal systemic infection. Infect Immun 2015; 83:3704–3711 [View Article][PubMed]
    [Google Scholar]
  12. Arthur JC, Perez-Chanona E, Mühlbauer M, Tomkovich S, Uronis JM et al. Intestinal inflammation targets cancer-inducing activity of the microbiota. Science 2012; 338:120–123 [View Article]
    [Google Scholar]
  13. Cougnoux A, Dalmasso G, Martinez R, Buc E, Delmas J et al. Bacterial genotoxin colibactin promotes colon tumour growth by inducing a senescence-associated secretory phenotype. Gut 2014; 63:1932–1942 [View Article][PubMed]
    [Google Scholar]
  14. Cuevas-Ramos G, Petit CR, Marcq I, Boury M, Oswald E et al. Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells. Proc Natl Acad Sci U S A 2010; 107:11537–11542 [View Article][PubMed]
    [Google Scholar]
  15. Bossuet-Greif N, Vignard J, Taieb F, Mirey G, Dubois D et al. The colibactin genotoxin generates DNA interstrand cross-links in infected cells. mBio 2018; 9:e02393-17 20 03 2018 [View Article][PubMed]
    [Google Scholar]
  16. Taieb F, Petit C, Nougayrède JP, Oswald E. The enterobacterial genotoxins: cytolethal distending toxin and colibactin. EcoSal Plus 2016; 7: [View Article][PubMed]
    [Google Scholar]
  17. Brotherton CA, Balskus EP. A prodrug resistance mechanism is involved in colibactin biosynthesis and cytotoxicity. J Am Chem Soc 2013; 135:3359–3362 [View Article][PubMed]
    [Google Scholar]
  18. Wallenstein A, Rehm N, Brinkmann M, Selle M, Bossuet-Greif N et al. ClbR is the key transcriptional activator of colibactin gene expression in Escherichia coli. mSphere 2020; 5:
    [Google Scholar]
  19. Shine EE, Xue M, Patel JR, Healy AR, Surovtseva YV et al. Model Colibactins exhibit human cell genotoxicity in the absence of host bacteria. ACS Chem Biol 2018; 13:3286–3293 [View Article][PubMed]
    [Google Scholar]
  20. Vizcaino MI, Engel P, Trautman E, Crawford JM. Comparative metabolomics and structural characterizations illuminate colibactin pathway-dependent small molecules. J Am Chem Soc 2014; 136:9244–9247 [View Article][PubMed]
    [Google Scholar]
  21. Pérez-Berezo T, Pujo J, Martin P, Le Faouder P, Galano JM et al. Identification of an analgesic lipopeptide produced by the probiotic Escherichia coli strain Nissle 1917. Nat Commun 2017; 8:1314 [View Article][PubMed]
    [Google Scholar]
  22. Massip C, Branchu P, Bossuet-Greif N, Chagneau CV, Gaillard D et al. Deciphering the interplay between the genotoxic and probiotic activities of Escherichia coli Nissle 1917. PLoS Pathog 2019; 15:e1008029 [View Article][PubMed]
    [Google Scholar]
  23. Dubois D, Delmas J, Cady A, Robin F, Sivignon A et al. Cyclomodulins in urosepsis strains of Escherichia coli. J Clin Microbiol 2010; 48:2122–2129 [View Article][PubMed]
    [Google Scholar]
  24. Johnson JR, Johnston B, Kuskowski MA, Nougayrede JP, Oswald E. Molecular epidemiology and phylogenetic distribution of the Escherichia coli pks genomic island. J Clin Microbiol 2008; 46:3906–3911 [View Article][PubMed]
    [Google Scholar]
  25. Arimizu Y, Kirino Y, Sato MP, Uno K, Sato T et al. Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains. Genome Res 2019; 29:1495–1505 [View Article][PubMed]
    [Google Scholar]
  26. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article][PubMed]
    [Google Scholar]
  27. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article][PubMed]
    [Google Scholar]
  28. Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom 2016; 2:e000056 [View Article][PubMed]
    [Google Scholar]
  29. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article][PubMed]
    [Google Scholar]
  30. Letunic I, Bork P. Interactive tree of life (iTOL) V3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242–W245 [View Article][PubMed]
    [Google Scholar]
  31. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12 [View Article][PubMed]
    [Google Scholar]
  32. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  33. Revell LJ. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol 2012; 3:217–223 [View Article]
    [Google Scholar]
  34. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG et al. Act: the ARTEMIS comparison tool. Bioinformatics 2005; 21:3422–3423 [View Article][PubMed]
    [Google Scholar]
  35. Gordon DM, Geyik S, Clermont O, O'Brien CL, Huang S et al. Fine-Scale structure analysis shows epidemic patterns of clonal complex 95, a cosmopolitan Escherichia coli lineage responsible for extraintestinal infection. mSphere 2017; 2: [View Article][PubMed]
    [Google Scholar]
  36. Bossuet-Greif N, Belloy M, Boury M, Oswald E, Nougayrede J-P. Protocol for HeLa cells infection with Escherichia coli strains producing colibactin and quantification of the induced DNA-damage. BIO-PROTOCOL 2017; 7:e2520 [View Article]
    [Google Scholar]
  37. Tronnet S, Oswald E. Quantification of Colibactin-associated genotoxicity in HeLa cells by in cell Western (ICW) using γ-H2AX as a marker. Bio Protoc 2018; 8:e2771 [View Article]
    [Google Scholar]
  38. Schubert S, Dufke S, Sorsa J, Heesemann J. A novel integrative and conjugative element (ICE) of Escherichia coli: the putative progenitor of the Yersinia high-pathogenicity island. Mol Microbiol 2004; 51:837–848 [View Article][PubMed]
    [Google Scholar]
  39. Fabian NJ, Mannion AJ, Feng Y, Madden CM, Fox JG. Intestinal colonization of genotoxic Escherichia coli strains encoding colibactin and cytotoxic necrotizing factor in small mammal pets. Vet Microbiol 2020; 240:108506 [View Article][PubMed]
    [Google Scholar]
  40. Kurnick SA, Mannion AJ, Feng Y, Madden CM, Chamberlain P et al. Genotoxic Escherichia coli strains encoding Colibactin, Cytolethal Distending Toxin, and Cytotoxic necrotizing factor in laboratory rats. Comp Med 2019; 69:103–113 [View Article][PubMed]
    [Google Scholar]
  41. Buchrieser C, Brosch R, Bach S, Guiyoule A, Carniel E. The high-pathogenicity island of Yersinia pseudotuberculosis can be inserted into any of the three chromosomal Asn tRNA genes. Mol Microbiol 1998; 30:965–978 [View Article][PubMed]
    [Google Scholar]
  42. Schubert S, Darlu P, Clermont O, Wieser A, Magistro G et al. Role of intraspecies recombination in the spread of pathogenicity islands within the Escherichia coli species. PLoS Pathog 2009; 5:e1000257 [View Article][PubMed]
    [Google Scholar]
  43. Rakin A, Noelting C, Schropp P, Heesemann J. Integrative module of the high-pathogenicity island of Yersinia. Mol Microbiol 2001; 39:407–416 [View Article][PubMed]
    [Google Scholar]
  44. Messerer M, Fischer W, Schubert S. Investigation of horizontal gene transfer of pathogenicity islands in Escherichia coli using next-generation sequencing. PLoS One 2017; 12:e0179880 [View Article][PubMed]
    [Google Scholar]
  45. Manges AR, Geum HM, Guo A, Edens TJ, Fibke CD et al. Global extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Clin Microbiol Rev 2019; 32: [View Article][PubMed]
    [Google Scholar]
  46. Oliveira PH, Touchon M, Rocha EP. Regulation of genetic flux between bacteria by restriction-modification systems. Proc Natl Acad Sci U S A 2016; 113:5658–5663 [View Article][PubMed]
    [Google Scholar]
  47. Massip C, Chagneau CV, Boury M, Oswald E. The synergistic triad between microcin, colibactin, and salmochelin gene clusters in uropathogenic Escherichia coli. Microbes Infect 2020; 22:144–147 [View Article][PubMed]
    [Google Scholar]
  48. Molan K, Podlesek Z, Hodnik V, Butala M, Oswald E et al. The Escherichia coli colibactin resistance protein ClbS is a novel DNA binding protein that protects DNA from nucleolytic degradation. DNA Repair 2019; 79:50–54 [View Article][PubMed]
    [Google Scholar]
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