1887

Microbial Genomics logo

Volume 7, Issue 11

Genome structural variation in O157:H7 Open Access

Abstract

The human zoonotic pathogen O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype. We demonstrate that LCRs are a major source of genomic variation across all lineages of O157:H7 and by using both optical mapping and Oxford Nanopore long-read sequencing prove that LCRs are generated in laboratory cultures started from a single colony and that these variants can be recovered from colonized cattle. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga-toxin production, type-3 secretion and motility can be affected by LCRs. In summary, O157:H7 has acquired multiple prophage regions over time that act to continually produce structural variants of the genome. These findings raise important questions about the significance of this prophage-mediated genome contingency to enhance adaptability between environments.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): cattle , duplication , E. coli , genome structure , inversion , O157:H7 , optical mapping , PFGE , prophage , Shiga toxin and type 3 secretion
Funding
This study was supported by the:
  • Food Standards Agency (Award FS101055)
    • Principle Award Recipient: DavidL. Gally
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/D/20002173)
    • Principle Award Recipient: DavidL. Gally
  • Biotechnology and Biological Sciences Research Council (Award BB/P02095X/1)
    • Principle Award Recipient: DavidL. Gally
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000682
2021-11-09
2024-04-29
Loading full text...

Full text loading...

/deliver/fulltext/mgen/7/11/mgen000682.html?itemId=/content/journal/mgen/10.1099/mgen.0.000682&mimeType=html&fmt=ahah

References

  1. Brussow H, Canchaya C, Hardt WD. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 2004; 68:560–602 [View Article] [PubMed]
     [Google Scholar]
  2. Taylor VL, Fitzpatrick AD, Islam Z, Maxwell KL. The diverse impacts of phage morons on bacterial fitness and virulence. Adv Virus Res 2019; 103:1–31S0065-3527(18)30043-5 [View Article] [PubMed]
     [Google Scholar]
  3. Argov T, Azulay G, Pasechnek A, Stadnyuk O, Ran-Sapir S. Temperate bacteriophages as regulators of host behavior. Curr Opin Microbiol 2017; 38:81–87 [View Article] [PubMed]
     [Google Scholar]
  4. Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS. Prophages mediate defense against phage infection through diverse mechanisms. ISME J 2016; 10:2854–2866 [View Article] [PubMed]
     [Google Scholar]
  5. Davies EV, Winstanley C, Fothergill JL, James CE. The role of temperate bacteriophages in bacterial infection. FEMS Microbiol Lett 2016; 363:fnw015 [View Article] [PubMed]
     [Google Scholar]
  6. Wang X, Kim Y, Ma Q, Hong SH, Pokusaeva K. Cryptic prophages help bacteria cope with adverse environments. Nat Commun 2010; 1:147 [View Article] [PubMed]
     [Google Scholar]
  7. Tree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL. Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli. Mol Cell 2014; 55:199–213 [View Article] [PubMed]
     [Google Scholar]
  8. Ferens WA, Hovde CJ. Escherichia coli O157:H7: animal reservoir and sources of human infection. Foodborne Pathog Dis 2011; 8:465–487 [View Article] [PubMed]
     [Google Scholar]
  9. Shaaban SC, McAteer LA, Jenkins SP, Dallman C, Bono JL et al. Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing. Microb Genom 2016 [View Article]
     [Google Scholar]
  10. Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 2001; 409:529–533 [View Article] [PubMed]
     [Google Scholar]
  11. Dallman TJ, Ashton PM, Byrne L, Perry NT, Petrovska L et al. Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK. Microb Genom 2015; 1:e000029 [View Article]
     [Google Scholar]
  12. Heiman KE, Mody RK, Johnson SD, Griffin PM, Gould LH. Escherichia coli O157 Outbreaks in the United States, 2003-2012. Emerging Infect Dis 2015; 21:1293–1301
     [Google Scholar]
  13. Karmali MA. Host and pathogen determinants of verocytotoxin-producing Escherichia coli-associated hemolytic uremic syndrome. Kidney Int Suppl 2009S4–7 [View Article] [PubMed]
     [Google Scholar]
  14. Obrig TG, Karpman D. Shiga toxin pathogenesis: kidney complications and renal failure. Curr Top Microbiol Immunol 2012; 357:105–136 [View Article] [PubMed]
     [Google Scholar]
  15. Brandal LT, Wester AL, Lange H, Lobersli I, Lindstedt BA. Shiga toxin-producing Escherichia coli infections in Norway, 1992-2012: characterization of isolates and identification of risk factors for haemolytic uremic syndrome. BMC Infect Dis 2015; 15:324 [View Article] [PubMed]
     [Google Scholar]
  16. Iyoda S, Manning SD, Seto K, Kimata K, Isobe J. Phylogenetic Clades 6 and 8 of Enterohemorrhagic Escherichia coli O157:H7 with particular stx subtypes are more frequently found in isolates from hemolytic uremic syndrome patients than from asymptomatic carriers. Open Forum Infect Dis 2014; 1:ofu061 [View Article] [PubMed]
     [Google Scholar]
  17. Buvens G, De Gheldre Y, Dediste A, de Moreau AI, Mascart G. Incidence and virulence determinants of verocytotoxin-producing Escherichia coli infections in the Brussels-Capital Region, Belgium, in 2008-2010. J Clin Microbiol 2012; 50:1336–1345 [View Article] [PubMed]
     [Google Scholar]
  18. Fuller CA, Pellino CA, Flagler MJ, Strasser JE, Weiss AA. Shiga toxin subtypes display dramatic differences in potency. Infect Immun 2011; 79:1329–1337 [View Article] [PubMed]
     [Google Scholar]
  19. Iguchi A, Iyoda S, Terajima J, Watanabe H, Osawa R. Spontaneous recombination between homologous prophage regions causes large-scale inversions within the Escherichia coli O157:H7 chromosome. Gene 2006; 372:199–207 [View Article] [PubMed]
     [Google Scholar]
  20. Kotewicz ML, Jackson SA, LeClerc JE, Cebula TA. Optical maps distinguish individual strains of Escherichia coli O157: H7. Microbiology (Reading) 2007; 153:1720–1733 [View Article] [PubMed]
     [Google Scholar]
  21. Periwal V, Scaria V. Insights into structural variations and genome rearrangements in prokaryotic genomes. Bioinformatics 2015; 31:1–9 [View Article] [PubMed]
     [Google Scholar]
  22. Hughes D. Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes. Genome Biol 2000; 1:REVIEWS0006 [View Article] [PubMed]
     [Google Scholar]
  23. Clawson ML, Keen JE, Smith TP, Durso LM, McDaneld TG. Phylogenetic classification of Escherichia coli O157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms. Genome Biol 2009; 10:R56 [View Article] [PubMed]
     [Google Scholar]
  24. Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 2013; 14:R101 [View Article] [PubMed]
     [Google Scholar]
  25. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
     [Google Scholar]
  26. Stewart AC, Osborne B, Read TD. DIYA: a bacterial annotation pipeline for any genomics lab. Bioinformatics 2009; 25:962–963 [View Article] [PubMed]
     [Google Scholar]
  27. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PloS one 2014; 9:e112963 [View Article]
     [Google Scholar]
  28. Luo H, Zhang CT, Gao F. Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes. Front Microbiol 2014; 5:482 [View Article] [PubMed]
     [Google Scholar]
  29. Arndt D, Grant JR, Marcu A, Sajed T, Pon A. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
     [Google Scholar]
  30. Green MR, Sambrook J. Isolation and quantification of DNA. Cold Spring Harb Protoc 2018; 2018:pdb. top093336
     [Google Scholar]
  31. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 2018; 34:3094–3100 [View Article] [PubMed]
     [Google Scholar]
  32. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25:2078–2079 [View Article] [PubMed]
     [Google Scholar]
  33. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010; 26:841–842 [View Article] [PubMed]
     [Google Scholar]
  34. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011; 27:1009–1010 [View Article] [PubMed]
     [Google Scholar]
  35. Okonechnikov K, Golosova O, Fursov M, team U. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012; 28:1166–1167 [View Article] [PubMed]
     [Google Scholar]
  36. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  37. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R. Circos: an information aesthetic for comparative genomics. Genome Res 2009; 19:1639–1645 [View Article] [PubMed]
     [Google Scholar]
  38. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  39. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PloS one 2010; 5:e9490 [View Article] [PubMed]
     [Google Scholar]
  40. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [View Article] [PubMed]
     [Google Scholar]
  41. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010; 26:589–595 [View Article] [PubMed]
     [Google Scholar]
  42. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20:1297–1303 [View Article] [PubMed]
     [Google Scholar]
  43. Dallman T, Ashton P, Schafer U, Jironkin A, Painset A. SnapperDB: a database solution for routine sequencing analysis of bacterial isolates. Bioinformatics 2018; 34:3028–3029 [View Article] [PubMed]
     [Google Scholar]
  44. Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 2015; 43:e15 [View Article] [PubMed]
     [Google Scholar]
  45. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
     [Google Scholar]
  46. Ribot EM, Fair MA, Gautom R, Cameron DN, Hunter SB. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog Dis 2006; 3:59–67 [View Article] [PubMed]
     [Google Scholar]
  47. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013; 29:15–21 [View Article] [PubMed]
     [Google Scholar]
  48. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  49. Nikolayeva O, Robinson MD. edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods Mol Biol 2014; 1150:45–79 [View Article] [PubMed]
     [Google Scholar]
  50. Dykhuizen DE. Experimental studies of natural selection in bacteria. Annu Rev Ecol Syst 1990; 21:373–398 [View Article]
     [Google Scholar]
  51. Lenski RE. Quantifying fitness and gene stability in microorganisms. Biotechnology 1991; 15:173–192 [View Article] [PubMed]
     [Google Scholar]
  52. Fitzgerald SF, Beckett AE, Palarea-Albaladejo J, McAteer S, Shaaban S et al. Shiga toxin sub-type 2a increases the efficiency of Escherichia coli O157 transmission between animals and restricts epithelial regeneration in bovine enteroids PLoS pathogens. Research 2019
     [Google Scholar]
  53. Fernandez-Brando RJ, Yamaguchi N, Tahoun A, McAteer SP, Gillespie T. Type III secretion-dependent sensitivity of Escherichia coli O157 to specific ketolides. Antimicrob Agents Chemother 2016; 60:459–470 [View Article] [PubMed]
     [Google Scholar]
  54. Wang D, Roe AJ, McAteer S, Shipston MJ, Gally DL. Hierarchal type III secretion of translocators and effectors from Escherichia coli O157:H7 requires the carboxy terminus of SepL that binds to Tir. Mol Microbiol 2008; 69:1499–1512 [View Article] [PubMed]
     [Google Scholar]
  55. Holden N, Totsika M, Dixon L, Catherwood K, Gally DL. Regulation of P-fimbrial phase variation frequencies in Escherichia coli CFT073. Infect Immun 2007; 75:3325–3334 [View Article] [PubMed]
     [Google Scholar]
  56. Xu X, McAteer SP, Tree JJ, Shaw DJ, Wolfson EB. Lysogeny with Shiga toxin 2-encoding bacteriophages represses type III secretion in enterohemorrhagic Escherichia coli. PLoS Pathog 2012; 8:e1002672 [View Article] [PubMed]
     [Google Scholar]
  57. Doyle M, Fookes M, Ivens A, Mangan MW, Wain J. An H-NS-like stealth protein aids horizontal DNA transmission in bacteria. Science 2007; 315:251–252 [View Article] [PubMed]
     [Google Scholar]
  58. Darmon E, Leach DR. Bacterial genome instability. Microbiol Mol Biol Rev 2014; 78:1–39 [View Article] [PubMed]
     [Google Scholar]
  59. Ooka T, Ogura Y, Asadulghani M, Ohnishi M, Nakayama K. Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes. Genome Res 2009; 19:1809–1816 [View Article] [PubMed]
     [Google Scholar]
  60. Corbishley A, Ahmad NI, Hughes K, Hutchings MR, McAteer SP. Strain-dependent cellular immune responses in cattle following Escherichia coli O157:H7 colonization. Infect Immun 2014; 82:5117–5131 [View Article] [PubMed]
     [Google Scholar]
  61. Taylor DE, Rooker M, Keelan M, Ng LK, Martin I. Genomic variability of O islands encoding tellurite resistance in enterohemorrhagic Escherichia coli O157:H7 isolates. J Bacteriol 2002; 184:4690–4698 [View Article] [PubMed]
     [Google Scholar]
  62. Landstorfer R, Simon S, Schober S, Keim D, Scherer S. Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces. BMC genomics 2014; 15:353 [View Article] [PubMed]
     [Google Scholar]
  63. Cowley LA, Dallman TJ, Fitzgerald S, Irvine N, Rooney PJ et al. Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks. Microb Genom 2016; 2:e000084 [View Article]
     [Google Scholar]
  64. Bobay LM, Touchon M, Rocha EP. Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability. PLoS Genet 2013; 9:e1003825 [View Article] [PubMed]
     [Google Scholar]
  65. De Paepe M, Hutinet G, Son O, Amarir-Bouhram J, Schbath S. Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases. PLoS Genet 2014; 10:e1004181 [View Article] [PubMed]
     [Google Scholar]
  66. Asadulghani M, Ogura Y, Ooka T, Itoh T, Sawaguchi A. The defective prophage pool of Escherichia coli O157: prophage-prophage interactions potentiate horizontal transfer of virulence determinants. PLoS Pathog 2009; 5:e1000408 [View Article] [PubMed]
     [Google Scholar]
  67. Schmidt H. Shiga-toxin-converting bacteriophages. Res Microbiol 2001; 152:687–695 [View Article] [PubMed]
     [Google Scholar]
  68. Chen C, Lewis CR, Goswami K, Roberts EL, DebRoy C. Identification and characterization of spontaneous deletions within the Sp11-Sp12 prophage region of Escherichia coli O157:H7 Sakai. Appl Environ Microbiol 2013; 79:1934–1941 [View Article] [PubMed]
     [Google Scholar]
  69. Henry MK, Tongue SC, Evans J, Webster C, MC KI. British Escherichia coli O157 in Cattle Study (BECS): to determine the prevalence of E. coli O157 in herds with cattle destined for the food chain. Epidemiol Infect 2017; 145:3168–3179 [View Article] [PubMed]
     [Google Scholar]
  70. Matthews L, McKendrick IJ, Ternent H, Gunn GJ, Synge B. Super-shedding cattle and the transmission dynamics of Escherichia coli O157. Epidemiol Infect 2006; 134:131–142 [View Article] [PubMed]
     [Google Scholar]
  71. Pearce MC, Jenkins C, Vali L, Smith AW, Knight HI. Temporal shedding patterns and virulence factors of Escherichia coli serogroups O26, O103, O111, O145, and O157 in a cohort of beef calves and their dams. Appl Environ Microbiol 2004; 70:1708–1716 [View Article] [PubMed]
     [Google Scholar]
  72. Vali L, Wisely KA, Pearce MC, Turner EJ, Knight HI. High-level genotypic variation and antibiotic sensitivity among Escherichia coli O157 strains isolated from two Scottish beef cattle farms. Appl Environ Microbiol 2004; 70:5947–5954 [View Article] [PubMed]
     [Google Scholar]
  73. Stanton E, Wahlig TA, Park D, Kaspar CW. Chronological set of E. coli O157:H7 bovine strains establishes a role for repeat sequences and mobile genetic elements in genome diversification. BMC genomics 2020; 21:562 [View Article] [PubMed]
     [Google Scholar]
  74. Yoshii N, Ogura Y, Hayashi T, Ajiro T, Sameshima T. Pulsed-field gel electrophoresis profile changes resulting from spontaneous chromosomal deletions in enterohemorrhagic Escherichia coli O157:H7 during passage in cattle. Appl Environ Microbiol 2009; 75:5719–5726 [View Article] [PubMed]
     [Google Scholar]
  75. Scott AE, Timms AR, Connerton PL, Loc Carrillo C, Adzfa Radzum K. Genome dynamics of Campylobacter jejuni in response to bacteriophage predation. PLoS Pathog 2007; 3:e119 [View Article] [PubMed]
     [Google Scholar]
  76. Darling AE, Miklos I, Ragan MA. Dynamics of genome rearrangement in bacterial populations. PLoS Genet 2008; 4:e1000128 [View Article] [PubMed]
     [Google Scholar]
  77. Guerillot R, Kostoulias X, Donovan L, Li L, Carter GP. Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections. Proc Natl Acad Sci U S A 2019; 116:20135–20140 [View Article] [PubMed]
     [Google Scholar]
  78. Sun S, Ke R, Hughes D, Nilsson M, Andersson DI. Genome-wide detection of spontaneous chromosomal rearrangements in bacteria. PloS one 2012; 7:e42639
     [Google Scholar]
  79. Brandis G, Hughes D. The SNAP hypothesis: Chromosomal rearrangements could emerge from positive selection during niche adaptation. PLoS Genet 2020; 16:e1008615 [View Article] [PubMed]
     [Google Scholar]
  80. Lesterlin C, Pages C, Dubarry N, Dasgupta S, Cornet F. Asymmetry of chromosome replichores renders the DNA translocase activity of FTSK essential for cell division and cell shape maintenance in Escherichia coli. PLoS Genet 2008; 4:e1000288 [View Article]
     [Google Scholar]
  81. Ackermann M. A functional perspective on phenotypic heterogeneity in microorganisms. Nat Rev Microbiol 2015; 13:497–508 [View Article] [PubMed]
     [Google Scholar]
  82. Martins BM, Locke JC. Microbial individuality: how single-cell heterogeneity enables population level strategies. Curr Opin Microbiol 2015; 24:104–112S1369-5274(15)00004-1 [View Article] [PubMed]
     [Google Scholar]
  83. Grimbergen AJ, Siebring J, Solopova A, Kuipers OP. Microbial bet-hedging: the power of being different. Curr Opin Microbiol 2015; 25:67–72S1369-5274(15)00052-1 [View Article] [PubMed]
     [Google Scholar]
  84. Zhang Z, Du C, de Barsy F, Liem M, Liakopoulos A et al. Antibiotic production in Streptomyces is organized by a division of labor through terminal genomic differentiation. Sci Adv 2020; 6:eaay5781
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000682
Loading
Genome structural variation in Escherichia coli O157:H7
M Gen 7, 000682 (2021); https://doi.org/10.1099/mgen.0.000682
/content/journal/mgen/10.1099/mgen.0.000682
/content/journal/mgen/10.1099/mgen.0.000682
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error