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Microbial Genomics logo Microbial Genomics

Volume 7, Issue 12

The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing O121:H19 Open Access

Abstract

Shiga toxin (Stx)-producing (STEC) are foodborne pathogens causing serious diseases, such as haemorrhagic colitis and haemolytic uraemic syndrome. Although O157:H7 STEC strains have been the most prevalent, incidences of STEC infections by several other serotypes have recently increased. O121:H19 STEC is one of these major non-O157 STECs, but systematic whole genome sequence (WGS) analyses have not yet been conducted on this STEC. Here, we performed a global WGS analysis of 638 O121:H19 strains, including 143 sequenced in this study, and a detailed comparison of 11 complete genomes, including four obtained in this study. By serotype-wide WGS analysis, we found that O121:H19 strains were divided into four lineages, including major and second major lineages (named L1 and L3, respectively), and that the locus of enterocyte effacement (LEE) encoding a type III secretion system (T3SS) was acquired by the common ancestor of O121:H19. Analyses of 11 complete genomes belonging to L1 or L3 revealed remarkable interlineage differences in the prophage pool and prophage-encoded T3SS effector repertoire, independent acquisition of virulence plasmids by the two lineages, and high conservation in the prophage repertoire, including that for Stx2a phages in lineage L1. Further sequence determination of complete Stx2a phage genomes of 49 strains confirmed that Stx2a phages in lineage L1 are highly conserved short-tailed phages, while those in lineage L3 are long-tailed lambda-like phages with notable genomic diversity, suggesting that an Stx2a phage was acquired by the common ancestor of L1 and has been stably maintained. Consistent with these genomic features of Stx2a phages, most lineage L1 strains produced much higher levels of Stx2a than lineage L3 strains. Altogether, this study provides a global phylogenetic overview of O121:H19 STEC and shows the interlineage genomic differences and the highly conserved genomic features of the major lineage within this serotype of STEC.

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  • Accepted:
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Keyword(s): bacteriophage , comparative genomics , phylogenetic analysis , plasmid , population structure and Shiga toxin-producing Escherichia coli O121:H19
Funding
This study was supported by the:
  • the Japan Society for the Promotion of Science (Award 21K07006)
    • Principal Award Recipient: KeijiNakamura
  • the Japan Society for the Promotion of Science (Award 18K07116)
    • Principal Award Recipient: KeijiNakamura
  • Health, Labour and Welfare Sciences Research Grants, Research on Food Safety Program (Award JPMH20KA1004)
    • Principal Award Recipient: TetsuyaHayashi
  • Japan Agency for Medical Research and Development (Award 21fk0108611h0501)
    • Principal Award Recipient: TetsuyaHayashi
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2021-12-08
2026-02-16

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References

  1. Tarr PI, Gordon CA, Chandler WL. Shiga-toxin-producing Escherichia coli and haemolytic uraemic syndrome. Lancet 2005; 365:1073–1086 [View Article] [PubMed]
     [Google Scholar]
  2. Centers for Disease Control and Prevention National Shiga toxin-producing Escherichia coli (STEC) surveillance annual report, 2016 US Department of Health and Human Services, CDC: 2018
     [Google Scholar]
  3. European Food Safety Authority and European Centre for Disease Prevention and Control The European union one health 2018 zoonoses report. EFSA J 2019; 17:5926
     [Google Scholar]
  4. Croxen MA, Law RJ, Scholz R, Keeney KM, Wlodarska M et al. Recent advances in understanding enteric pathogenic Escherichia coli. Clin Microbiol Rev 2013; 26:822–880 [View Article] [PubMed]
     [Google Scholar]
  5. Boerlin P, McEwen SA, Boerlin-Petzold F, Wilson JB, Johnson RP et al. Associations between virulence factors of Shiga toxin-producing Escherichia coli and disease in humans. J Clin Microbiol 1999; 37:497–503 [View Article] [PubMed]
     [Google Scholar]
  6. Deng W, Puente JL, Gruenheid S, Li Y, Vallance BA et al. Dissecting virulence: systematic and functional analyses of a pathogenicity island. Proc Natl Acad Sci U S A 2004; 101:3597–3602 [View Article] [PubMed]
     [Google Scholar]
  7. Tobe T, Beatson SA, Taniguchi H, Abe H, Bailey CM et al. An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Proc Natl Acad Sci U S A 2006; 103:14941–14946 [View Article] [PubMed]
     [Google Scholar]
  8. Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M et al. Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci U S A 2009; 106:17939–17944 [View Article] [PubMed]
     [Google Scholar]
  9. Abu-Ali GS, Lacher DW, Wick LM, Qi W, Whittam TS. Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex. BMC Genomics 2009; 10:296 [View Article] [PubMed]
     [Google Scholar]
  10. Reid SD, Herbelin CJ, Bumbaugh AC, Selander RK, Whittam TS. Parallel evolution of virulence in pathogenic Escherichia coli. Nature 2000; 406:64–67 [View Article] [PubMed]
     [Google Scholar]
  11. Ohnishi M, Terajima J, Kurokawa K, Nakayama K, Murata T et al. Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning. Proc Natl Acad Sci U S A 2002; 99:17043–17048 [View Article] [PubMed]
     [Google Scholar]
  12. Ogura Y, Kurokawa K, Ooka T, Tashiro K, Tobe T et al. Complexity of the genomic diversity in enterohemorrhagic Escherichia coli O157 revealed by the combinational use of the O157 Sakai OligoDNA microarray and the whole genome PCR scanning. DNA Res 2006; 13:3–14 [View Article] [PubMed]
     [Google Scholar]
  13. Ogura Y, Ooka T, Terajima J, Nougayrède J-P et al. Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes. Genome Biol 2007; 8:1 [View Article] [PubMed]
     [Google Scholar]
  14. Shaaban S, Cowley LA, McAteer SP, Jenkins C, Dallman TJ et al. Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing. Microb Genom 2016; 2:e000096 [View Article] [PubMed]
     [Google Scholar]
  15. Asadulghani M, Ogura Y, Ooka T, Itoh T, Sawaguchi A et al. 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]
  16. Ogura Y, Gotoh Y, Itoh T, Sato MP, Seto K et al. Population structure of Escherichia coli O26: H11 with recent and repeated stx2 acquisition in multiple lineages. Microb Genom 2017; 3:e000141 [View Article]
     [Google Scholar]
  17. Ishijima N, Lee K-I, Kuwahara T, Nakayama-Imaohji H, Yoneda S et al. Identification of a new virulent clade in enterohemorrhagic Escherichia coli O26:H11/H- sequence type 29. Sci Rep 2017; 7:43136 [View Article] [PubMed]
     [Google Scholar]
  18. Bielaszewska M, Mellmann A, Bletz S, Zhang W, Köck R et al. Enterohemorrhagic Escherichia coli O26:H11/H-: a new virulent clone emerges in Europe. Clin Infect Dis 2013; 56:1373–1381 [View Article] [PubMed]
     [Google Scholar]
  19. Ison SA, Delannoy S, Bugarel M, Nagaraja TG, Renter DG et al. Targeted amplicon sequencing for single-nucleotide-polymorphism genotyping of attaching and effacing Escherichia coli O26:H11 cattle strains via a high-throughput library preparation technique. Appl Environ Microbiol 2016; 82:640–649 [View Article] [PubMed]
     [Google Scholar]
  20. Zhang WL, Bielaszewska M, Liesegang A, Tschäpe H, Schmidt H et al. Molecular characteristics and epidemiological significance of Shiga toxin-producing Escherichia coli O26 strains. J Clin Microbiol 2000; 38:2134–2140 [View Article] [PubMed]
     [Google Scholar]
  21. Ogura Y, Mondal SI, Islam MR, Mako T, Arisawa K et al. The shiga toxin 2 production level in Escherichia coli O157:H7 is correlated with the subtypes of toxin-encoding phage. Sci Rep 2015; 5: [View Article]
     [Google Scholar]
  22. Brooks JT, Sowers EG, Wells JG, Greene KD, Griffin PM et al. Non-O157 Shiga toxin-producing Escherichia coli infections in the United States, 1983-2002. J Infect Dis 2005; 192:1422–1429 [View Article] [PubMed]
     [Google Scholar]
  23. McCarthy TA, Barrett NL, Hadler JL, Salsbury B, Howard RT et al. Hemolytic-uremic syndrome and Escherichia coli O121 at a lake in connecticut, 1999. Pediatrics 2001; 108:e59 [View Article] [PubMed]
     [Google Scholar]
  24. Crowe SJ, Bottichio L, Shade LN, Whitney BM, Corral N et al. Shiga toxin-producing E. coli infections associated with flour. N Engl J Med 2017; 377:2036–2043 [View Article] [PubMed]
     [Google Scholar]
  25. National institute of infectious disease Infectious agents surveillance report (iasr). NIID 2021; 42:87–90
     [Google Scholar]
  26. Käppeli U, Hächler H, Giezendanner N, Beutin L, Stephan R. Human infections with non-O157 Shiga toxin-producing Escherichia coli, Switzerland, 2000-2009. Emerg Infect Dis 2011; 17:180–185 [View Article] [PubMed]
     [Google Scholar]
  27. Lee K, Morita-Ishihara T, Iyoda S, Ogura Y, Hayashi T et al. A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121. Front Microbiol 2017; 8:1–9 [View Article]
     [Google Scholar]
  28. Kikuchi K, Lee K, Ueno H, Tomari K, Kobori S et al. Enterohaemorrhagic Escherichia coli O121:H19 acquired an extended-spectrum β-lactamase gene during the development of an outbreak in two nurseries. Microb Genom 2019; 5:e000278 [View Article] [PubMed]
     [Google Scholar]
  29. Wirth T, Falush D, Lan R, Colles F, Mensa P et al. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 2006; 60:1136–1151 [View Article] [PubMed]
     [Google Scholar]
  30. Carter MQ, Tan ZF, Pham A, Carychao DK, Cooley MB. A clonal Shiga toxin-producing Escherichia coli O121:H19 population exhibits diverse carbon utilization patterns. Foodborne Pathog Dis 2019; 16:384–393 [View Article] [PubMed]
     [Google Scholar]
  31. Zhou Z, Alikhan N-F, Mohamed K, Fan Y. Agama Study Group et al. The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res 2020; 30:138–152 [View Article] [PubMed]
     [Google Scholar]
  32. Nakamura K, Murase K, Sato MP, Toyoda A, Itoh T et al. Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28. Microb Genom 2020; 6:e000323 [View Article] [PubMed]
     [Google Scholar]
  33. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  34. Nakamura K, Ogura Y, Gotoh Y, Hayashi T. Prophages integrating into prophages: a mechanism to accumulate type III secretion effector genes and duplicate Shiga toxin-encoding prophages in Escherichia coli. PLoS Pathog 2021; 17:e1009073 [View Article] [PubMed]
     [Google Scholar]
  35. Joensen KG, Tetzschner AMM, Iguchi A, Aarestrup FM, Scheutz F. Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data. J Clin Microbiol 2015; 53:2410–2426 [View Article] [PubMed]
     [Google Scholar]
  36. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008; 18:1851–1858 [View Article] [PubMed]
     [Google Scholar]
  37. Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom 2017; 3:e000132 [View Article] [PubMed]
     [Google Scholar]
  38. De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 2018; 34:2666–2669 [View Article] [PubMed]
     [Google Scholar]
  39. 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]
  40. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 2016; 35:173–184 [View Article] [PubMed]
     [Google Scholar]
  41. Ohtsubo Y, Ikeda-Ohtsubo W, Nagata Y, Tsuda M. GenomeMatcher: A graphical user interface for DNA sequence comparison. BMC Bioinformatics 2008; 9:1–9 [View Article]
     [Google Scholar]
  42. Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al. 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]
  43. 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]
  44. 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]
  45. Cheng L, Connor TR, Sirén J, Aanensen DM, Corander J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol Biol Evol 2013; 30:1224–1228 [View Article] [PubMed]
     [Google Scholar]
  46. 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]
     [Google Scholar]
  47. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
     [Google Scholar]
  48. Ooka T, Ogura Y, Katsura K, Seto K, Kobayashi H et al. Defining the genome features of Escherichia albertii, an emerging enteropathogen closely related to Escherichia coli. Genome Biol Evol 2015; 7:3170–3179 [View Article] [PubMed]
     [Google Scholar]
  49. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Research 2006; 34:D32–D36 [View Article]
     [Google Scholar]
  50. Ogura Y, Seto K, Morimoto Y, Nakamura K, Sato MP et al. Genomic Characterization of β-Glucuronidase–Positive Escherichia coli O157:H7 Producing Stx2a. Emerg Infect Dis 2018; 24:2219–2227 [View Article]
     [Google Scholar]
  51. Menardo F, Loiseau C, Brites D, Coscolla M, Gygli SM et al. Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC Bioinformatics 2018; 19:164 [View Article] [PubMed]
     [Google Scholar]
  52. Rambaut A, Lam TT, Max Carvalho L, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol 2016; 2:vew007 [View Article] [PubMed]
     [Google Scholar]
  53. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012; 29:1969–1973 [View Article] [PubMed]
     [Google Scholar]
  54. Robertson J, Lin J, Levett PN, Nadon C, Nash J et al. Complete genome sequence of an Escherichia coli O121:H19 strain from an outbreak in Canada associated with flour. Genome Announc 2018; 6:1–2 [View Article]
     [Google Scholar]
  55. Patel PN, Lindsey RL, Garcia-Toledo L, Rowe LA, Batra D et al. High-Quality Whole-Genome Sequences for 77 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing. Genome Announc 2018; 6:e00391-18 [View Article] [PubMed]
     [Google Scholar]
  56. Parker CT, Cooper KK, Huynh S, Smith TP, Bono JL et al. Genome sequences of eight shiga toxin-producing Escherichia coli strains isolated from a produce-growing region in California. Microbiol Resour Announc 2018; 7:e00807-18 [View Article] [PubMed]
     [Google Scholar]
  57. Tyson S, Peterson C-L, Olson A, Tyler S, Knox N et al. Eleven high-quality reference genome sequences and 360 draft assemblies of Shiga toxin-producing Escherichia coli isolates from human, food, animal, and environmental sources in Canada. Microbiol Resour Announc 2019; 8:1–17 [View Article]
     [Google Scholar]
  58. Lacher DW, Qi W, Bumbaugh AC, Hyma KE, Ouellette LM et al. EcMLST: an online database for multi locus sequence typing of pathogenic escherichia coli. In Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004 2004 IEEE computer society; 2004
     [Google Scholar]
  59. Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K et al. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 2001; 8:11–22 [View Article] [PubMed]
     [Google Scholar]
  60. Kusumoto M, Ooka T, Nishiya Y, Ogura Y, Saito T et al. Insertion sequence-excision enhancer removes transposable elements from bacterial genomes and induces various genomic deletions. Nat Commun 2011; 2:152 [View Article] [PubMed]
     [Google Scholar]
  61. Makendi C, Page AJ, Wren BW, Le Thi Phuong T, Clare S et al. A phylogenetic and phenotypic analysis of Salmonella enterica serovar Weltevreden, an emerging agent of diarrheal disease in tropical regions. PLoS Negl Trop Dis 2016; 10:e0004446 [View Article] [PubMed]
     [Google Scholar]
  62. Plunkett G, Rose DJ, Durfee TJ, Blattner FR. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J Bacteriol 1999; 181:1767–1778 [View Article] [PubMed]
     [Google Scholar]
  63. Tyler JS, Mills MJ, Friedman DI. The operator and early promoter region of the Shiga toxin type 2-encoding bacteriophage 933W and control of toxin expression. J Bacteriol 2004; 186:7670–7679 [View Article] [PubMed]
     [Google Scholar]
  64. Ohnishi M, Kurokawa K, Hayashi T. Diversification of Escherichia coli genomes: are bacteriophages the major contributors?. Trends Microbiol 2001; 9:481–485 [View Article] [PubMed]
     [Google Scholar]
/content/journal/mgen/10.1099/mgen.0.000716
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The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19
M Gen 7, 000716 (2021); https://doi.org/10.1099/mgen.0.000716
/content/journal/mgen/10.1099/mgen.0.000716
/content/journal/mgen/10.1099/mgen.0.000716
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