1887

Abstract

Shiga toxin ()-producing O157 : H7 is a prominent food-borne pathogen. Symptoms in human infections range from asymptomatic to haemorrhagic colitis and haemolytic uraemic syndrome, and there is a need for methods that yield information that can be used to better predict clinical and epidemiological outcomes. IS is an insertion sequence notable for its prevalence and variable distribution in the chromosome of O157 : H7, which has been exploited for subtyping and strain characterization. In particular, IS distribution is closely aligned with the major phylogenetic lineages that are known to be distinctive in their genome structure and virulence potential. In the present study, a comprehensive subtyping method in which IS-typing was combined with genotyping was developed using a conventional PCR approach. This method consisted of a set of 32 markers based on the unique distribution of IS in the three major phylogenetic lineages of O157 : H7 and six additional markers to determine the genotype, a key virulence signature associated with each lineage. The analysis of IS loci variation with the 32 markers allowed us to determine the IS distribution profile (IDP), phylogenetic lineage and genetic relatedness of the 31 O157 : H7 strains examined. An association between IDP typing and genotype was observed. The use of both IDP and the genotype for strain characterization provided confirmative and complementary data in support of lineage placement of closely related strains. In addition, IS/ profiles were in agreement with strain segregation based on LSPA-6 (lineage-specific polymorphism assay) and PFGE subtyping, demonstrating its potential as a subtyping and strain tracking method.

Funding
This study was supported by the:
  • National Science Foundation (Award NSF-EF-0913042)
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2014-03-01
2024-12-03
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References

  1. Asadulghani M., Ogura Y., Ooka T., Itoh T., Sawaguchi A., Iguchi A., Nakayama K., Hayashi T. ( 2009). The defective prophage pool of Escherichia coli O157: prophage-prophage interactions potentiate horizontal transfer of virulence determinants. PLoS Pathog 5:e1000408 [View Article][PubMed]
    [Google Scholar]
  2. Bell B. P., Goldoft M., Griffin P. M., Davis M. A., Gordon D. C., Tarr P. I., Bartleson C. A., Lewis J. H., Barrett T. J. & other authors ( 1994). A multistate outbreak of Escherichia coli O157 : H7-associated bloody diarrhea and hemolytic uremic syndrome from hamburgers. The Washington experience. JAMA 272:1349–1353 [View Article][PubMed]
    [Google Scholar]
  3. Blattner F. R., Plunkett G. III, Bloch C. A., Perna N. T., Burland V., Riley M., Collado-Vides J., Glasner J. D., Rode C. K. & other authors ( 1997). The complete genome sequence of Escherichia coli K-12. Science 277:1453–1462 [View Article][PubMed]
    [Google Scholar]
  4. Boerlin P., McEwen S. A., Boerlin-Petzold F., Wilson J. B., Johnson R. P., Gyles C. L. ( 1999). Associations between virulence factors of Shiga toxin-producing Escherichia coli and disease in humans. J Clin Microbiol 37:497–503[PubMed]
    [Google Scholar]
  5. Chen C.-C., Hu S.-T. ( 2006). Two frameshift products involved in the transposition of bacterial insertion sequence IS629. . J Biol Chem 281:21617–21628 [View Article][PubMed]
    [Google Scholar]
  6. Darling A. E., Mau B., Perna N. T. ( 2010). ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5:e11147 [View Article][PubMed]
    [Google Scholar]
  7. Eppinger M., Mammel M. K., Leclerc J. E., Ravel J., Cebula T. A. ( 2011a). Genome signatures of Escherichia coli O157 : H7 isolates from the bovine host reservoir. Appl Environ Microbiol 77:2916–2925 [View Article][PubMed]
    [Google Scholar]
  8. Eppinger M., Mammel M. K., Leclerc J. E., Ravel J., Cebula T. A. ( 2011b). Genomic anatomy of Escherichia coli O157 : H7 outbreaks. Proc Natl Acad Sci U S A 108:20142–20147 [View Article][PubMed]
    [Google Scholar]
  9. Griffin P. M., Tauxe R. V. ( 1991). The epidemiology of infections caused by Escherichia coli O157 : H7, other enterohemorrhagic E. coli, and the associated hemolytic uremic syndrome. Epidemiol Rev 13:60–98[PubMed]
    [Google Scholar]
  10. Griffin P. M., Ostroff S. M., Tauxe R. V., Greene K. D., Wells J. G., Lewis J. H., Blake P. A. ( 1988). Illnesses associated with Escherichia coli O157 : H7 infections: a broad clinical spectrum. Ann Intern Med 109:705–712 [View Article][PubMed]
    [Google Scholar]
  11. Hayashi T., Makino K., Ohnishi M., Kurokawa K., Ishii K., Yokoyama K., Han C. G., Ohtsubo E., Nakayama K. & other authors ( 2002). Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 8:11–22 [CrossRef]
    [Google Scholar]
  12. Iguchi A., Iyoda S., Terajima J., Watanabe H., Osawa R. ( 2006). Spontaneous recombination between homologous prophage regions causes large-scale inversions within the Escherichia coli O157 : H7 chromosome. Gene 372:199–207 [View Article][PubMed]
    [Google Scholar]
  13. Jeong K. C., Hiki O., Kang M. Y., Park D., Kaspar C. W. ( 2013). Prevalent and persistent Escherichia coli O157 : H7 strains on farms are selected by bovine passage. Vet Microbiol 162:912–920 [View Article][PubMed]
    [Google Scholar]
  14. Johannes L., Römer W. ( 2010). Shiga toxins–from cell biology to biomedical applications. Nat Rev Microbiol 8:105–116[PubMed]
    [Google Scholar]
  15. Karmali M. A., Petric M., Steele B. T., Lim C. ( 1983). Sporadic cases of haemolytic-uraemic syndrome associated with faecal cytotoxin and cytotoxin-producing Escherichia coli in stools. Lancet 1:619–620 [View Article][PubMed]
    [Google Scholar]
  16. Kim J., Nietfeldt J., Benson A. K. ( 1999). Octamer-based genome scanning distinguishes a unique subpopulation of Escherichia coli O157 : H7 strains in cattle. Proc Natl Acad Sci U S A 96:13288–13293 [View Article][PubMed]
    [Google Scholar]
  17. Krzywinski M., Schein J., Birol I., Connors J., Gascoyne R., Horsman D., Jones S. J., Marra M. A. ( 2009). Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645 [View Article][PubMed]
    [Google Scholar]
  18. Kudva I. T., Evans P. S., Perna N. T., Barrett T. J., Ausubel F. M., Blattner F. R., Calderwood S. B. ( 2002). Strains of Escherichia coli O157 : H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms. J Bacteriol 184:1873–1879 [View Article][PubMed]
    [Google Scholar]
  19. Kulasekara B. R., Jacobs M., Zhou Y., Wu Z., Sims E., Saenphimmachak C., Rohmer L., Ritchie J. M., Radey M. & other authors ( 2009). Analysis of the genome of the Escherichia coli O157 : H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence. Infect Immun 77:3713–3721 [View Article][PubMed]
    [Google Scholar]
  20. Kusumoto M., Nishiya Y., Kawamura Y., Shinagawa K. ( 1999). Identification of an insertion sequence, IS1203 variant, in a Shiga toxin 2 gene of Escherichia coli 0157:H7. J Biosci Bioeng 87:93–96 [CrossRef]
    [Google Scholar]
  21. Kusumoto M., Ooka T., Nishiya Y., Ogura Y., Saito T., Sekine Y., Iwata T., Akiba M., Hayashi T. ( 2011). Insertion sequence-excision enhancer removes transposable elements from bacterial genomes and induces various genomic deletions. Nat Commun 2:152 [View Article][PubMed]
    [Google Scholar]
  22. Laing C., Pegg C., Yawney D., Ziebell K., Steele M., Johnson R., Thomas J. E., Taboada E. N., Zhang Y., Gannon V. P. J. ( 2008). Rapid determination of Escherichia coli O157 : H7 lineage types and molecular subtypes by using comparative genomic fingerprinting. Appl Environ Microbiol 74:6606–6615 [View Article][PubMed]
    [Google Scholar]
  23. Laing C. R., Buchanan C., Taboada E. N., Zhang Y., Karmali M. A., Thomas J. E., Gannon V. P. ( 2009). In silico genomic analyses reveal three distinct lineages of Escherichia coli O157 : H7, one of which is associated with hyper-virulence. BMC Genomics 10:287 [View Article][PubMed]
    [Google Scholar]
  24. Lee M., Kaspar C. W., Brosch R., Shere J., Luchansky J. B. ( 1996). Genomic analysis using pulsed-field gel electrophoresis of Escherichia coli 0157 : H7 isolated from dairy calves during the United States national dairy heifer evaluation project (1991–1992). 48:223–230
    [Google Scholar]
  25. Manning S. D., Motiwala A. S., Springman A. C., Qi W., Lacher D. W., Ouellette L. M., Mladonicky J. M., Somsel P., Rudrik J. T. & other authors ( 2008). Variation in virulence among clades of Escherichia coli O157 : H7 associated with disease outbreaks. Proc Natl Acad Sci U S A 105:4868–4873 [View Article][PubMed]
    [Google Scholar]
  26. Matsutani S., Ohtsubo E. ( 1990). Complete sequence of IS629. . Nucleic Acids Res 18:1899 [View Article][PubMed]
    [Google Scholar]
  27. Obrig T. G. ( 2010). Escherichia coli Shiga toxin mechanisms of action in renal disease. Toxins (Basel) 2:2769–2794 [View Article][PubMed]
    [Google Scholar]
  28. Ohnishi M., Terajima J., Kurokawa K., Nakayama K., Murata T., Tamura K., Ogura Y., Watanabe H., Hayashi T. ( 2002). Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning. Proc Natl Acad Sci U S A 99:17043–17048 [View Article][PubMed]
    [Google Scholar]
  29. Ooka T., Ogura Y., Asadulghani M., Ohnishi M., Nakayama K., Terajima J., Watanabe H., Hayashi T. ( 2009a). 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 19:1809–1816 [View Article][PubMed]
    [Google Scholar]
  30. Ooka T., Terajima J., Kusumoto M., Iguchi A., Kurokawa K., Ogura Y., Asadulghani M., Nakayama K., Murase K. & other authors ( 2009b). Development of a multiplex PCR-based rapid typing method for enterohemorrhagic Escherichia coli O157 strains. J Clin Microbiol 47:2888–2894 [View Article][PubMed]
    [Google Scholar]
  31. Park D., Stanton E., Ciezki K., Parrell D., Bozile M., Pike D., Forst S. A., Jeong K. C., Ivanek R. & other authors ( 2013). Evolution of the Stx2-encoding prophage in persistent bovine Escherichia coli O157 : H7 strains. Appl Environ Microbiol 79:1563–1572 [View Article][PubMed]
    [Google Scholar]
  32. Perna N. T., Plunkett G. III, Burland V., Mau B., Glasner J. D., Rose D. J., Mayhew G. F., Evans P. S., Gregor J. & other authors ( 2001). Genome sequence of enterohaemorrhagic Escherichia coli O157 : H7. Nature 409:529–533 [View Article][PubMed]
    [Google Scholar]
  33. Rangel J. M., Sparling P. H., Crowe C., Griffin P. M., Swerdlow D. L. ( 2005). Epidemiology of Escherichia coli O157 : H7 outbreaks, United States, 1982-2002. Emerg Infect Dis 11:603–609 [View Article][PubMed]
    [Google Scholar]
  34. Riley L. W., Remis R. S., Helgerson S. D., McGee H. B., Wells J. G., Davis B. R., Hebert R. J., Olcott E. S., Johnson L. M. & other authors ( 1983). Hemorrhagic colitis associated with a rare Escherichia coli serotype. N Engl J Med 308:681–685 [View Article][PubMed]
    [Google Scholar]
  35. Rump L. V., Fischer M., Gonzalez-Escalona N. ( 2011a). Prevalence, distribution and evolutionary significance of the IS629 insertion element in the stepwise emergence of Escherichia coli O157 : H7. BMC Microbiol 11:133 [View Article][PubMed]
    [Google Scholar]
  36. Rump L. V., Fischer M., González-Escalona N. ( 2011b). Different IS629 transposition frequencies exhibited by Escherichia coli O157 : H7 strains in the stepwise evolutionary model. Appl Environ Microbiol 77:5030–5033 [View Article][PubMed]
    [Google Scholar]
  37. Shere J. A., Bartlett K. J., Kaspar C. W. ( 1998). Longitudinal study of Escherichia coli O157 : H7 dissemination on four dairy farms in Wisconsin. Appl Environ Microbiol 64:1390–1399[PubMed]
    [Google Scholar]
  38. Shringi S., García A., Lahmers K. K., Potter K. A., Muthupalani S., Swennes A. G., Hovde C. J., Call D. R., Fox J. G., Besser T. E. ( 2012). Differential virulence of clinical and bovine-biased enterohemorrhagic Escherichia coli O157 : H7 genotypes in piglet and Dutch belted rabbit models. Infect Immun 80:369–380 [View Article][PubMed]
    [Google Scholar]
  39. Steele M., Ziebell K., Zhang Y., Benson A., Johnson R., Laing C., Taboada E., Gannon V. ( 2009). Genomic regions conserved in lineage II Escherichia coli O157:H7 strains. Appl Environ Microbiol 75:3271–3280 [View Article][PubMed]
    [Google Scholar]
  40. Strauch E., Schaudinn C., Beutin L. ( 2004). First-time isolation and characterization of a bacteriophage encoding the Shiga toxin 2c variant, which is globally spread in strains of Escherichia coli O157. Infect Immun 72:7030–7039 [View Article][PubMed]
    [Google Scholar]
  41. Strauch E., Hammerl J. A., Konietzny A., Schneiker-Bekel S., Arnold W., Goesmann A., Pühler A., Beutin L. ( 2008). Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157 : H7. Infect Immun 76:5466–5477 [View Article][PubMed]
    [Google Scholar]
  42. Suzuki M., Matsumoto M., Hata M., Takahashi M., Sakae K. ( 2004). Development of a rapid PCR method using the insertion sequence IS1203 for genotyping Shiga toxin-producing Escherichia coli O157. J Clin Microbiol 42:5462–5466 [View Article][PubMed]
    [Google Scholar]
  43. Vallenet D., Labarre L., Rouy Z., Barbe V., Bocs S., Cruveiller S., Lajus A., Pascal G., Scarpelli C., Médigue C. ( 2006). MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34:53–65 [View Article][PubMed]
    [Google Scholar]
  44. Vanaja S. K., Springman A. C., Besser T. E., Whittam T. S., Manning S. D. ( 2010). Differential expression of virulence and stress fitness genes between Escherichia coli O157 : H7 strains with clinical or bovine-biased genotypes. Appl Environ Microbiol 76:60–68 [View Article][PubMed]
    [Google Scholar]
  45. Vogt R. L., Dippold L. ( 2005). Escherichia coli O157 : H7 outbreak associated with consumption of ground beef, June-July 2002. Public Health Rep 120:174–178[PubMed]
    [Google Scholar]
  46. Wachsmuth I. K., Griffin P. M., Wells J. G. ( 1991). Escherichia coli O157 : H7, a cause of hemorrhagic colitis and hemolytic uremic syndrome. Acta Paediatr Jpn 33:603–612 [View Article][PubMed]
    [Google Scholar]
  47. Yang Z., Kovar J., Kim J., Nietfeldt J., Smith D. R., Moxley R. A., Olson M. E., Fey P. D., Benson A. K. ( 2004). Identification of common subpopulations of non-sorbitol-fermenting, β-glucuronidase-negative Escherichia coli O157 : H7 from bovine production environments and human clinical samples. Appl Environ Microbiol 70:6846–6854 [View Article][PubMed]
    [Google Scholar]
  48. Yokoyama E., Hashimoto R., Etoh Y., Ichihara S., Horikawa K., Uchimura M. ( 2011). Biased distribution of IS629 among strains in different lineages of enterohemorrhagic Escherichia coli serovar O157. Infect Genet Evol 11:78–82 [View Article][PubMed]
    [Google Scholar]
  49. Young R., Bläsi U. ( 1995). Holins: form and function in bacteriophage lysis. FEMS Microbiol Rev 17:191–205 [View Article][PubMed]
    [Google Scholar]
  50. Zhang Y., Laing C., Steele M., Ziebell K., Johnson R., Benson A. K., Taboada E., Gannon V. P. J. ( 2007). Genome evolution in major Escherichia coli O157 : H7 lineages. BMC Genomics 8:121 [View Article][PubMed]
    [Google Scholar]
  51. Zhang Y., Laing C., Zhang Z., Hallewell J., You C., Ziebell K., Johnson R. P., Kropinski A. M., Thomas J. E. & other authors ( 2010). Lineage and host source are both correlated with levels of Shiga toxin 2 production by Escherichia coli O157 : H7 strains. Appl Environ Microbiol 76:474–482 [View Article][PubMed]
    [Google Scholar]
  52. Zhou Z., Li X., Liu B., Beutin L., Xu J., Ren Y., Feng L., Lan R., Reeves P. R., Wang L. ( 2010). Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PLoS ONE 5:e8700 [View Article][PubMed]
    [Google Scholar]
  53. Zhou Y., Liang Y., Lynch K. H., Dennis J. J., Wishart D. S. ( 2011). PHAST: a fast phage search tool. Nucleic Acids Res 39:Suppl. 2W347–W352 [View Article][PubMed]
    [Google Scholar]
  54. Ziebell K., Steele M., Zhang Y., Benson A., Taboada E. N., Laing C., McEwen S., Ciebin B., Johnson R., Gannon V. ( 2008). Genotypic characterization and prevalence of virulence factors among Canadian Escherichia coli O157 : H7 strains. Appl Environ Microbiol 74:4314–4323 [View Article][PubMed]
    [Google Scholar]
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