1887

Abstract

Optical maps for five representative clinical, food-borne and bovine-derived isolates from the 2006 O157 : H7 outbreak linked to fresh spinach in the United States showed a common set of 14 distinct chromosomal markers that define the outbreak strain. Partial 454 DNA sequencing was used to characterize the optically mapped chromosomal markers. The markers included insertions, deletions, substitutions and a simple single nucleotide polymorphism creating a HI site. The Shiga toxin gene profile of the spinach-associated outbreak isolates ( ) correlated with prophage insertions different from those in the prototypical EDL933 and Sakai reference strains ( ). The prophage occupying the chromosomal position in the spinach-associated outbreak isolates was similar to the EDL933 cryptic prophage V, but it lacked the gene. In EDL933, the genes are within prophage BP933-W at the chromosomal locus; this locus was unoccupied in the spinach outbreak isolates. Instead, the genes were found within a chimeric BP933-W-like prophage with a different integrase, inserted at the locus in the outbreak isolates. An extra set of Shiga toxin genes, , was found in the outbreak isolates within a prophage integrated at the locus. The optical maps of two additional clinical isolates from the outbreak showed a single, different prophage variation in each, suggesting that changes occurred in the source strain during the course of this widespread, multi-state outbreak.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2008/019026-0
2008-11-01
2019-12-12
Loading full text...

Full text loading...

/deliver/fulltext/micro/154/11/3518.html?itemId=/content/journal/micro/10.1099/mic.0.2008/019026-0&mimeType=html&fmt=ahah

References

  1. Bielaszewska, M., Köck, R., Friedrich, A. W., von Eiff, C., Zimmerhackl, L. B., Karch, H. & Mellmann, A. ( 2007a; ). Shiga toxin-mediated hemolytic uremic syndrome: time to change the diagnostic paradigm? PLoS ONE 2, e1024 [CrossRef]
    [Google Scholar]
  2. Bielaszewska, M., Prager, R., Köck, R., Mellmann, A., Zhang, W., Tschäpe, H., Tarr, P. I. & Karch, H. ( 2007b; ). Shiga toxin gene loss and transfer in vitro and in vivo during enterohemorrhagic Escherichia coli O26 infection in humans. Appl Environ Microbiol 73, 3144–3150.[CrossRef]
    [Google Scholar]
  3. Brüssow, H., Canchaya, C. & Hardt, W.-D. ( 2004; ). Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 68, 560–602.[CrossRef]
    [Google Scholar]
  4. CDC ( 2006; ). Ongoing multistate outbreak of Escherichia coli serotype O157 : H7 infections associated with consumption of fresh spinach – United States, September 2006. MMWR Morb Mortal Wkly Rep 55, 1045–1046.
    [Google Scholar]
  5. Chen, Q., Savarino, S. J. & Venkatesan, M. M. ( 2006; ). Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12. Microbiology 152, 1041–1054.[CrossRef]
    [Google Scholar]
  6. Cooley, M., Carychao, D., Crawford-Miksza, L., Jay, M. T., Myers, C., Rose, C., Keys, C., Farrar, J. & Mandrell, R. E. ( 2007; ). Incidence and tracking of Escherichia coli O157 : H7 in a major produce production region in California. PLoS ONE 14, e1159
    [Google Scholar]
  7. Eklund, M., Leino, K. & Siitonen, A. ( 2002; ). Clinical Escherichia coli strains carrying stx genes: stx variants and stx-positive virulence profiles. J Clin Microbiol 40, 4585–4593.[CrossRef]
    [Google Scholar]
  8. Feng, P. C., Monday, S. R., Lacher, D. W., Allison, L., Siitonen, A., Keys, C., Eklund, M., Nagano, H., Karch, H. & other authors ( 2007; ). Genetic diversity among clonal lineages within Escherichia coli O157 : H7 stepwise evolutionary model. Emerg Infect Dis 13, 1701–1706.[CrossRef]
    [Google Scholar]
  9. Friedrich, A. W., Bielaszewska, M., Zhang, W. L., Pulz, M., Kuczius, T., Ammon, A. & Karch, H. ( 2002; ). Escherichia coli harboring Shiga toxin 2 gene variants: frequency and association with clinical symptoms. J Infect Dis 185, 74–84.[CrossRef]
    [Google Scholar]
  10. Fukiya, S., Mizoguchi, H., Tobe, T. & Mori, H. ( 2004; ). Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray. J Bacteriol 186, 3911–3921.[CrossRef]
    [Google Scholar]
  11. 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.
    [Google Scholar]
  12. Hayashi, T., Makino, K., Ohnishi, M., Kurokawa, K., Ishii, K., Yokoyama, K., Han, C. G., Ohtsubo, E., Nakayama, K. & other authors ( 2001; ). 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]
  13. Herold, S., Karch, H. & Schmidt, H. ( 2004; ). Shiga toxin-encoding bacteriophages – genomes in motion. Int J Med Microbiol 294, 115–121.[CrossRef]
    [Google Scholar]
  14. 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.[CrossRef]
    [Google Scholar]
  15. Jackson, S. A., Mammel, M. K., Patel, I. R., Mays, T., Albert, T. J., LeClerc, J. E. & Cebula, T. A. ( 2007; ). Interrogating genomic diversity of Escherichia coli O157 : H7 using DNA tiling arrays. Forensic Sci Int 168, 183–199.[CrossRef]
    [Google Scholar]
  16. Johansen, B. K., Wasteson, Y., Granum, P. E. & Brynestad, S. ( 2001; ). Mosaic structure of Shiga-toxin-2-encoding phages isolated from Escherichia coli O157 : H7 indicates frequent gene exchange between lambdoid phage genomes. Microbiology 147, 1929–1936.
    [Google Scholar]
  17. Karch, H., Friedrich, A. W., Gerber, A., Zimmerhackl, L. B., Schmidt, M. A. & Bielaszewska, M. ( 2006; ). New aspects in the pathogenesis of enteropathic hemolytic uremic syndrome. Semin Thromb Hemost 32, 105–112.[CrossRef]
    [Google Scholar]
  18. Kohler, B., Karch, H. & Schmidt, H. ( 2000; ). Antibacterials that are used as growth promoters in animal husbandry can affect the release of Shiga-toxin-2-converting bacteriophages and Shiga toxin 2 from Escherichia coli strains. Microbiology 146, 1085–1090.
    [Google Scholar]
  19. Koitabashi, T., Vuddhakul, V., Radu, S., Morigaki, T., Asai, N., Nakaguchi, Y. & Nishibuchi, M. ( 2006; ). Genetic characterization of Escherichia coli O157 : H7 strains carrying the stx2 gene but not producing Shiga toxin 2. Microbiol Immunol 50, 135–148.[CrossRef]
    [Google Scholar]
  20. Kotewicz, M. L., Jackson, S. A., LeClerc, J. E. & Cebula, T. A. ( 2007; ). Optical maps distinguish individual strains of Escherichia coli O157 : H7. Microbiology 153, 1720–1733.[CrossRef]
    [Google Scholar]
  21. Kudva, I. T., Evans, P. S., Perna, N. T., Barrett, T. J., DeCastro, G. J., Ausubel, F. M., Blattner, F. R. & Calderwood, S. B. ( 2002a; ). Polymorphic amplified typing sequences provide a novel approach to Escherichia coli O157 : H7 strain typing. J Clin Microbiol 40, 1152–1159.[CrossRef]
    [Google Scholar]
  22. Kudva, I. T., Evans, P. S., Perna, N. T., Barrett, T. J., Ausubel, F. M., Blattner, F. R. & Calderwood, S. B. ( 2002b; ). Strains of Escherichia coli O157 : H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms. J Bacteriol 184, 1873–1879.[CrossRef]
    [Google Scholar]
  23. Lim, A., Dimalanta, E. T., Potamousis, K. D., Yen, G., Apodoca, J., Tao, C., Lin, J., Qi, R., Skiadas, J. & other authors ( 2001; ). Shotgun optical maps of the whole Escherichia coli O157 : H7 genome. Genome Res 11, 1584–1593.[CrossRef]
    [Google Scholar]
  24. 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.[CrossRef]
    [Google Scholar]
  25. Ogura, Y., Kurokawa, K., Ooka, T., Tashiro, K., Tobe, T., Ohnishi, M., Nakayama, K., Morimoto, T., Terajima, J. & other authors ( 2006; ). Complexity of the genomic diversity in enterohemorrhagic Escherichia coli O157 revealed by the combinational use of the O157 Sakai oligo DNA microarray and the whole genome PCR scanning. DNA Res 13, 3–14.[CrossRef]
    [Google Scholar]
  26. 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.[CrossRef]
    [Google Scholar]
  27. Orth, D., Grif, K., Khan, A. B., Naim, A., Dierich, M. P. & Würzner, R. ( 2007; ). The Shiga toxin genotype rather than the amount of Shiga toxin or the cytotoxicity of Shiga toxin in vitro correlates with the appearance of the hemolytic uremic syndrome. Diagn Microbiol Infect Dis 59, 235–242.[CrossRef]
    [Google Scholar]
  28. 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 (Erratum in Nature 410, 240).[CrossRef]
    [Google Scholar]
  29. Ribot, E. M., Fair, M. A., Gautom, R., Cameron, D. N., Hunter, S. B., Swaminathan, B. & Barrett, T. J. ( 2006; ). Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157 : H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog Dis 3, 59–67.[CrossRef]
    [Google Scholar]
  30. Ritchie, J. M., Wagner, P. L., Acheson, D. W. & Waldor, M. K. ( 2003; ). Comparison of Shiga toxin production by hemolytic-uremic syndrome-associated and bovine-associated Shiga toxin-producing Escherichia coli isolates. Appl Environ Microbiol 69, 1059–1066.[CrossRef]
    [Google Scholar]
  31. Serra-Moreno, R., Jofre, J. & Muniesa, M. ( 2007; ). Insertion site occupancy by stx2 bacteriophages depends on the locus availability of the host strain chromosome. J Bacteriol 189, 6645–6654.[CrossRef]
    [Google Scholar]
  32. Shaikh, N. & Tarr, P. I. ( 2003; ). Escherichia coli O157 : H7 Shiga toxin-encoding bacteriophages: integrations, excisions, truncations, and evolutionary implications. J Bacteriol 185, 3596–3605.[CrossRef]
    [Google Scholar]
  33. Shima, K., Wu, Y., Sugimoto, N., Asakura, M., Nishimura, K. & Yamasaki, S. ( 2006; ). Comparison of a PCR-restriction fragment length polymorphism (PCR-RFLP) assay to pulsed-field gel electrophoresis to determine the effect of repeated subculture and prolonged storage on RFLP patterns of Shiga toxin-producing Escherichia coli O157 : H7. J Clin Microbiol 44, 3963–3968.[CrossRef]
    [Google Scholar]
  34. Su, C. & Brandt, L. J. ( 1995; ). Escherichia coli O157 : H7 infection in humans. Ann Intern Med 123, 698–714.[CrossRef]
    [Google Scholar]
  35. Wick, L. M., Qi, W., Lacher, D. W. & Whittam, T. S. ( 2005; ). Evolution of genomic content in the stepwise emergence of Escherichia coli O157 : H7. J Bacteriol 187, 1783–1791.[CrossRef]
    [Google Scholar]
  36. Zhang, W., Bielaszewska, M., Friedrich, A. W., Kuczius, T. & Karch, H. ( 2005; ). Transcriptional analysis of genes encoding Shiga toxin 2 and its variants in Escherichia coli. Appl Environ Microbiol 71, 558–561.[CrossRef]
    [Google Scholar]
  37. Zhang, W., Qi, W., Albert, T. J., Motiwala, A. S., Alland, D., Hyytia-Trees, E. K., Ribot, E. M., Fields, P. I., Whittam, T. S. & Swaminathan, B. ( 2006; ). Probing genomic diversity and evolution of Escherichia coli O157 by single-nucleotide polymorphisms. Genome Res 16, 757–767.[CrossRef]
    [Google Scholar]
  38. Zhou, S., Kile, A., Bechner, M., Place, M., Kvikstad, E., Deng, W., Wei, J., Severin, J., Runnheim, R. & other authors ( 2004; ). Single-molecule approach to bacterial genomic comparisons via optical mapping. J Bacteriol 186, 7773–7782.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2008/019026-0
Loading
/content/journal/micro/10.1099/mic.0.2008/019026-0
Loading

Data & Media loading...

Supplements

Chromosomal markers 1 and 2 in the 2006 US spinach-associated outbreak strain, insertion sequence RFLP and RFLP in prophage H/I. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (269 kb) Chromosomal markers 3 and 9 in the 2006 US spinach-associated outbreak strain, a P4-like prophage and R prophage. Aligned fragments are highlighted in green; white fragments indicate non-alignment. As the R prophage is found within an inversion in EDL933, the EDL933 segment was inverted to show the alignment; note the reverse in the Mbp coordinates for EDL933. [ PDF] (288 kb) Chromosomal markers 13 and 14 in the 2006 US spinach-associated outbreak strain, a non-insertion of a Mu-like prophage found in Sakai and an 11 kb phage scar. Sequence data demonstrates the 11 kb insertion occurred relative to the BamHI EDL933 restriction fragment at 5.150 Mbp. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (265 kb) Chromosomal markers in clinical variants of 2006 US spinach-associated outbreak, isolate EC4076, containing deletion of prophage T, and isolate EC4115, containing a 41 kb insertion within the V-like prophage at chromosome locus yehV. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (387 kb)

PDF

Chromosomal markers 1 and 2 in the 2006 US spinach-associated outbreak strain, insertion sequence RFLP and RFLP in prophage H/I. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (269 kb) Chromosomal markers 3 and 9 in the 2006 US spinach-associated outbreak strain, a P4-like prophage and R prophage. Aligned fragments are highlighted in green; white fragments indicate non-alignment. As the R prophage is found within an inversion in EDL933, the EDL933 segment was inverted to show the alignment; note the reverse in the Mbp coordinates for EDL933. [ PDF] (288 kb) Chromosomal markers 13 and 14 in the 2006 US spinach-associated outbreak strain, a non-insertion of a Mu-like prophage found in Sakai and an 11 kb phage scar. Sequence data demonstrates the 11 kb insertion occurred relative to the BamHI EDL933 restriction fragment at 5.150 Mbp. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (265 kb) Chromosomal markers in clinical variants of 2006 US spinach-associated outbreak, isolate EC4076, containing deletion of prophage T, and isolate EC4115, containing a 41 kb insertion within the V-like prophage at chromosome locus yehV. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (387 kb)

PDF

Chromosomal markers 1 and 2 in the 2006 US spinach-associated outbreak strain, insertion sequence RFLP and RFLP in prophage H/I. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (269 kb) Chromosomal markers 3 and 9 in the 2006 US spinach-associated outbreak strain, a P4-like prophage and R prophage. Aligned fragments are highlighted in green; white fragments indicate non-alignment. As the R prophage is found within an inversion in EDL933, the EDL933 segment was inverted to show the alignment; note the reverse in the Mbp coordinates for EDL933. [ PDF] (288 kb) Chromosomal markers 13 and 14 in the 2006 US spinach-associated outbreak strain, a non-insertion of a Mu-like prophage found in Sakai and an 11 kb phage scar. Sequence data demonstrates the 11 kb insertion occurred relative to the BamHI EDL933 restriction fragment at 5.150 Mbp. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (265 kb) Chromosomal markers in clinical variants of 2006 US spinach-associated outbreak, isolate EC4076, containing deletion of prophage T, and isolate EC4115, containing a 41 kb insertion within the V-like prophage at chromosome locus yehV. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (387 kb)

PDF

Chromosomal markers 1 and 2 in the 2006 US spinach-associated outbreak strain, insertion sequence RFLP and RFLP in prophage H/I. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (269 kb) Chromosomal markers 3 and 9 in the 2006 US spinach-associated outbreak strain, a P4-like prophage and R prophage. Aligned fragments are highlighted in green; white fragments indicate non-alignment. As the R prophage is found within an inversion in EDL933, the EDL933 segment was inverted to show the alignment; note the reverse in the Mbp coordinates for EDL933. [ PDF] (288 kb) Chromosomal markers 13 and 14 in the 2006 US spinach-associated outbreak strain, a non-insertion of a Mu-like prophage found in Sakai and an 11 kb phage scar. Sequence data demonstrates the 11 kb insertion occurred relative to the BamHI EDL933 restriction fragment at 5.150 Mbp. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (265 kb) Chromosomal markers in clinical variants of 2006 US spinach-associated outbreak, isolate EC4076, containing deletion of prophage T, and isolate EC4115, containing a 41 kb insertion within the V-like prophage at chromosome locus yehV. Aligned fragments are highlighted in green; white fragments indicate non-alignment. [ PDF] (387 kb)

PDF
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