1887

Abstract

Optical maps of 11 O157 : H7 strains have been generated by the assembly of contiguous sets of restriction fragments across their entire 5.3 to 5.6 Mbp chromosomes. Each strain showed a distinct, highly individual configuration of 500–700 HI fragments, yielding a map resembling a DNA ‘bar code’. The accuracy of optical mapping was assessed by comparing directly the restriction maps of two wholly sequenced reference genomes of O157 : H7, i.e. EDL933 and the Sakai isolate (RIMD 0509952), with the optical maps of the same strains. The optical maps of nine other O157 : H7 strains were compared similarly, using the sequence-based maps of the Sakai and EDL933 strains as references. A total of 91 changes at 28 loci were positioned and sized; these included complex chromosomal inversions, insertions, deletions, substitutions, as well as a number of simple RFLPs. The optical maps defined unique genome landmarks in each of the strains and demonstrated the ability of optical mapping to distinguish and differentiate, at the individual level, strains of this important pathogen.

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2007-06-01
2024-03-28
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References

  1. Alokam S., Liu S. L., Said K., Sanderson K. E. 2002; Inversions over the terminus region in Salmonella and Escherichia coli : IS200s as the sites of homologous recombination inverting the chromosome of Salmonella enterica serovar typhi. J Bacteriol 184:6190–6197 [CrossRef]
    [Google Scholar]
  2. Bielaszewska M., Prager R., Zhang W., Friedrich A. W., Mellmann A., Tschape H., Karch H. 2006; Chromosomal dynamism in progeny of outbreak-related sorbitol-fermenting enterohemorrhagic Escherichia coli O157 : NM. Appl Environ Microbiol 72:1900–1909 [CrossRef]
    [Google Scholar]
  3. Brussow 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. Budowle B., Johnson M. D., Fraser C. M., Leighton T. J., Murch R. S., Chakraborty R. 2005; Genetic analysis and attribution of microbial forensics evidence. Crit Rev Microbiol 31:233–254 [CrossRef]
    [Google Scholar]
  5. Cai W., Jing J., Irvin B., Ohler L., Rose E., Shizuya H., Kim U. J., Simon M., Anantharaman T. other authors 1998; High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping. Proc Natl Acad Sci U S A 95:3390–3395 [CrossRef]
    [Google Scholar]
  6. Cebula T. A., Brown E. W., Jackson S. A., Mammel M. K., Mukherjee A., LeClerc J. E. 2005; Molecular applications for identifying microbial pathogens in the post-9/11 era. Expert Rev Mol Diagn 5:431–445 [CrossRef]
    [Google Scholar]
  7. 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]
  8. Feil E. J., Enright M. C. 2004; Analyses of clonality and the evolution of bacterial pathogens. Curr Opin Microbiol 7:308–313 [CrossRef]
    [Google Scholar]
  9. Foley S. L., Simjee S., Meng J., White D. G., McDermott P. F., Zhao S. 2004; Evaluation of molecular typing methods for Escherichia coli O157 : H7 isolates from cattle, food, and humans. J Food Prot 67:651–657
    [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. 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 [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. 2006; Interrogating genomic diversity of Escherichia coli O157 : H7 using DNA tiling arrays. Forensic Sci Int 2006 23: Epub ahead of print
    [Google Scholar]
  16. Kimmitt P. T., Harwood C. R., Barer M. R. 2000; Toxin gene expression by shiga toxin-producing Escherichia coli : the role of antibiotics and the bacterial SOS response. Emerg Infect Dis 6:458–465 [CrossRef]
    [Google Scholar]
  17. 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]
  18. 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]
  19. Kotewicz M. L., Brown E. W., LeClerc J. E., Cebula T. A. 2003; Genomic variability among enteric pathogens: the case of the mutS-rpoS intergenic region. Trends Microbiol 11:2–6 [CrossRef]
    [Google Scholar]
  20. 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]
  21. 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]
  22. 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]
  23. Liu S. L., Sanderson K. E. 1995; The chromosome of Salmonella paratyphi A is inverted by recombination between rrnH and rrnG. J Bacteriol 177:6585–6592
    [Google Scholar]
  24. Mead P. S., Griffin P. M. 1998; Escherichia coli O157 : H7. Lancet 352:1207–1212 [CrossRef]
    [Google Scholar]
  25. Miesel L., Segall A., Roth J. R. 1994; Construction of chromosomal rearrangements in Salmonella by transduction: inversions of non-permissive segments are not lethal. Genetics 137:919–932
    [Google Scholar]
  26. Nemoy L. L., Kotetishvili M., Tigno J., Keefer-Norris A., Harris A. D., Perencevich E. N., Johnson J. A., Torpey D., Sulakvelidze A. other authors 2005; Multilocus sequence typing versus pulsed-field gel electrophoresis for characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolates. J Clin Microbiol 43:1776–1781 [CrossRef]
    [Google Scholar]
  27. Ochman H. 2005; Genomes on the shrink. Proc Natl Acad Sci U S A 102:11959–11960 [CrossRef]
    [Google Scholar]
  28. 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 OligoDNA microarray and the Whole Genome PCR scanning. DNA Res 13:3–14 [CrossRef]
    [Google Scholar]
  29. 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]
  30. Perna N. T., Burland V., Mau B., Glasner J. D., Rose D. J., Mayhew G. F., Evans P. S., Gregor J. other authors Plunkett G. III 2001; Genome sequence of enterohaemorrhagic Escherichia coli O157 : H7. Nature 409:529–533 Erratum in Nature 2001 410, 240 [CrossRef]
    [Google Scholar]
  31. Plunkett G. III, Rose D. J., Durfee T. J., Blattner F. R. 1999; Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157 : H7: shiga toxin as a phage late-gene product. J Bacteriol 181:1767–1778
    [Google Scholar]
  32. 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]
  33. 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 [CrossRef]
    [Google Scholar]
  34. Schmidt H. 2001; Shiga-toxin-converting bacteriophages. Res Microbiol 152:687–695 [CrossRef]
    [Google Scholar]
  35. 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]
  36. 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]
  37. Su C., Brandt L. J. 1995; Escherichia coli O157 : H7 infection in humans. Ann Intern Med 123:698–714 [CrossRef]
    [Google Scholar]
  38. Urwin R., Maiden M. C. 2003; Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol 11:479–487 [CrossRef]
    [Google Scholar]
  39. Welch R. A., Burland V., Redford P., Roesch P., Rasko D., Buckles E. L., Liou S. R., Boutin A. other authors Plunkett G. III 2002; Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci U S A 99:17020–17024 [CrossRef]
    [Google Scholar]
  40. Whittam T. S., Wolfe M. L., Wachsmuth I. K., Orskov F., Orskov I., Wilson R. A. 1993; Clonal relationships among Escherichia coli strains that cause hemorrhagic colitis and infantile diarrhea. Infect Immun 61:1619–1629
    [Google Scholar]
  41. 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]
  42. 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]
  43. 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]
  44. Zhang X., McDaniel A. D., Wolf L. E., Keusch G. T., Waldor M. K., Acheson D. W. 2000; Quinolone antibiotics induce Shiga toxin-encoding bacteriophages, toxin production, and death in mice. J Infect Dis 181:664–670 [CrossRef]
    [Google Scholar]
  45. 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]
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