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Volume 152, Issue 4

Subtractive hybridization and optical mapping of the enterotoxigenic H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of K-12 Free

Abstract

Enterotoxigenic (ETEC) is a primary cause of diarrhoea in infants in developing countries and in travellers to endemic regions. While several virulence genes have been identified on ETEC plasmids, little is known about the ETEC chromosome, although it is expected to share significant homology in backbone sequences with K-12. In the absence of genomic sequence information, the subtractive hybridization method and the more recently described optical mapping technique were carried out to determine the degree of genomic variation between virulent ETEC strain H10407 and the non-pathogenic K-12 strain MG1655. In one round of PCR-based suppression subtractive hybridization, 153 fragments representing sequences unique to strain H10407 were identified. searches indicated that few unique sequences showed homology to known pathogenicity island genes identified in related pathogens. A total of 65 fragments contained sequences that were either linked to hypothetical proteins or showed no homology to any known sequence in the database. The remaining sequences were either phage or prophage related or displayed homology to classifiable genes that function in various aspects of bacterial metabolism. The 153 unique sequences showed variable distribution across different ETEC strains including ETEC strain B7A, which is attenuated in virulence and lacked several H10407-specific sequences. Restriction-enzyme-based optical maps of strain H10407 were compared to restriction maps of strain MG1655 and related pathogens. The 5·1 Mb ETEC chromosome was ∼500 kb greater in length than the chromosome of K-12, collinear with it and indicated several discrete regions where insertions and/or deletions had occurred relative to the chromosome of strain MG1655. No major inversions, transpositions or gross rearrangements were observed on the ETEC chromosome. Based on comparisons with known genomic sequences and related optical-map-based restriction site similarity, the sequence of the H10407 chromosome is expected to demonstrate ∼96 % identity with that of K-12.

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Keyword(s): CF, colonization factor , CFA, colonization factor antigen , EHEC, enterohaemorrhagic Escherichia coli , ETEC, enterotoxigenic E. coli , LEE, locus of enterocyte effacement , LT, heat-labile enterotoxin , PAI, pathogenicity island , PCF, putative colonization factor , SSH, suppression subtraction hybridization , ST, heat-stable enterotoxin and UPEC, uropathogenic E. coli
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2006-04-01
2024-04-26
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References

  1. Arduino R. C, DuPont H. L. 1993; Travellers' diarrhoea. Baillieres Clin Gastroenterol 7:365–385 [CrossRef]
     [Google Scholar]
  2. Blattner F. R, Plunkett G., 3rd, Bloch C. A. 14 other authors 1997; The complete genome sequence of Escherichia coli K-12. Science 277:1453–1474 [CrossRef]
     [Google Scholar]
  3. Byrd W, Mog S. R, Cassels F. J. 2003; Pathogenicity and immune response measured in mice following intranasal challenge with enterotoxigenic Escherichia coli strains H10407 and B7A. Infect Immun 71:13–21 [CrossRef]
     [Google Scholar]
  4. Cai W, Jing J, Irvin B. 8 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]
  5. Cartwright R. Y. 1993; Travellers' diarrhoea. Br Med Bull 49:348–362
     [Google Scholar]
  6. Diatchenko L, Lau Y. F, Campbell A. P. 8 other authors 1996; Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci U S A 93:6025–6030 [CrossRef]
     [Google Scholar]
  7. Dobrindt U, Reidl J. 2000; Pathogenicity islands and phage conversion: evolutionary aspects of bacterial pathogenesis. Int J Med Microbiol 290:519–527 [CrossRef]
     [Google Scholar]
  8. Dobrindt U, Agerer F, Michaelis K. 7 other authors 2003; Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J Bacteriol 185:1831–1840 [CrossRef]
     [Google Scholar]
  9. Elsinghorst E. A, Kopecko D. J. 1992; Molecular cloning of epithelial cell invasion determinants from enterotoxigenic Escherichia coli . Infect Immun 60:2409–2417
     [Google Scholar]
  10. Elsinghorst E. A, Weitz J. A. 1994; Epithelial cell invasion and adherence directed by the enterotoxigenic Escherichia coli tib locus is associated with a 104-kilodalton outer membrane protein. Infect Immun 62:3463–3471
     [Google Scholar]
  11. Evans D. G, Silver R. P, Gorbach S. L, Evans D. J., Jr, Chase D. G. 1975; Plasmid-controlled colonization factor associated with virulence in Escherichia coli enterotoxigenic for humans. Infect Immun 12:656–667
     [Google Scholar]
  12. Evans D. J., Jr, Evans D. G. 1973; Three characteristics associated with enterotoxigenic Escherichia coli isolated from man. Infect Immun 8:322–328
     [Google Scholar]
  13. Fleckenstein J. M, Kopecko D. J, Warren R. L, Elsinghorst E. A. 1996; Molecular characterization of the tia invasion locus from enterotoxigenic Escherichia coli . Infect Immun 64:2256–2265
     [Google Scholar]
  14. Fleckenstein J. M, Lindler L. E, Elsinghorst E. A, Dale J. B. 2000; Identification of a gene within a pathogenicity island of enterotoxigenic Escherichia coli H10407 required for maximal secretion of the heat-labile enterotoxin. Infect Immun 68:2766–2774 [CrossRef]
     [Google Scholar]
  15. Freedman D. J, Tacket C. O, Delehanty A, Maneval D. R, Nataro J, Crabb J. H. 1998; Milk immunoglobulin with specific activity against purified colonization factor antigens can protect against oral challenge with enterotoxigenic Escherichia coli . J Infect Dis 177:662–667 [CrossRef]
     [Google Scholar]
  16. 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]
  17. Gilligan P. H. 1999; Escherichia coli . EAEC, EHEC, EIEC, ETEC. Clin Lab Med 19:505–521
     [Google Scholar]
  18. Gupta A, Phung L. T, Taylor D. E, Silver S. 2001; Diversity of silver resistance genes in IncH incompatibility group plasmids. Microbiology 147:3393–3402
     [Google Scholar]
  19. Hayashi T, Makino K, Ohnishi M. 19 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]
  20. Jerse A. E, Yu J, Tall B. D, Kaper J. B. 1990; A genetic locus of enteropathogenic Escherichia coli necessary for the production of attaching and effacing lesions on tissue culture cells. Proc Natl Acad Sci U S A 87:7839–7843 [CrossRef]
     [Google Scholar]
  21. Jin Q, Yuan Z, Xu J. 30 other authors 2002; Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res 30:4432–4441 [CrossRef]
     [Google Scholar]
  22. Knutton S, Lloyd D. R, McNeish A. S. 1987; Identification of a new fimbrial structure in enterotoxigenic Escherichia coli (ETEC) serotype O148 : H28 which adheres to human intestinal mucosa: a potentially new human ETEC colonization factor. Infect Immun 55:86–92
     [Google Scholar]
  23. Lai Z, Jing J, Aston C. 12 other authors 1999; A shotgun optical map of the entire Plasmodium falciparum genome. Nat Genet 23:309–313 [CrossRef]
     [Google Scholar]
  24. Levine M. M, Nalin D. R, Hoover D. L, Bergquist E. J, Hornick R. B, Young C. R. 1979; Immunity to enterotoxigenic Escherichia coli . Infect Immun 23:729–736
     [Google Scholar]
  25. Levine M. M, Kaper J. B, Black R. E, Clements M. L. 1983; New knowledge on pathogenesis of bacterial enteric infections as applied to vaccine development. Microbiol Rev 47:510–550
     [Google Scholar]
  26. Levine M. M, Ristaino P, Marley G. 8 other authors 1984; Coli surface antigens 1 and 3 of colonization factor antigen II-positive enterotoxigenic Escherichia coli : morphology, purification, and immune responses in humans. Infect Immun 44:409–420
     [Google Scholar]
  27. Lim A, Dimalanta E. T, Potamousis K. D. 16 other authors 2001; Shotgun optical maps of the whole Escherichia coli O157 : H7 genome. Genome Res 11:1584–1593 [CrossRef]
     [Google Scholar]
  28. Lin J, Qi R, Aston C. 8 other authors 1999; Whole-genome shotgun optical mapping of Deinococcus radiodurans . Science 285:1558–1562 [CrossRef]
     [Google Scholar]
  29. Lindenthal C, Elsinghorst E. A. 1999; Identification of a glycoprotein produced by enterotoxigenic Escherichia coli . Infect Immun 67:4084–4091
     [Google Scholar]
  30. McConnell M. M, Hibberd M, Field A. M, Chart H, Rowe B. 1990; Characterization of a new putative colonization factor (CS17) from a human enterotoxigenic Escherichia coli of serotype O114 : H21 which produces only heat-labile enterotoxin. J Infect Dis 161:343–347 [CrossRef]
     [Google Scholar]
  31. Myers E. W, Huang X. 1992; An O (N2 log N) restriction map comparison and search algorithm. Bull Math Biol 54:599–618
     [Google Scholar]
  32. Patel S. K, Dotson J, Allen K. P, Fleckenstein J. M. 2004; Identification and molecular characterization of EatA, an autotransporter protein of enterotoxigenic Escherichia coli . Infect Immun 72:1786–1794 [CrossRef]
     [Google Scholar]
  33. Perna N. T, Mayhew G. F, Posfai G, Elliott S, Donnenberg M. S, Kaper J. B, Blattner F. R. 1998; Molecular evolution of a pathogenicity island from enterohemorrhagic Escherichia coli O157 : H7. Infect Immun 66:3810–3817
     [Google Scholar]
  34. Perna N. T, Plunkett G., 3rd, Burland V. 25 other authors 2001; Genome sequence of enterohaemorrhagic Escherichia coli O157 : H7. Nature 409:529–533 [CrossRef]
     [Google Scholar]
  35. Qadri F, Svennerholm A. M, Faruque A. S, Sack R. B. 2005; Enterotoxigenic Escherichia coli in developing countries: epidemiology, microbiology, clinical features, treatment, and prevention. Clin Microbiol Rev 18:465–483 [CrossRef]
     [Google Scholar]
  36. Reid R. H, Boedeker E. C, McQueen C. E. 8 other authors 1993; Preclinical evaluation of microencapsulated CFA/II oral vaccine against enterotoxigenic E coli. Vaccine 11:159–167 [CrossRef]
     [Google Scholar]
  37. Reiter W. D, Palm P, Yeats S. 1989; Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res 17:1907–1914 [CrossRef]
     [Google Scholar]
  38. Reslewic S, Zhou S, Place M. 11 other authors 2005; Whole-genome shotgun optical mapping of Rhodospirillum rubrum . Appl Environ Microbiol 71:5511–5522 [CrossRef]
     [Google Scholar]
  39. Sambrook J, Russell W. D. 2001 Molecular Cloning: a Laboratory Manual, 3rd edn.. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  40. Schmidt H, Hensel M. 2004; Pathogenicity islands in bacterial pathogenesis. Clin Microbiol Rev 17:14–56 [CrossRef]
     [Google Scholar]
  41. Sherlock O, Vejborg R. M, Klemm P. 2005; The TibA adhesin/invasin from enterotoxigenic Escherichia coli is self recognizing and induces bacterial aggregation and biofilm formation. Infect Immun 73:1954–1963 [CrossRef]
     [Google Scholar]
  42. Smith H. R, Cravioto A, Willshaw G. A, McConnell M. M, Scotland S. M, Gross R. J, Rowe B. 1979; A plasmid coding for the production of colonisation factor antigen I and heat-stable enterotoxin in strains of Escherichia coli of serogroup O78. FEMS Microbiol Lett 6:255–266 [CrossRef]
     [Google Scholar]
  43. Smyth C. J. 1982; Two mannose-resistant haemagglutinins on enterotoxigenic Escherichia coli of serotype O6 : K15 : H16 or H-isolated from travellers' and infantile diarrhoea. J Gen Microbiol 128:2081–2096
     [Google Scholar]
  44. Tacket C. O, Losonsky G, Link H, Hoang Y, Guesry P, Hilpert H, Levine M. M. 1988; Protection by milk immunoglobulin concentrate against oral challenge with enterotoxigenic Escherichia coli . N Engl J Med 318:1240–1243 [CrossRef]
     [Google Scholar]
  45. Tang M, Waterman M. S. 2001; Local matching of random restriction maps. J Appl Probab 38:335–356 [CrossRef]
     [Google Scholar]
  46. Tauschek M, Gorrell R. J, Strugnell R. A, Robins-Browne R. M. 2002; Identification of a protein secretory pathway for the secretion of heat-labile enterotoxin by an enterotoxigenic strain of Escherichia coli . Proc Natl Acad Sci U S A 99:7066–7071 [CrossRef]
     [Google Scholar]
  47. Waterman M. S, Smith T. F, Katcher H. L. 1984; Algorithms for restriction map comparisons. Nucleic Acids Res 12:237–242 [CrossRef]
     [Google Scholar]
  48. Wei J, Goldberg M. B, Burland V. 14 other authors 2003; Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun 71:2775–2786 [CrossRef]
     [Google Scholar]
  49. Welch R. A, Burland V, Plunkett G. 16 other authors 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]
  50. Wenneras C, Erling V. 2004; Prevalence of enterotoxigenic Escherichia coli -associated diarrhoea and carrier state in the developing world. J Health Popul Nutr 22:370–382
     [Google Scholar]
  51. Winstanley C. 2002; Spot the difference: applications of subtractive hybridisation to the study of bacterial pathogens. J Med Microbiol 51:459–467
     [Google Scholar]
  52. Wolf M. K. 1997; Occurrence, distribution, and associations of O and H serogroups, colonization factor antigens, and toxins of enterotoxigenic Escherichia coli . Clin Microbiol Rev 10:569–584
     [Google Scholar]
  53. Wolf M. K, Taylor D. N, Boedeker E. C, Hyams K. C, Maneval D. R, Levine M. M, Tamura K, Wilson R. A, Echeverria P. 1993; Characterization of enterotoxigenic Escherichia coli isolated from U.S. troops deployed to the Middle East. J Clin Microbiol 31:851–856
     [Google Scholar]
  54. Yamamoto T, Yokota T. 1983; Plasmids of enterotoxigenic Escherichia coli H10407: evidence for two heat-stable enterotoxin genes and a conjugal transfer system. J Bacteriol 153:1352–1360
     [Google Scholar]
  55. Zhou S, Kile A, Bechner M. 13 other authors 2004a; Single-molecule approach to bacterial genomic comparisons via optical mapping. J Bacteriol 186:7773–7782 [CrossRef]
     [Google Scholar]
  56. Zhou S, Kile A, Kvikstad E. 11 other authors 2004b; Shotgun optical mapping of the entire Leishmania major Friedlin genome. Mol Biochem Parasitol 138:97–106 [CrossRef]
     [Google Scholar]
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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 (2006); https://doi.org/10.1099/mic.0.28648-0
/content/journal/micro/10.1099/mic.0.28648-0
/content/journal/micro/10.1099/mic.0.28648-0
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