Aspects of genome plasticity in pathogenic Escherichia coli

International Journal of Medical Microbiology

Volumn 297, Issue 7-8, 2007, Pages 625-639

  Bielaszewska, Martina ^a   Dobrindt, Ulrich ^b   Gärtner, Julia ^c,d   Gallitz, Inka ^c   Hacker, Jörg ^b   Karch, Helge ^a   Müller, Daniel ^c   Schubert, Sören ^e   Alexander Schmidt, M ^c   Sorsa, Liisa Johanna ^e   Zdziarski, Jaroslaw ^b  

^a UNIVERSITY HOSPITAL MÜNSTER   (Germany)

^b UNIVERSITY OF WÜRZBURG   (Germany)

^c UNIVERSITY OF MÜNSTER   (Germany)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF MUNICH   (Germany)

Author keywords

ATEC; CDT; DNA pathoarray; EHEC; Enterohemorrhagic Escherichia coli; EPEC; EXPEC; Genome plasticity; Genomic diversity; Multiplex PCR; Pathogenicity islands; SF EHEC O157

Indexed keywords

BACTERIAL DNA; BACTERIAL TOXIN; SHIGA TOXIN; VIRULENCE FACTOR;

ASYMPTOMATIC BACTERIURIA; BACTERIAL CHROMOSOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; CHROMOSOME REARRANGEMENT; CYTOTOXICITY; DIAGNOSTIC VALUE; DNA MICROARRAY; ENTEROHEMORRHAGIC ESCHERICHIA COLI; ESCHERICHIA COLI; EVOLUTION; EXCISION REPAIR; GENE IDENTIFICATION; GENE TRANSFER; GENETIC ANALYSIS; GENETIC STABILITY; GENETIC VARIABILITY; GENOME; GENOME SIZE; GENOMICS; INTESTINE FLORA; INTESTINE INFECTION; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENESIS; SEROTYPE; SHORT SURVEY; SUBTRACTIVE HYBRIDIZATION;

EID: 35348836137     PISSN: 14384221     EISSN: 16180607     Source Type: Journal    
DOI: 10.1016/j.ijmm.2007.03.001     Document Type: Short Survey

References (82)

1. Bagshaw S.M., and Laupland K.B. Epidemiology of intensive care unit - acquired urinary tract infections. Curr. Opin. Infect. Dis. 19 (2006) 67-71
2. Beinke C., Laarmann S., Wachter C., Karch H., Greune L., and Schmidt M.A. Diffusely adhering Escherichia coli strains induce attaching and effacing phenotypes and secrete homologs of Esp proteins. Infect. Immun. 66 (1998) 528-539
3. Bergsten G., Wullt B., and Svanborg C. Escherichia coli, fimbriae, bacterial persistence and host response induction in the human urinary tract. Int. J. Med. Microbiol. 295 (2005) 487-502
4. Bielaszewska M., Fell M., Greune L., Prager R., Fruth A., Tschäpe H., Schmidt M.A., and Karch H. Characterization of cytolethal distending toxin genes and expression in Shiga toxin-producing Escherichia coli strains of non-O157 serogroups. Infect. Immun. 72 (2004) 1812-1816
5. Bielaszewska M., Tarr P.I., Karch H., Zhang W., and Mathys W. Phenotypic and molecular analysis of tellurite resistance among enterohemorrhagic Escherichia coli O157:H7 and sorbitol-fermenting O157:NM clinical isolates. J. Clin. Microbiol. 43 (2005) 452-454
6. Bielaszewska M., Sinha B., Kuczius T., and Karch H. Cytolethal distending toxin from Shiga toxin-producing Escherichia coli O157 causes irreversible G2/M arrest, inhibition of proliferation and death of human endothelial cells. Infect. Immun. 73 (2005) 552-562
7. Bielaszewska M., Prager R., Zhang W., Friedrich A.W., Mellmann A., Tschäpe H., and Karch H. Chromosomal dynamism in progeny of outbreak-related sorbitol-fermenting enterohemorrhagic Escherichia coli O157:NM. Appl. Environ. Microbiol. 72 (2006) 1900-1909
8. Bingen-Bidois M., Clermont O., Bonacorsi S., Terki M., Brahimi N., Loukil C., Barraud D., and Bingen E. Phylogenetic analysis and prevalence of urosepsis strains of Escherichia coli bearing pathogenicity island-like domains. Infect. Immun. 70 (2002) 3216-3226
9. Blattner F.R., Plunkett III G., Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., and Shao Y. The complete genome sequence of Escherichia coli K-12. Science 277 (1997) 1453-1474
10. Brunder W., Karch H., and Schmidt H. Complete sequence of the large virulence plasmid pSFO157 of the sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H- strain 3072/96. Int. J. Med. Microbiol. 296 (2006) 467-474
11. Brzuszkiewicz E., Brüggemann H., Liesegang H., Emmerth M., Ölschläger T., Nagy G., Albermann K., Wagner C., Buchrieser C., Emödy L., Gottschalk G., Hacker J., and Dobrindt U. How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc. Natl. Acad. Sci. USA 103 (2006) 12879-12884
12. Buckles E.L., Bahrani-Mougeot F.K., Molina A., Lockatell C.V., Johnson D.E., Drachenberg C.B., Burland V., Blattner F.R., and Donnenberg M.S. Identification and characterization of a novel uropathogenic Escherichia coli-associated fimbrial gene cluster. Infect. Immun. 72 (2004) 3890-3901
13. Ceelen L.M., Decostere A., Ducatelle R., and Haesebrouck F. Cytolethal distending toxin generates cell death by inducing a bottleneck in the cell cycle. Microbiol. Res. 161 (2006) 109-120
14. Chen S.L., Hung C.S., Xu J., Reigstad C.S., Magrini V., Sabo A., Blasiar D., Bieri T., Meyer R.R., Ozersky P., Armstrong J.R., Fulton R.S., Latreille J.P., Spieth J.P., Hooton T.M., Mardis E.R., Hultgren S.J., and Gordon J.I. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc. Natl. Acad. Sci. USA 103 (2006) 5977-5982
15. Clermont O., Bonacorsi S., and Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66 (2000) 4555-4558
16. Clermont O., Cordevant C., Bonacorsi S., Marecat A., Lange M., and Bingen E. Automated ribotyping provides rapid phylogenetic subgroup affiliation of clinical extraintestinal pathogenic Escherichia coli strains. J. Clin. Microbiol. 39 (2001) 4549-4553
17. Cornelis G.R. The type III secretion injectisome. Nat. Rev. Microbiol. 4 (2006) 811-825
18. Cortes-Bratti X., Frisan T., and Thelestam M. The cytolethal distending toxins induce DNA damage and cell cycle arrest. Toxicon 39 (2001) 1729-1736
19. Dobrindt U. (Patho-)Genomics of Escherichia coli. Int. J. Med. Microbiol. 295 (2005) 357-371
20. Dobrindt U., and Hacker J. Whole genome plasticity in pathogenic bacteria. Curr. Opin. Microbiol. 4 (2001) 550-557
21. Dobrindt U., Blum-Oehler G., Nagy G., Schneider G., Johann A., Gottschalk G., and Hacker J. Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536. Infect. Immun. 70 (2002) 6365-6372
22. Dobrindt U., Agerer F., Michaelis K., Janka A., Buchrieser C., Samuelson M., Svanborg C., Gottschalk G., Karch H., and Hacker J. Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J. Bacteriol. 185 (2003) 1831-1840
23. Dobrindt U., Hochhut B., Hentschel U., and Hacker J. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2 (2004) 414-424
24. Foxman B., and Brown P. Epidemiology of urinary tract infections: transmission and risk factors, incidence, and costs. Infect. Dis. Clin. North Am. 17 (2003) 227-241
25. Foxman B., Barlow R., D'Arcy H., Gillespie B., and Sobel J.D. Urinary tract infection: self-reported incidence and associated costs. Ann. Epidemiol. 10 (2000) 509-515
26. Friedrich A.W., Nierhoff K.V., Bielaszewska M., Mellmann A., and Karch H. Phylogeny, clinical associations, and diagnostic utility of the pilin subunit gene (sfpA) of sorbitol-fermenting, enterohemorrhagic Escherichia coli O157:H-. J. Clin. Microbiol. 42 (2004) 4697-4701
27. Friedrich A.W., Köck R., Bielaszewska M., Zhang W., Karch H., and Mathys W. Distribution of the urease gene cluster and urease activity among enterohemorrhagic Escherichia coli O157 from humans. J. Clin. Microbiol. 43 (2005) 546-550
28. Friedrich A.W., Lu S., Bielaszewska M., Prager R., Bruns P., Xu J.G., Tschäpe H., and Karch H. Cytolethal distending toxin in Escherichia coli O157:H7: spectrum of conservation, structure, and endothelial toxicity. J. Clin. Microbiol. 44 (2006) 1844-1846
29. Gal-Mor O., and Finlay B.B. Pathogenicity islands: a molecular toolbox for bacterial virulence. Cell. Microbiol. 8 (2006) 1707-1719
30. Gärtner J.F., and Schmidt M.A. Comparative analysis of locus of enterocyte effacement pathogenicity islands of atypical enteropathogenic Escherichia coli. Infect. Immun. 72 (2004) 6722-6728
31. Gaynes R., and Edwards J.R. Overview of nosocomial infections caused by gram-negative bacilli. Clin. Infect. Dis. 41 (2005) 848-854
32. Gomes T.A.T., Irino K., Girão D.M., Girão V.B.C., Guth B.E.C., Vaz T.M.I., Moreira F.C., Chinarelli S.H., and Vieira M.A.M. Emerging enteropathogenic Escherichia coli strains?. Emerg. Infect. Dis. 10 (2004) 1851-1855
33. Goosney D.L., DeVinney R., and Finlay B.B. Recruitment of cytoskeletal and signalling proteins to enteropathogenic and enterohemorrhagic Escherichia coli pedestals. Infect. Immun. 69 (2001) 3315-3322
34. Grozdanov L., Raasch C., Schulze J., Sonnenborn U., Gottschalk G., Hacker J., and Dobrindt U. Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917. J. Bacteriol. 186 (2004) 5432-5441
35. Gyles C.L. Shiga toxin-producing Escherichia coli: an overview. J. Anim. Sci. 85 13 Suppl. (2007) E45-E62
36. Hacker J., and Carniel E. Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep. 2 (2001) 376-381
37. Hayashi T., Makino K., Ohnishi M., Kurokawa K., Ishii K., Yokoyama K., Han C.G., Ohtsubo E., Nakayama K., Murata T., Tanaka M., Tobe T., Iida T., Takami H., Honda T., Sasakawa C., Ogasawara N., Yasunaga T., Kuhara S., Shiba T., Hattori M., and Shinagawa H. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8 (2001) 11-22
38. Herzer P.J., Inouye S., Inouye M., and Whittam T.S. Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. J. Bacteriol. 172 (1990) 6175-6181
39. Janka A., Bielaszewska M., Dobrindt U., and Karch H. Identification and distribution of the enterohemorrhagic Escherichia coli factor for adherence (efa1) gene in sorbitol-fermenting E. coli O157:H-. Int. J. Med. Microbiol. 292 (2002) 207-214
40. Janka A., Bielaszewska M., Dobrindt U., Greune L., Schmidt M.A., and Karch H. The cytolethal distending toxin (cdt) gene cluster in enterohemorrhagic Escherichia coli O157:H- and O157:H7: characterization and evolutionary considerations. Infect. Immun. 71 (2003) 3634-3638
41. Janka A., Becker G., Sonntag A.-K., Bielaszewska M., Dobrindt U., and Karch H. Presence and characterization of a mosaic genomic island which distinguishes sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H- from Escherichia coli O157:H7. Appl. Environ. Microbiol. 71 (2005) 4875-4878
42. Jantunen M.E., Saxen H., Lukinmaa S., Ala-Houhala M., and Siitonen A. Genomic identity of pyelonephritogenic Escherichia coli isolated from blood, urine and faeces of children with urosepsis. J. Med. Microbiol. 50 (2001) 650-652
43. Johnson J.R., and Russo T.A. Molecular epidemiology of extraintestinal pathogenic (uropathogenic) Escherichia coli. Int. J. Med. Microbiol. 295 (2005) 383-404
44. Johnson J.R., and Stell A.L. PCR for specific detection of H7 flagellar variant of fliC among extraintestinal pathogenic Escherichia coli. J. Clin. Microbiol. 39 (2001) 3712-3717
45. Kaper J.B., Nataro J.P., and Mobley H.L.T. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2 (2004) 123-140
46. Karch H., Tarr P.I., and Bielaszewska M. Enterohaemorrhagic Escherichia coli in human medicine. Int. J. Med. Microbiol. 295 (2005) 405-418
47. Karch H., Friedrich A.W., Gerber A., Zimmerhackl L.B., Schmidt M.A., and Bielaszewska M. New aspects in the pathogenesis of enteropathic hemolytic uremic syndrome. Sem. Thromb. Hemost. 32 (2006) 105-112
48. Kim K.S. Pathogenesis of bacterial meningitis: from bacteraemia to neuronal injury. Nat. Rev. Neurosci. 4 (2003) 376-385
49. Klapproth J.M.A., Scaletsky I.C.A., McNamara B.P., Lai L.-C., Malstrom C., James S.P., and Donnenberg M.S. A large toxin from pathogenic Escherichia coli strains that inhibits lymphocyte activation. Infect. Immun. 68 (2000) 2148-2155
50. Klemm P., Roos V., Ulett G.C., Svanborg C., and Schembri M.A. Molecular characterisation of the Escherichia coli asymptomatic bacteriuria strain 83972: the taming of a pathogen. Infect. Immun. 74 (2006) 781-785
51. Le Bouguénec C., and Servin A.L. Diffusely adherent Escherichia coli strains expressing Afa/Dr adhesins (Afa/Dr DAEC): hitherto unrecognized pathogens. FEMS Microbiol. Lett. 256 (2006) 185-194
52. Lerat E., Daubin V., Ochman H., and Moran N.A. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3 (2005) e130
53. Marrs C.F., Zhang L., Tallman P., Manning S.D., Somsel P., Raz P., Colodner R., Jantunen M.E., Siitonen A., Saxen H., and Foxman B. Variations in 10 putative uropathogen virulence genes among urinary, faecal and peri-urethral Escherichia coli. J. Med. Microbiol. 51 (2002) 138-142
54. Mereghetti L., Tayoro J., Watt S., Lanotte P., Loulergue J., Perrotin D., and Quentin R. Genetic relationship between Escherichia coli strains isolated from the intestinal flora and those responsible for infectious diseases among patients hospitalized in intensive care units. J. Hosp. Infect. 52 (2002) 43-51
55. Morin M.D., and Hopkins W.J. Identification of virulence genes in uropathogenic Escherichia coli by multiplex polymerase chain reaction and their association with infectivity in mice. Urology 60 (2002) 537-541
56. Müller D., Hagedorn P., Brast S., Heusipp G., Bielaszewska M., Friedrich A.W., Karch H., and Schmidt M.A. Rapid identification and differentiation of clinical isolates of enteropathogenic Escherichia coli (EPEC), atypical EPEC, and Shiga toxin-producing Escherichia coli by a one-step multiplex PCR method. J. Clin. Microbiol. 44 (2006) 2626-2629
57. Müller, D., Greune, L., Heusipp, G., Karch, H., Fruth, A., Tschäpe, H., Schmidt, M.A., 2007. Identification of unconventional intestinal pathogenic Escherichia coli isolates expressing intermediate virulence factor profiles using a novel single-step multiplex PCR. Appl. Environ. Microbiol. 73, in press.
58. Nataro J.P. Enteroaggregative Escherichia coli pathogenesis. Curr. Opin. Gastroenterol. 21 (2005) 4-8
59. Nataro J.P., and Kaper J.B. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11 (1998) 142-201
60. Neilands J.B. Mechanism and regulation of synthesis of aerobactin in Escherichia coli K12 (pColV-K30). Can. J. Microbiol. 38 (1992) 728-733
61. Nguyen R.N., Taylor L.S., Tauschek M., and Robins-Browne R.M. Atypical enteropathogenic Escherichia coli infection and prolonged diarrhea in children. Emerg. Infect. Dis. 12 (2006) 597-603
62. Nicholls L., Grant T.H., and Robins-Browne R.M. Identification of a novel genetic locus that is required for in vitro adhesion of a clinical isolate of enterohaemorrhagic Escherichia coli to epithelial cells. Mol. Microbiol. 35 (2000) 275-288
63. Ochman H., and Selander R.K. Evidence for clonal population structure in Escherichia coli. Proc. Natl. Acad. Sci. USA 81 (1984) 198-201
64. Ochman H., Lerat E., and Daubin V. Examining bacterial species under the specter of gene transfer and exchange. Proc. Natl. Acad. Sci. USA 102 Suppl. 1 (2005) 6595-6599
65. Oelschlaeger T.A., Dobrindt U., and Hacker J. Virulence factors of uropathogens. Curr. Opin. Urol. 12 (2002) 33-38
66. Perna N.T., Plunkett Jr. G., Burland V., Mau B., Glasner J.D., Rose D.J., Mayhew G.F., Evans P.S., Gregor J., Kirkpatrick H.A., Posfai G., Hackett J., Klink S., Boutin A., Shao Y., Miller L., Grotbeck E.J., Davis N.W., Lim A., Dimalanta E.T., Potamousis K.D., Apodaca J., Anantharaman T.S., Lin J., Yen G., Schwartz D.C., Welch R.A., and Blattner F.R. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409 (2001) 529-533
67. Pupo G.M., Karaolis D.K., Lan R., and Reeves P.R. Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies. Infect. Immun. 65 (1997) 2685-2692
68. Purdy G.E., and Payne S.M. The SHI-3 iron transport island of Shigella boydii 0-1392 carries the genes for aerobactin synthesis and transport. J. Bacteriol. 183 (2001) 4176-4182
69. Roos V., and Klemm P. Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract. Infect. Immun. 74 (2006) 3565-3575
70. Roos V., Glen C., Ulett G.C., Schembri M.A., and Klemm P. The asymptomatic bacteriuria Escherichia coli strain 83972 outcompetes uropathogenic E. coli strains in human urine. Infect. Immun. 74 (2006) 615-624
71. Roos V., Schembri M.A., Ulett G.C., and Klemm P. Asymptomatic bacteriuria Escherichia coli strain 83972 carries mutations in the foc locus and is unable to express F1C fimbriae. Microbiology 152 (2006) 1799-1806
72. Sharp P.M., and Li W.H. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15 (1987) 1281-1295
73. Snyder J.A., Haugen B.J., Buckles E.L., Lockatell C.V., Johnson D.E., Donnenberg M.S., Welch R.A., and Mobley H.L.T. Transcriptome of uropathogenic Escherichia coli during urinary tract infection. Infect. Immun. 72 (2004) 6373-6381
74. Sorsa L.J., Dufke S., Heesemann J., and Schubert S. Characterization of an iroBCDEN gene cluster on a transmissible plasmid of uropathogenic Escherichia coli: evidence for horizontal transfer of a chromosomal virulence factor. Infect. Immun. 71 (2003) 3285-3293
75. Sorsa L.J., Dufke S., and Schubert S. Identification of novel virulence-associated loci in uropathogenic Escherichia coli by suppression subtractive hybridization. FEMS Microbiol. Lett. 230 (2004) 203-208
76. Stevens M.P., van Diemen P.M., Frankel G., Phillips A.D., and Wallis T.S. Efa1 influences colonization of the bovine intestine by Shiga toxin-producing Escherichia coli serotypes O5 and O111. Infect. Immun. 70 (2002) 5158-5166
77. Tarr P.I., Gordon C.A., and Chandler W.L. Shiga toxin-producing Escherichia coli and the haemolytic uraemic syndrome. Lancet 365 (2005) 1073-1086
78. Welch R.A., Burland V., Plunkett III G., Redford P., Roesch P., Rasko D., Buckles E.L., Liou S.R., Boutin A., Hackett J., Stroud D., Mayhew G.F., Rose D.J., Zhou S., Schwartz D.C., Perna N.T., Mobley H.L., Donnenberg M.S., and Blattner F.R. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99 (2002) 17020-17024
79. Wirth T., Falush D., Lan R., Colles F., Mensa P., Wieler L.H., Karch H., Reeves P.R., Maiden M.C., Ochman H., and Achtman M. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol. Microbiol. 60 (2006) 1136-1151
80. Xie Y., Kim K.J., and Kim K.S. Current concepts on Escherichia coli K1 trans-location of the blood-brain barrier. FEMS Immunol. Med. Microbiol. 42 (2004) 271-279
81. Zhang W.L., Kohler B., Oswald E., Beutin L., Karch H., Morabito S., Caprioli A., Suerbaum S., and Schmidt H. Genetic diversity of intimin genes of attaching and effacing Escherichia coli strains. J. Clin. Microbiol. 40 (2002) 4486-4492
82. Zhang W., Mellmann A., Sonntag A.-K., Wieler L., Bielaszewska M., Tschäpe H., Karch H., and Friedrich A.W. Structural and functional differences between disease-associated genes of enterohaemorrhagic Escherichia coli O111. Int. J. Med. Microbiol. 297 (2007) 17-26