Characterization of four novel genomic regions of uropathogenic Escherichia coli highly associated with the extraintestinal virulent phenotype: A jigsaw puzzle of genetic modules

International Journal of Medical Microbiology

Volumn 297, Issue 2, 2007, Pages 83-95

  Sorsa, Liisa Johanna ^a   Feldmann, Friederike ^a   Hildinger, Kirsten ^a   Dufke, Severin ^a   Schubert, Sören ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

DNA microarray; Extraintestinal pathogenic Escherichia coli; Genomic variation; Virulence determinant

Indexed keywords

BACTERIAL DNA; DNA FRAGMENT; GENOMIC DNA;

ARTICLE; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL MENINGITIS; BACTERIAL STRAIN; BACTERIAL VIRULENCE; CODON; COMMENSAL ESCHERICHIA COLI; DNA MICROARRAY; DNA SEQUENCE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENICITY ISLAND; PREVALENCE; SCR GENE; SEPSIS; TRANSPOSON; URINARY TRACT INFECTION; UROPATHOGENIC ESCHERICHIA COLI;

EID: 33847720721     PISSN: 14384221     EISSN: 16180607     Source Type: Journal    
DOI: 10.1016/j.ijmm.2006.11.007     Document Type: Article

References (35)

1. Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., and Struhl K. Current Protocols in Molecular Biology (1989), Wiley, New York
2. Bernier-Febreau C., du Merle L., Turlin E., Labas V., Ordonez J., Gilles A.M., and Le Bougouenec C. Use of deoxyribose by intestinal and extraintestinal pathogenic Escherichia coli strains: a metabolic adaptation involved in competitiveness. Infect. Immun. 72 (2004) 6151-6156
3. Bidet P., Bonacorsi S., Clermont O., De Montille C., Brahimi N., and Bingen E. Multiple insertional events, restricted by the genetic background, have led to acquisition of pathogenicity island IIJ96-like domains among E. coli strains of different clinical origins. Infect. Immun. 73 (2005) 4081-4087
4. Blatch G.L., and Lassle M. The tetratricopeptide repeat: a structural motif mediating protein-protein interactions. Bioessays 21 (1999) 932-939
5. Bullen J.J., Rogers H.J., Spalding P.B., and Ward C.G. Iron and infection: the heart of the matter. FEMS Immunol. Med. Microbiol. 43 (2005) 325-330
6. Caprioli A., Morabito S., Brugereb H., and Oswald E. Enterohaemorrhagic E. coli: emerging issues on virulence and modes of transmission. Vet. Res. 36 (2005) 289-311
7. Chang D.E., Smalley D.J., Tucker D.L., Leatham M.P., Norris W.E., Stevenson S.J., Anderson A.B., Grissom J.E., Laux D.C., Cohen P.S., and Conway T. Carbon nutrition of Escherichia coli in the mouse intestine. Proc. Natl. Acad. Sci. USA 101 (2004) 7427-7432
8. Clermont O., Bonacorsi S., and Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66 (2000) 4555-4558
9. Cowan P.J., Nagesha H., Leonard L., Howard J.L., and Pittard A.J. Characterization of the major promoter for the plasmid-encoded sucrose genes scrY, scrA, and scrB. J. Bacteriol. 173 (1991) 7464-7470
10. 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
11. Dobrindt U., Hochhut B., Hentschel U., and Hacker J. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2 (2004) 414-424
12. Doroshenko V.G., and Livshits V.A. Structure and mode of transposition of Tn2555 carrying sucrose utilization genes. FEMS Microbiol. Lett. 233 (2004) 353-359
13. Escobar-Paramo P., Clermont O., Blanc-Potard A.B., Bui H., Le Bouguenec C., and Denamur E. A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Mol. Biol. Evol. 21 (2004) 1085-1094
14. Fischer D., and Eisenberg D. Finding families for genomic ORFans. Bioinformatics 15 (1999) 759-762
15. 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
16. 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
17. Hochhut B., Dobrindt U., and Hacker J. Pathogenicity islands and their role in bacterial virulence and survival. Contrib. Microbiol. 12 (2005) 234-254
18. Huber W., von Heydebreck A., Sultmann H., Poustka A., and Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 Suppl. 1 (2002) S96-S104
19. Johnson J.R. Microbial virulence determinants and the pathogenesis of urinary tract infection. Infect. Dis. Clin. North Am. 17 (2003) 261-278 viii
20. Johnson J.R., Jerome C., Boster D.R., Stapleton A.E., and Tarr P.I. Analysis of urinary Escherichia coli isolates for ability to produce Shiga toxin. J Clin Microbiol 40 (2002) 2247-2248
21. Johnson J.R., Kuskowski M.A., Gajewski A., Soto S., Horcajada J.P., Jimenez de Anta M.T., and Vila J. Extended virulence genotypes and phylogenetic background of Escherichia coli isolates from patients with cystitis, pyelonephritis, or prostatitis. J. Infect. Dis. 191 (2005) 46-50
22. Le Bouguenec 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
23. Le Gall T., Darlu P., Escobar-Paramo P., Picard B., and Denamur E. Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species. Genome Res. 15 (2005) 260-268
24. Lerat E., Daubin V., Ochman H., and Moran N.A. Evolutionary origins of genomic repertoires in bacteria. PLoS. Biol. 3 (2005) e130
25. Mellmann A., Bielaszewska M., Zimmerhackl L.B., Prager R., Harmsen D., Tschape H., and Karch H. Enterohemorrhagic Escherichia coli in human infection: in vivo evolution of a bacterial pathogen. Clin. Infect. Dis. 41 (2005) 785-792
26. Nataro J.P. Enteroaggregative Escherichia coli pathogenesis. Curr. Opin. Gastroenterol. 21 (2005) 4-8
27. Nougayrede J.P., Taieb F., De Rycke J., and Oswald E. Cyclomodulins: bacterial effectors that modulate the eukaryotic cell cycle. Trends Microbiol. 13 (2005) 103-110
28. 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
29. Pal C., Papp B., and Lercher M.J. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37 (2005) 1372-1375
30. Roesch P.L., Redford P., Batchelet S., Moritz R.L., Pellett S., Haugen B.J., Blattner F.R., and Welch R.A. Uropathogenic Escherichia coli use d-serine deaminase to modulate infection of the murine urinary tract. Mol. Microbiol. 49 (2003) 55-67
31. Russo T.A., and Johnson J.R. Medical and economic impact of extraintestinal infections due to Escherichia coli: focus on an increasingly important endemic problem. Microbes Infect. 5 (2003) 449-456
32. 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
33. 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
34. Wang H.C., Badger J., Kearney P., and Li M. Analysis of codon usage patterns of bacterial genomes using the self-organizing map. Mol. Biol. Evol. 18 (2001) 792-800
35. 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