Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays

Journal of Bacteriology

Volumn 185, Issue 6, 2003, Pages 1831-1840

  Dobrindt, Ulrich ^a   Agerer, Franziska ^a   Michaelis, Kai ^a   Janka, Andreas ^a   Buchrieser, Carmen ^d   Samuelson, Martin ^e   Svanborg, Catharina ^e   Gottschalk, Gerhard ^b   Karch, Helge ^c   Hacker, Jörg ^a  

^a UNIVERSITY OF WÜRZBURG   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c UNIVERSITY HOSPITAL MÜNSTER   (Germany)

^d INSTITUT PASTEUR   (France)

^e LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ARTICLE; BACTERIAL GENOME; BACTERIAL VIRULENCE; BACTERIUM ISOLATE; DNA MICROARRAY; DNA SEQUENCE; ESCHERICHIA COLI; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS;

ELECTROPHORESIS, GEL, PULSED-FIELD; ESCHERICHIA COLI; ESCHERICHIA COLI INFECTIONS; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; HUMANS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPEN READING FRAMES; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS); VIRULENCE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 0037337509     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.6.1831-1840.2003     Document Type: Article

References (58)

1. Achtman, M., K. Zurth, G. Morelli, G. Torrea, A. Guiyoule, and E. Carniel. 1999. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 96:14043-14048.
2. Akman, L., and S. Aksoy. 2001. A novel application of gene arrays: Escherichia coli array provides insight into the biology of the obligate endosymbiont of tsetse flies. Proc. Natl. Acad. Sci. USA 98:7546-7551.
3. Andersson, P., I. Engberg, G. Lidin-Janson, K. Lincoln, R. Hull, S. Hull, and C. Svanborg. 1991. Persistence of Escherichia coli bacteriuria is not determined by bacterial adherence. Infect. Immun. 59:2915-2921.
4. Behr, M. A., M. A. Wilson, W. P. Gill, H. Salamon, G. K. Schoolnik, S. Rane, and P. M. Small. 1999. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284:1520-1523.
5. Bergthorsson, U., and H. Ochman. 1998. Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol. Biol. Evol. 15:6-16.
6. Blattner, F. R., G, Plunkett, C. A. Bloch, N. T. Perna, V. Burland, M, Riley, J. Collado-Villes, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462.
7. Blum, G., M. Ott, A, Lischewski, A. Ritter, H. Imrich, H. Tschäpe, and J. Hacker. 1994. Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen. Infect. Immun. 62:606-614.
8. Blum, G., V. Falbo, A. Caprioli, and J. Hacker, 1995. Gene clusters encoding the cytotoxic necrotizing factor type 1, Prs-fimbriae and alpha-hemolysin form the pathogenicity island II of the uropathogenic Escherichia coli strain J96. FEMS Microbiol. Lett. 126:189-195.
9. Bonacorsi, S. P. P., O. Clermont, C. Tinsley, I. Le Gall, J.-C. Beaudoin, J. Elion, X. Nassif, and E. Bingen. 2000. Identification of regions of the Escherichia coli chromosome specific for neonatal meningitis-associated strains. Infect. Immun. 68:2096-2101.
10. Boyd, E. F., and D. L. Hartl. 1998. Chromosomal regions specific to pathogenic isolates of Escherichia coli have a phylogenetically clustered distribution. J. Bacteriol. 180:1159-1165.
11. Cheetham, B. F., and M. E. Katz. 1995. A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol. Microbiol. 18:201-208.
12. Chizhikov, V., A. Rasooly, K. Chumakov, and D. D. Levy. 2001. Microarray analysis of microbial virulence factors. Appl. Environ. Microbiol. 67:3258-3263.
13. Clermont, O., S. Bonacorsi, and E. Bingen. 2000. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66:4555-4558.
14. Dobrindt, U., and J. Hacker. 1999. Plasmids, phages and pathogenicity islands: lessons on the evolution of bacterial toxins, p. 3-23. In J. E. Alouf and J. H. Freer (ed.), The comprehensive sourcebook of bacterial protein toxins, 2nd ed. Academic Press, London, United Kingdom.
15. 536) of uropathogenic Escherichia coli strain 536. Infect. Immun. 70:6365-6372.
16. 536 of uropathogenic Escherichia coli strain 536. Infect. Immun. 69:4248-4256.
17. Dobrindt, U., U. Hentschel, J. B. Kaper, and J. Hacker. 2002. Genome plasticity in pathogenic and nonpathogenic enterobacteria. Curr. Top. Microbiol. Immunol. 264:157-175.
18. Dong, Y., J. D. Glasner, F. R. Blattner, and E. W. Triplett. 2001. Genomic interspecies microarray hybridization: rapid discovery of three thousand genes in the maize endophyte, Klebsiella pneumoniae 342, by microarray hybridization with Escherichia coli K-12 open reading frames. Appl. Environ. Microbiol. 67:1911-1921.
19. Dorrell, N., J. A. Mangan, K. G. Laing, J. Hinds, D. Linton, H. Al-Ghusein, B. G. Barrell, J. Parkhill, N. G. Stoker, A. V. Karlyshev, P, D. Butcher, and B. W. Wren. 2001. Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Res. 11:1706-1715.
20. Falkow, S, 1996. The evolution of pathogenicity in Escherichia coli, Shigella and Salmonella, p. 2723-2729. In F. C. Neidhardt, R. Curtis III, J. L. Ingraham, E. C. C. Lin, K. Brooks Low, Jr., B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology, 2nd ed. ASM Press, Washington, D.C.
21. Gill, R. T., S. Wildt, Y. T. Yang, S. Ziesman, and G. Stephanopoulos. 2002. Genome-wide screening for trait conferring genes using DNA microarrays. Proc. Natl. Acad. Sci. USA 99:7033-7038.
22. Hacker, J., and J. B. Kaper. 2000. Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol. 54:641-679.
23. Hayashi, T., K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii, K. Yokoyama, C. G. Han, E. Ohtsubo, K. Nakayama, T. Murata, M. Tanaka, T, Tobe, T. Iida, H. Takami, T. Honda, C. Sasakawa, N. Ogasawara, T. Yasunaga, S. Kuhara, T. Shiba, M. Hattori, and H. Shinagawa. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8:11-22.
24. Huang, S. H., C. Wass, Q. Fu, N. V. Prasadarao, M. Stins, and K. S. Kim. 1995. Escherichia coli invasion of brain microvascular endothelial cells in vitro and in vivo: molecular cloning and characterization of invasion gene ibe10. Infect. Immun. 63:4470-4475.
25. Hull, R. A., E. R. Gill, P. Hsu, B. H. Minshew, and S. Falkow. 1981. Construction and expression of recombinant plasmids encoding type 1 or D-mannose-resistant pili from a urinary tract infection Escherichia coli isolate. Infect. Immun. 33:933-938.
26. Jackson, R. W., J. W. Mansfield, D. L. Arnold, A. Sesma, C. D. Paynter, J. Murillo, J. D. Taylor, and A. Vivian. 2000. Excision from tRNA genes of a large chromosomal region, carrying avrPphB, associated with race change in the bean pathogen, Pseudomonas syringae pv. phaseolicola. Mol. Microbiol. 38:186-197.
27. Janke, B., U. Dobrindt, J. Hacker, and G. Blum-Oehler. 2001. A subtractive hybridisation analysis of genomic differences between the uropathogenic E. coli strain 536 and the E. coli K-12 strain MG1655. FEMS Microbiol. Lett. 199:61-66.
28. Johnson, J. R., and A. L. Stell. 2000. Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise. J. Infect. Dis. 181:261-272.
29. Johnson, J. R., T. T. O'Bryan, M. Kuskowski, and J. N. Maslow. 2001. Ongoing horizontal and vertical transmission of virulence genes and papa alleles among Escherichia coli blood isolates from patients with diverse-source bacteremia. Infect. Immun. 69:5363-5374.
30. Kaper, J. B., and J. Hacker. 1999. Pathogenicity islands, plasmids and other mobile elements. ASM Press, Washington, D.C.
31. -. J. Clin. Microbiol. 31:1200-1205.
32. Karch, H., S. Schubert, D. Zhang, W. Zhang, H. Schmidt, T. Ölschläger, and J. Hacker. 1999. A genomic island, termed high-pathogenicity island, is present in certain non-O157 Shiga toxin-producing Escherichia coli clonal lineages. Infect. Immun. 67:5994-6001.
33. Kiewitz, C., K. Larbig, J. Klockgether, C. Weinel, and B. Tümmler. 2000. Monitoring genome evolution ex vivo: reversible chromosomal integration of a 106 kb plasmid at two tRNA(Lys) gene loci in sequential Pseudomonas aeruginosa airway isolates. Microbiology 146:2365-2373.
34. Knapp, S., J. Hacker, I. Then, D. Müller, and W. Goebel. 1984. Multiple copies of hemolysin genes and associated sequences in the chromosomes of uropathogenic Escherichia coli strains. J. Bacteriol. 159:1027-1033.
35. Korhonen, T. K., M. V. Valtonen, J. Parkkinen, V. Väisänen-Rhen, J. Finne, I. Ørskov, F. Ørskov, S. B. Svenson, and P. H. Mäkelä. 1985. Serotypes, hemolysin production, and receptor recognition of Escherichia coli strains associated with neonatal sepsis and meningitis. Infect. Immun. 48:486-491.
36. Lawrence, J. G., and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:9413-9417.
37. Levine, M. M., E. J. Bergquist, D. R. Nalin, D. H. Waterman, R. B. Hornick, C. R. Young, S. Sotman, and B. Rowe. 1978. Escherichia coli strains that cause diarrhoea but do not produce heat-labile or heat-stable enterotoxins and are non-invasive. Lancet i:1119-1122.
38. Maurelli, A. T., R. E. Fernández, C. A. Bloch, C. K. Rode, and A. Fasano. 1998. "Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc. Natl. Acad. Sci. USA 95:3943-3948.
39. Melkerson-Watson, L. J., C. K. Rode, L. Zhang, B. Foxman, and C. A. Bloch. 2000. Integrated genomic map from uropathogenic Escherichia coli J96. Infect. Immun. 68:5933-5942.
40. Mellies, J. L., F. Navarro-Garcia, I. Okeke, J. Frederickson, J. P. Nataro, and J. B. Kaper. 2001. espC pathogenicity island of enteropathogenic Escherichia coli encodes an enterotoxin. Infect. Immun. 69:315-324.
41. Mühldorfer, I., G. Blum, A. Donohue-Rolfe, H. Heier, T. Ölschläger, H. Tschäpe, U. Wallner, and J. Hacker. 1996. Characterization of Escherichia coli strains isolated from environmental water habitats and from stool samples of healthy volunteers. Res. Microbiol. 147:625-635.
42. Nataro, J. P., and J. B. Kaper. 1998. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11:142-201.
43. Ochman, H., and I. B. Jones. 2000. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19:6637-6643.
44. Ochman, H., J. G. Lawrence, and E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
45. Ørskov, F., and I. Ørskov. 1992. Escherichia coli serotyping and disease in man and animals. Can. J. Microbiol. 38:699-704.
46. Ott, M., J. Hacker, T. Schmoll, T. Jarchau, T. K. Korhonen, and W. Goebel. 1986. Analysis of the genetic determinants coding for the S-fimbrial adhesin (sfa) in different Escherichia coli strains causing meningitis or urinary tract infections. Infect. Immun. 54:646-653.
47. Perna, N. T., G. Plunkett III, V. Burland, B. Mau, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Posfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. T. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, and F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529-533.
48. Reiter, W., D. P. Palm, and S. Yeats. 1989. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 17:1907-1914.
49. Rode, C. K., L. J. Melkerson-Watson, A. T. Johnson, and C. A. Bloch. 1999. Type-specific contributions to chromosome size differences in Escherichia coli. Infect. Immun. 19:230-236.
50. Salama, N., K. Guillemin, T. K. McDaniel, G. Sherlock, L. Tompkins, and S, Falkow. 2000. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc. Natl. Acad. Sci. USA 97:14668-14673.
51. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
52. Schmidt, H., C. Geitz, P. I. Tarr, M. Frosch, and H Karch. 1999. Non-O157:H7 pathogenic Shiga toxin-producing Escherichia coli: phenotypic and genetic profiling of virulence traits and evidence for clonality. J. Infect. Dis. 179:115-123.
53. Smoot, J. C., K. D. Barbian, J. J. Van Gompel, L. M. Smoot, M. S. Chaussee, G. L. Sylva, D. E. Sturdevant, S. M. Ricklefs, S. F. Porcella, L. D. Parkins, S. B. Beres, D. S. Campbell, T. M. Smith, Q. Zhang, V. Kapur, J. A. Daly, L. G. Veasy, and J. M. Musser. 2002. Genome sequence and comparative microarray analysis of serotype M 18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Proc. Natl. Acad. Sci. USA 99:4668- 4673.
54. Taylor, D. E., M. Rooker, M. Keelan, L. K. Ng, I. Martin, N. T. Perna, N. T. Burland, and F. R. Blattner. 2002. Genomic variability of O islands encoding tellurite resistance in enterohemorrhagic Escherichia coli O157:H7 isolates. J. Bacteriol. 184:4690-4698.
55. Van Vliet, F., A. Boyen, and N. Glansdorff. 1988. On interspecies gene transfer: the case of the argF gene of Escherichia coli. Ann. Inst. Pasteur Microbiol. 139:493-496.
56. Wriston, J. C., and T. O. Yellin. 1973. L-Asparaginase: a review. Adv. Enzymol. Relat. Areas Mol. Biol. 39:185-248.
57. York, H. K., and M. Stodolsky. 1981. Characterization of P1argF derivatives from Escherichia coli K12 transduction. I. IS1 elements flank the argF gene segment. Mol. Gen. Genet. 181:230-240.
58. Zhang, L., B. Foxman, S. D. Manning, P. Tallman, and C. F. Marrs. 2000. Molecular epidemiologic approaches to urinary tract infection gene discovery in uropathogenic Escherichia coli. Infect. Immun. 68:2009-2015.