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Journal of Bacteriology, March 2003, p. 1831-1840, Vol. 185, No. 6
0021-9193/03/$08.00+0     DOI: 10.1128/JB.185.6.1831-1840.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays

Ulrich Dobrindt,1* Franziska Agerer,1 Kai Michaelis,1 Andreas Janka,2 Carmen Buchrieser,3 Martin Samuelson,4 Catharina Svanborg,4 Gerhard Gottschalk,5 Helge Karch,6 and Jörg Hacker1

Institut für Molekulare Infektionsbiologie der Universität Würzburg, 97070 Würzburg,1 Institut für Hygiene und Mikrobiologie der Universität Würzburg, 97080 Würzburg,2 Institut für Mikrobiologie und Genetik, Göttingen Genomics Laboratory, 37077 Göttingen,5 Institut für Hygiene der Universität Münster, 48149 Münster, Germany,6 Laboratoire de Génomique des Microorganismes Pathogènes, Institut Pasteur, 75724 Paris Cedex 15, France,3 Department of Microbiology, Immunology and Glycobiology, Institute of Laboratory Medicine, Lund University, 223 62 Lund, Sweden4

Received 16 August 2002/ Accepted 18 December 2002

Genomes of prokaryotes differ significantly in size and DNA composition. Escherichia coli is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal E. coli isolates, a whole-genome approach was applied. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic E. coli K-12 strain MG1655 was investigated in 26 E. coli isolates, including various extraintestinal and intestinal pathogenic E. coli isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of E. coli was determined using a DNA "pathoarray" developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different E. coli strains. Up to 10% of the E. coli K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic E. coli are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal E. coli isolates. Based on these results, the conserved E. coli core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among E. coli strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.

* Corresponding author. Mailing address: Institut für Molekulare Infektionsbiologie, Röntgenring 11, D-97070 Würzburg, Germany. Phone: 49 (0)931 312155. Fax: 49 (0)931 312578. E-mail: ulrich.dobrindt{at}mail.uni-wuerzburg.de.

Journal of Bacteriology, March 2003, p. 1831-1840, Vol. 185, No. 6
0021-9193/03/$08.00+0     DOI: 10.1128/JB.185.6.1831-1840.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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