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

Abstract

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.

FIG. 1.

Analysis of the presence of virulence-associated genes among pathogenic, commensal, and laboratory E. coli strains using the E. coli pathoarray. (A) Signal intensities after DNA-DNA hybridization with labeled genomic DNA of the UPEC strain 536. (B) Signal intensities after DNA-DNA hybridization with labeled genomic DNA of the commensal E. coli isolate MGS 73 isolated from a healthy volunteer.

FIG. 2.

Detection of genomic alterations among pathogenic, commensal, and laboratory E. coli strains using DNA arrays. (A) Comparison of genomes of different pathogenic, commensal, and laboratory E. coli isolates and the E. coli K-12 strain MG1655 using Panorama E. coli gene arrays. The individual chromosomes are displayed linearly and in equal lengths. Missing-undetectable ORFs are marked by vertical black lines in the individual chromosomes. The positions of the undetectable ORFs refer to the E. coli MG1655 chromosome. The positions of tRNA genes frequently used as chromosomal insertion sites of horizontally acquired DNA elements and those of 10 prophages of strain MG1655, as well as the chromosomal origin and terminus of replication, are marked within the map of E. coli strain MG1655. (B) Detection of virulence-associated genes of E. coli and Shigella among pathogenic and commensal E. coli isolates using the E. coli pathoarray. Virulence-associated genes are grouped with regard to typical E. coli pathotypes. Missing-undetectable ORFs are marked by vertical black lines.