Comparative Genomics Using DNA Arrays

The genomes of several different pathogenic and nonpathogenic E. coli as well as those of Shigella isolates have been compared in different studies by DNA-DNA hybridization using DNA arrays. Comparative genomic hybridization using a K-12-specific array allows detection of chromosomal regions that have been replaced by acquisition and chromosomal insertion of horizontally acquired DNA and gene loss. The K-12-specific genome content of different E. coli isolates has been compared to assess the incidence of gene transfer and gene loss for E. coli genome evolution: a total of 67 events, including 37 additions and 30 deletions, were required to account for the distribution of all genes present in the chromosome of K-12 strain MG1655 [38]. The genome content of 26 different ExPEC and IPEC strains was compared using a K-12-specific array in combination with an array comprising many probes specific for virulence-associated genes of ExPEC and IPEC. The conserved chromosomal E. coli backbone was assessed to comprise about 3100 genes and the majority of variable ORFs of the K-12 genome were functionally grouped as hypothetical, unclassified, or as prophages and cell envelope genes. Analysis of the genome content using the so-called "E. coli pathoarray" revealed that many virulence-associated ORFs of ExPEC are also widespread among nonpathogenic, commensal isolates [39]. Another more recent study of 22 ExPEC, IPEC, and Shigella strains confirmed the range of order of the common backbone of the E. coli genome as estimated by Dobrindt and coworkers [39] to contain about 2800 ORFs. The mosaic distribution of absent regions indicated that the genomes of pathogenic strains were highly diversified because of insertions and deletions [40]. An array based on the E. coli K-12 genome has also been used to determine the common E. coli core gene pool in O26 verotoxigenic E. coli strains [41].

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