Unique DNA sequences of avian pathogenic Escherichia coli isolates as determined by genomic suppression subtractive hybridization

Genomic suppression subtractive hybridization was carried out between an avian pathogenic Escherichia coli (APEC) and an E. coli isolate from apparently healthy poultry (avian fecal E. coli or AFEC) to understand the genomic differences between APEC and AFEC and to identify potential virulence genes. In an effort to ensure that the genes identified were novel, tester and driver strains were chosen by their similarities in certain known virulence genes. In total, 24 subtractive hybridization fragments specific for APEC were obtained. Eight of the fragments were phage or plasmid related, 13 matched to chromosomal regions and three did not show homology to any known genes. We further determined the association of APEC-specific fragments with virulence by screening a collection of APEC, AFEC and human uropathogenic E. coli (UPEC) using the PCR. Chromosomally located fragments that matched to the ireA iron-responsive element gene, the tia invasion determinant gene, the ibeA invasion gene, genes encoding P pili and a gene encoding aldo/keto reductase were present at significantly higher frequencies in APEC and UPEC than in AFEC, suggesting their contribution to the virulence of extraintestinal pathogenic E. coli. No genes were found to be specific to APEC alone.