COMPARATIVE GENOME ANALYSIS OF E. coli O157:H7 POPULATIONS

Deaprtment of Food Science and technology, University of Nebraska, 330 Food Industry Complex, Lincoln, NE 68583-0919

E. coli O157:H7 is recognized as a leading cause of hemorrhagic colitis in the United States and other countries. Multi-locus genotyping methods suggest that the O157:H7 serotype is a geographically dispersed clone. However, high-resolution methods such as PFGE demonstrate that substantial genomic diversity exists among O157:H7 isolates of bovine or human origin. To investigate the detailed structure and ecology of E. coli O157:H7 populations, we developed Octamer Based Genome Scanning (OBGS), a multi-locus method that compares the length of genome segments that lie between combinations of over-represented, strand-biased oligomers in the genome. Fragment analysis of OBGS products ranging from 200-1,500 bases can be achieved on Li-Cor 4200L automated DNA sequencers. Phylogenetic analysis of OBGS products at 20% genome coverage was conducted on O157:H7 isolates of bovine and human origin and demonstrated that the E. coli O157:H7 clone has diverged into two distinct lineages. Strikingly, the bovine and human isolates were non-randomly distributed between the lineages; many of the animal isolates form a clade of highly related strains within one lineage while clinical isolates are primarily confined to the other lineage. Southern hybridization with lambdoid phages indicates that prophage-mediated events are associated with divergence. Accordingly, DNA sequence analysis of the shiga toxin 1 converting phage, HB4, demonstrates that shiga toxin converting prophage have undergone divergence through extensive exchange of functional segments of their genomes, suggesting that recombination events between phage/prophage may be responsible for the generation of genome diversity and the ecological segregation of E. coli O157:H7 populations.