The genomic analysis of Escherichia coli O157:H7 populations

E. coli O157:H7 comprises a geographically distributed population of highly related strains each carrying the same set of known virulence factors. These organisms are the most common cause of foodborne hemorrhagic colitis in the U.S., Canada, the U.K., and Japan. Despite the minti-locus similarity of E. coli O157:H7 strains, considerable genome diversity has been observed by high-resolution methods such as pulse-field gel electrophoresis. We developed a method termed octamer-based genome scanning (OBGS) to assess the genetic relatedness of E. coli O157:H7 isolates in detail. Our initial work by OBGS has shown that the populations can be divided into two lineages termed lineage I and lineage II. Descendants of these two lineages can be found in separated continents, suggesting that their divergence preceded geographic spread. Analysis of polymorphic loci shared by all lineage II strains further suggests that lineage II is a derived state of lineage I. To understand the genetic basis for the divergence of the lineages, we have mapped lineage-specific polymorphisms by high-density OBGS analysis using a panel of 150 different primer combinations and a set of 40 representative lineage I and II strains. Of 4,527 polymorphic OBGS products observed, 1,284 were lineage-specific, suggesting that they arose during divergence of the lineages. Cloning and DNA sequence analysis of 95 lineage-specific, polymorphic OBGS products identified a total of 60 independent loci. The polymorphisms included single nucleotide changes that create or destroy OBGS priming sites as well as insertions and deletions in various sizes. The largest functional category of genes carrying lineage-specific polymorphisms includes prophage genes, implying that one of the largest genetic differences between the lineages is prophage content. Two prophage-encoded, one plasmid-encoded, and four genomic polymorphisms map to genes which share homology with putative or known proteins associated with E. coli virulence. A total of 6 polymorphisms could confer lineage-specific abilities to survive in a certain niche. Such functional categories included central metabolism-, transport-, and regulation-associated polymorphisms. These finding support the hypothesis that some of polymorphisms could confer quantitative, lineage-specific differences in virulence or transmissibility