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A comparative whole genome analysis was performed on three newly sequenced  Escherichia coli  O157:H7 strains with different  stx  profiles, previously isolated from feedlot cattle [C1-010 ( stx1− ,  stx2c +), C1-057 ( stx− ), and C1-067 ( stx1 +,  stx2a +)], as well as five foodborne outbreak strains and six  stx -negative strains from NCBI. Phylogenomic analysis demonstrated that the  stx2c -carrying C1-010 and  stx -negative C1-057 strains were grouped with the six NCBI  stx -negative  E. coli  O157:H7 strains in Cluster 1, whereas the  stx2a -carrying C1-067 and five foodborne outbreak strains were clustered together in Cluster 2. Based on different clusters, we selected the three newly sequenced strains, one  stx2a -carrying strain, and the six NCBI  stx -negative strains and identify their prophages at the  stx  insertion sites. All  stx -carrying prophages contained both the three Red recombination genes ( exo ,  bet ,  gam ) and their repressor  cI . On the other hand, the majority of the  stx -negative prophages carried only the three Red recombination genes, but their repressor  cI  was absent. In the absence of the repressor  cI , the consistent expression of the Red recombination genes in prophages might result in more frequent gene exchanges, potentially increasing the probability of the acquisition of  stx  genes. We further investigated each of the 10 selected  E. coli  O157:H7 strains for their respective unique metabolic pathway genes. Seven unique metabolic pathway genes in the two  stx2a -carrying strains and one in the single  stx2c -carrying and seven  stx -negative strains were found to be associated with an upstream insertion sequence 629 within a conserved region among these strains. The presence of more unique metabolic pathway genes in  stx2a -carrying  E. coli  O157:H7 strains may potentially increase their competitiveness in complex environments, such as feedlot cattle. For the  stx2c -carrying and  stx -negative  E. coli  O157:H7 strains, the fact that they were grouped into the same phylogenomic cluster and had the same unique metabolic pathway genes suggested that they may also share closely related evolutionary pathways. As a consequence, gene exchange between them is more likely to occur. Results from this study could potentially serve as a basis to help develop strategies to reduce the prevalence of pathogenic  E. coli  O157:H7 in livestock and downstream food production environments.

frontiers in microbiology

Comparative Whole Genome Analysis of Escherichia coli O157:H7 Isolates From Feedlot Cattle to Identify Genotypes Associated With the Presence and Absence of stx Genes