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

A comparative whole genome analysis was performed on three newly sequenced O157:H7 strains with different profiles, previously isolated from feedlot cattle [C1-010 ( , +), C1-057 ( ), and C1-067 ( +, +)], as well as five foodborne outbreak strains and six -negative strains from NCBI. Phylogenomic analysis demonstrated that the -carrying C1-010 and -negative C1-057 strains were grouped with the six NCBI -negative O157:H7 strains in Cluster 1, whereas the -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 -carrying strain, and the six NCBI -negative strains and identify their prophages at the insertion sites. All -carrying prophages contained both the three Red recombination genes ( , , ) and their repressor . On the other hand, the majority of the -negative prophages carried only the three Red recombination genes, but their repressor was absent. In the absence of the repressor , 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 genes. We further investigated each of the 10 selected O157:H7 strains for their respective unique metabolic pathway genes. Seven unique metabolic pathway genes in the two -carrying strains and one in the single -carrying and seven -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 -carrying O157:H7 strains may potentially increase their competitiveness in complex environments, such as feedlot cattle. For the -carrying and -negative 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 O157:H7 in livestock and downstream food production environments.