AUTHOR=Jia Mo , Geornaras Ifigenia , Martin Jennifer N. , Belk Keith E. , Yang Hua 

TITLE=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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.647434

DOI=10.3389/fmicb.2021.647434

ISSN=1664-302X

ABSTRACT=<p>A comparative whole genome analysis was performed on three newly sequenced <italic>Escherichia coli</italic> O157:H7 strains with different <italic>stx</italic> profiles, previously isolated from feedlot cattle [C1-010 (<italic>stx1−</italic>, <italic>stx2c</italic>+), C1-057 (<italic>stx−</italic>), and C1-067 (<italic>stx1</italic>+, <italic>stx2a</italic>+)], as well as five foodborne outbreak strains and six <italic>stx</italic>-negative strains from NCBI. Phylogenomic analysis demonstrated that the <italic>stx2c</italic>-carrying C1-010 and <italic>stx</italic>-negative C1-057 strains were grouped with the six NCBI <italic>stx</italic>-negative <italic>E. coli</italic> O157:H7 strains in Cluster 1, whereas the <italic>stx2a</italic>-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 <italic>stx2a</italic>-carrying strain, and the six NCBI <italic>stx</italic>-negative strains and identify their prophages at the <italic>stx</italic> insertion sites. All <italic>stx</italic>-carrying prophages contained both the three Red recombination genes (<italic>exo</italic>, <italic>bet</italic>, <italic>gam</italic>) and their repressor <italic>cI</italic>. On the other hand, the majority of the <italic>stx</italic>-negative prophages carried only the three Red recombination genes, but their repressor <italic>cI</italic> was absent. In the absence of the repressor <italic>cI</italic>, 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 <italic>stx</italic> genes. We further investigated each of the 10 selected <italic>E. coli</italic> O157:H7 strains for their respective unique metabolic pathway genes. Seven unique metabolic pathway genes in the two <italic>stx2a</italic>-carrying strains and one in the single <italic>stx2c</italic>-carrying and seven <italic>stx</italic>-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 <italic>stx2a</italic>-carrying <italic>E. coli</italic> O157:H7 strains may potentially increase their competitiveness in complex environments, such as feedlot cattle. For the <italic>stx2c</italic>-carrying and <italic>stx</italic>-negative <italic>E. coli</italic> 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 <italic>E. coli</italic> O157:H7 in livestock and downstream food production environments.</p>