Variability in the Occupancy of Escherichia coli O157 Integration Sites by Shiga Toxin-Encoding Prophages

Abstract

<i>Escherichia coli</i> O157:H7 strains often produce Shiga toxins encoded by genes on lambdoid bacteriophages that insert into multiple loci as prophages. O157 strains were classified into distinct clades that vary in virulence. Herein, we used PCR assays to examine Shiga toxin (Stx) prophage occupancy in <i>yehV</i>, <i>argW</i>, <i>wrbA</i>, and <i>sbcB</i> among 346 O157 strains representing nine clades. Overall, <i>yehV</i> was occupied in most strains (n = 334, 96.5%), followed by <i>wrbA</i> (n = 213, 61.6%), <i>argW</i> (n = 103, 29.8%), and <i>sbcB</i> (n = 93, 26.9%). Twelve occupancy profiles were identified that varied in frequency and differed across clades. Strains belonging to clade 8 were more likely to have occupied <i>sbcB</i> and <i>argW</i> sites compared to other clades (<i>p</i> < 0.0001), while clade 2 strains were more likely to have occupied <i>wrbA</i> sites (<i>p</i> < 0.0001). Clade 8 strains also had more than the expected number of occupied sites based on the presence of <i>stx</i> variants (<i>p</i> < 0.0001). Deletion of a 20 kb non-Stx prophage occupying <i>yehV</i> in a clade 8 strain resulted in an ~18-fold decrease in <i>stx2</i> expression. These data highlight the complexity of Stx prophage integration and demonstrate that clade 8 strains, which were previously linked to hemolytic uremic syndrome, have unique Stx prophage occupancy profiles that can impact <i>stx2</i> expression.