“…Colony lysates, prepared from each bacterial strain cultured on Luria Bertani agar plates, were each tested in triplicate to confirm the PATS profiles as described previously [49 -52]. Briefly, primer pairs targeting the 8 polymorphic XbaI-, 7 polymorphic AvrII-restriction enzyme sites, and the four virulence genes encoding Shiga toxin 1 and 2 (Stx1 and Stx2), Intimin-γ (eae), and hemolysin-A (hlyA) were used to generate amplicons from the colony lysates in a hot start, touchdown PCR reaction [47,49,50,52,53]. PCR reactions amplifying the AvrII-restriction enzyme site were purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA), and digested with the AvrII restriction enzyme (New England Biolabs, Beverly, MA) to confirm the presence of the restriction site.…”