The accessory genome of Shiga toxin-producing Escherichia coli (STEC) defines a persistent colonization type in cattle

Shiga toxin-producing Escherichia coli (STEC) strains can colonize cattle for several months and may, thus, serve as gene reservoir for the genesis of highly virulent zoonotic enterohemorrhagic E. coli (EHEC). Attempts to reduce the human risk for acquiring EHEC infections should include strategies to control such STEC strains persisting in cattle. We therefore aimed to identify genetic patterns associated with the STEC colonization type in the bovine host. We included 88 persistent (STECper, shedding ≥ 4 months) and 74 sporadically colonizing STEC (STECspo, shedding ≤ 2 months) isolates from cattle and 16 bovine STEC isolates with unknown colonization type. Genoserotype and MLST were determined and the isolates probed with a DNA microarray for virulence-associated genes (VAGs). All STECper belonged to only four genoserotypes (O26:H11, O156:H25, O165:H25, O182:H25) which formed three genetic clusters (ST21/396/1705, ST300/688, ST119). In contrast, STECspo were scattered among 28 genoserotypes and 30 MLST types with O157:H7 (ST11) and O6:H49 (ST1079) being the most prevalent. The microarray analysis identified 139 unique gene patterns that clustered with the genoserotypes and MLST types of the strains. While the STECper isolates possessed heterogeneous phylogenetic backgrounds, the accessory genome clustered these isolates together, separating them from STECspo. Given the vast genetic heterogeneity of bovine STEC strains, defining genetic patterns distinguishing STECper from STECspo will facilitate the targeted design of new intervention strategies counteracting these zoonotic pathogens at farm level.