Genetic and phenotypic factors associated with persistent Shiga toxin-producing Escherichia coli shedding in beef cattle.

Shiga toxin-producing Escherichia coli (STEC) is leading cause of foodborne infections. Cattle are an important STEC reservoir, though little is known about specific pathogen traits that impact persistence in the farm environment. Hence, we sought to evaluate STEC isolates recovered from beef cattle in a single herd in Michigan. To do this, we collected fecal grabs from 26 cattle and re-sampled 13 of these animals at three additional visits over a three-month period. In all, 66 STEC isolates were recovered for genomics and biofilm quantification using crystal violet assays. The STEC population was diverse representing seven serotypes including O157:H7, O26:H11 and O103:H2, which are commonly associated with human infections. Although a core genome analysis of 2,933 genes grouped isolates into clusters based on serogroups, some isolates within each cluster had variable biofilm levels and virulence gene profiles. Most (77.8%; n=49) isolates harbored stx2a, while 38 (57.5%) isolates formed strong biofilms. Isolates belonging to the predominant serogroup, O6 (n=36; 54.5%), were more likely to form strong biofilms, persistently colonize multiple cattle, and be acquired over time. A high-quality single nucleotide polymorphism (SNP) analysis of 33 O6 isolates detected only 0-13 SNP differences between strains, indicating that a highly similar strain type was persisting in this herd. Similar findings were observed for other persistent serogroups, though key genes were found to differ among strong and weak biofilm producers. Together, these data highlight the diversity and persistent nature of some STEC types in this important food animal reservoir.ImportanceFood animal reservoirs contribute to STEC evolution via the acquisition of horizontally acquired elements like Shiga toxin bacteriophages that enhance pathogenicity. In cattle, persistent fecal shedding of STEC contributes to contamination of beef and dairy products and to crops exposed to contaminated water systems. Hence, identifying factors important for STEC persistence is critical. This longitudinal study enhances understanding of the genetic diversity of STEC types circulating in a cattle herd and identifies genotypic and phenotypic traits associated with persistence. Key findings demonstrate that multiple STEC types readily persist in and are transmitted across cattle in a shared environment. These dynamics also enhance persistence of virulence genes that can be transferred between bacterial hosts, resulting in the emergence of novel STEC strain types. Understanding how pathogens persist and diversify in reservoirs is important for guiding new pre-harvest prevention strategies aimed at reducing foodborne transmission to humans.