Shiga toxin-producing Escherichia coli (STEC) is a leading cause of foodborne infection resulting in 265,000 illnesses and more than 3,600 hospitalizations annually. Since its identification in 1982 associated with an outbreak of haemorrhagic colitis, serotype O157:H7 has been the primary focus of research and surveillance. However, the increasing incidence of other serogroups, or non-O157 STEC, that are associated with clinical illness has since surpassed the incidence of O157 and has raised questions about the genetic diversity of this pathogen population. Six serogroups, O26, O45, O103, O111, O121, and O145, have been denoted as "big six" non-O157 STEC serogroups since they are frequently associated with clinical outcomes.In this dissertation, 895 non-O157 STEC isolates recovered from patients in Michigan between 2001-2018 were analyzed using whole genome sequencing (WGS) to identify virulence gene profiles and apply new typing methods to better discriminate closely related strains. The recovery of a wide range of serogroups from cases presenting with symptoms ranging from mild diarrhea to hemorrhagic colitis, indicates that genetic diversity and variation may have an impact on disease outcomes. The number and richness of serogroups identified over the past 18 years has been steadily increasing and serogroup alone lacks the discriminatory capabilities to classify related isolates. Indeed, strains representing the same sequence types (ST) were often found to be unrelated by serogroup. Notably, some serogroups, STs, virulence gene profiles and alleles were associated with clinical outcomes and patient demographics. Contrast to national surveillance, cases between 11 and 29 years of age had the highest frequency of STEC infections in Michigan.Additionally, a subset of 44 non-O157 STEC recovered from Michigan patients between 2000 and 2006 were examined more comprehensively while making comparisons to 114 clinical STEC isolates from Connecticut to examine the impact of geographic location on risk factors for non-O157 STEC infections. Lastly, a subset of STEC isolates associated with outbreaks in Michigan were examined to identify the impact of WGS on identification of strain relatedness for surveillance compared to pulsed-field gel electrophoresis.While most of the work outlined in this dissertation focused on characterizing clinical non-O157 STEC isolates, a comparative analysis of cattle isolates was also performed since cattle are an important reservoir of STEC. Indeed, numerous outbreaks and illnesses have been traced back to contaminated cattle-based food products or fecal contamination of water and crops. The ability of STEC to persist in the cattle reservoir and farm environment may give rise to more pathogenic strains due to the accumulation of horizontally acquired genes. 66 STEC isolates recovered from a beef herd over four samplings were examined to identify the genetic diversity within the cattle population and longitudinal persistence. The ability of a strain to form a strong biofilm was associated with the ability to persist and be recovered at multiple sampling phases from the same animal. Further, to better understand the genetic diversity of STEC recovered from the cattle reservoir, an additional 12 STEC isolates from three bovine herds (n = 78) and 241 clinical O157 STEC isolates (n = 1,135) were included to identify shared profiles. The similarity in serogroups and virulence gene profiles warrant a continued surveillance of the cattle environment to better understand crossover events and the ability of strains to evolve into new virulent STEC lineages. The work described in this dissertation helped to elucidate the genetic characteristics important for clinical outcomes and identified targets for future surveillance to better understand lineages that may be important for disease.
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