Escherichia coli O157:H7 Phylogenetics: Implications for Virulence and Disease Distribution
Tarr, Gillian A. M.
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This dissertation uses phylogenetic classifications to investigate heterogeneity in the epidemiology of Shiga toxin-producing Escherichia coli (STEC) O157:H7, one of the top causes of foodborne illness and hospitalization. Isolates of a given phylogenetic lineage may express similar traits. Understanding differences between lineages may increase our understanding of STEC O157:H7 incidence and its progression to hemolytic uremic syndrome (HUS). The goals of this study were to: 1) validate HUS case status and compare common definitions of HUS; 2) test the association between phylogenetic lineage and HUS, determine how age affects this association, and quantify the portion of the association due to Shiga toxin genes (stx); and 3) determine whether STEC O157:H7 isolates of the same lineage cluster together or are equally distributed with other lineages. I conducted a retrospective cohort study of all culture-confirmed STEC O157:H7 cases reported to the Washington State Department of Health from 2005 through 2014. Isolates were typed using an established single nucleotide polymorphism (SNP) assay and grouped into phylogenetic lineages. Lineage Ib was the most common, followed by IIa and IIb. The remaining lineages were grouped in a “rare” category. I abstracted medical records of all hospitalized cases to validate HUS status using stringent clinical criteria. Compared to other common definitions of HUS, these stringent criteria best identified cases with severe disease as evidenced by dialysis. The definition used for public health reporting performed poorly when judged against the stringent criteria, overestimating HUS burden by twofold. Using the validated HUS outcome, I assessed the association between phylogenetic lineage and HUS using generalized estimating equations to account for lack of independence among STEC O157:H7 isolates with the same pulsed field gel electrophoresis profile. In unadjusted analysis, lineage IIb was associated with a significantly higher odds of HUS than lineage Ib [odds ratio (OR) =1.65; 95% confidence interval (CI) 1.05, 2.60]. However, when assessing effect modification of the OR by age, both lineage IIa and IIb were associated with higher odds of HUS among adults 20-59 but not among children <10 years-old. Associations between lineages IIa or IIb and HUS appeared to be mediated by the stx2a genotype. The concept of spatial segregation was used to assess the distribution of STEC O157:H7 cases by phylogenetic lineage. Using a kernel estimation method, statistically significant spatial segregation was detected (p=0.001), with foci of segregation among lineage IIb in the southwest region of the state and among lineage IIa in the south-central region. A generalized additive model adjusted for age and sex identified increased risk of lineage IIb infections in the southwest, consistent with the spatial segregation detected. Two additional methods confirmed the results. In exploratory analysis, I identified multiple risk factors potentially associated with infection by particular STEC O157:H7 lineages. Distinguishing lineages of the STEC O157:H7 serotype can provide insight into its maintenance, transmission, and virulence. The heterogeneity between lineages provides an opportunity to target interventions, both clinical and public health, to the specific form of the pathogen dominant in an area. This dissertation furthers our understanding of STEC O157:H7, as well as uncovering multiple questions that should be addressed to effectively limit the incidence and impact of this disease.
- Epidemiology