Doctor of Philosophy / Department of Diagnostic Medicine and Pathobiology / Harvey Morgan Scott / The use of antibiotics in food animals is of major concern as a purported cause of antimicrobial resistance (AMR) in human pathogens; as a result, alternatives to in-feed antibiotics such as heavy metals have been proposed. The effect of copper and CTC supplementation in weaned pigs on AMR in the gut microbiota was evaluated. Four treatment groups: control, copper, chlortetracycline (CTC), and copper plus CTC were randomly allocated to 32 pens with five pigs per pen. Fecal samples (n = 576) were collected weekly from three pigs per pen over six weeks and two Escherichia coli isolates per sample were tested phenotypically for antimicrobial and copper susceptibilities and genotypically for the presence of tetracycline (tet), copper (pcoD) and ceftiofur bla[subscript]C[subscript]M[subscript]Y₋₂) resistance genes. CTC-supplementation significantly increased tetracycline resistance and susceptibility to copper when compared with the control group. Copper supplementation decreased resistance to most of the antibiotics, including cephalosporins, over all treatment periods. However, copper supplementation did not affect minimum inhibitory concentrations of copper or detection of pcoD. While tetA and bla[subscript]C[subscript]M[subscript]Y₋₂ genes were associated with a higher multi-drug resistance (MDR), tetB and pcoD were associated with lower MDR. Supplementations of CTC or copper alone were associated with increased tetB prevalence; however, their combination was paradoxically associated with reduced prevalence. These studies indicate that E. coli isolates from the weaned pigs studied exhibit high levels of antibiotic resistance with diverse multi-resistant phenotypic profiles. In a related study, total fecal community DNA (n = 569) was used to detect 14 tet genes and to quantify gene copies of tetA, tetB, pcoD and bla[subscript]C[subscript]M[subscript]Y₋₂. CTC and copper plus CTC supplementation increased both the prevalence and gene copies of tetA, while decreasing both the prevalence and gene copies of tetB, when compared with the control group. The diversity of tet genes were reduced over time in the gut bacterial community. The roles of copper supplementation in pig production and pco-mediated copper resistance in E. coli need to be further explored since a strong negative association of pcoD, with both tetA and bla[subscript]C[subscript]M[subscript]Y₋₂, suggests there exist opportunities to select for a more innocuous resistance profile.

Master of Science / Department of Biomedical Science / H. Morgan Scott / The modern phenomenon of increasing prevalence of antibiotic resistance in clinically relevant bacteria threatens humanity’s ability to use antibiotics to treat infection in both humans and animals. Despite the marked complexity of bacterial evolution, there is tremendous importance in unfolding the process by which antibiotic resistance genes emerge, disperse, and persist in the natural world. This thesis investigates certain aspects of this process in two experimental studies that differ primarily by scale but also by methodology. The first study examined the long-term annual prevalence of ceftiofur and tetracycline resistance in Canadian beef cattle from 2002 to 2011 at both phenotypic and genotypic levels. Ceftiofur was present at a very low prevalence (<4%) that did not statistically increase over the decade (p<0.05). Relative proportions of tetracycline genes tet(A), tet(B), and tet(C) also did not significantly change over the observation period. However, it was surprising that almost 20% of isolates recovered from nonselective agar harbored tet(C) given that current literature generally indicates that tet(C) is significantly less prevalent than tet(A) or tet(B). The usage of historical samples in addition to parallel selective plating using agar supplemented with antibiotics provided insight into systemic bias present in common microbial approaches. Long-term sample freezing significantly diminished the recoverability of E. coli over time. Additionally the usage of selective MacConkey agar containing tetracycline biased the proportions of tetracycline genes to over-represent the tet(B) gene in commensal E. coli compared to nonselective MacConkey agar. The second study attempted to explain the short-term selection effects of antibiotic treatment on the overall ecological fitness of commensal E. coli using bacterial growth parameters estimated from spectrophotometric growth curves as a simple surrogate of general fitness. Treating cattle with either tetracycline or ceftiofur was found to not only select in favor of tetracycline resistant bacteria, but also increased the overall fitness among the tetracycline resistant population. However, growth curves were unable able to explain why transiently selected resistant bacteria were eventually replaced by susceptible bacteria once the selection pressure was removed.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / K.R. Harkin / T.G. Nagaraja / Associations of land cover/land use, socio-economic and housing, and hydrological and soil-hydrological variables were evaluated retrospectively as potential risk factors for canine leptospirosis in Kansas and Nebraska using Geographic Information Systems (GIS). The sample included 94 dogs positive for leptospirosis based on a positive polymerase chain reaction test for leptospires in urine, isolation of leptospires on urine culture, a single reciprocal serum titer of 12,800 or greater, or a four-fold rise in reciprocal serum titers over a 2 to 4 week period; and 185 dogs negative for leptospirosis based on a negative polymerase chain reaction test and reciprocal serum titers less than 400. Publicly available geographic datasets representing land cover/land use, socio-economic and housing characteristics, and hydrologic and soil hydrologic themes were analyzed along with geocoded addresses of case/control locations in GIS. Among different land cover/land use variables evaluated, urban areas (high and medium intensity urban areas and urban areas in general) and evergreen forests and forest/woodlands in general were significant risk factors. Among socio-economic and demographic determinants evaluated, houses lacking complete plumbing facilities, poverty status by age (18-64), and living within 2500 meters of a university/college or parks/forests were significant risk factors. Proximity to water features, hydrologic density and frequently flooded areas were identified as significant risk factors for canine leptospirosis among hydrologic and soil-hydrologic variables. Pet owners whose dogs live in such areas or under these circumstances should consider vaccination to prevent canine leptospirosis.

No description available.

Objectives: To describe the use of standardized protocols (SPs) in emergency departments (EDs) across Ontario for childhood asthma and analyze the association of SPs with hospital admissions, 7-day ED re-visits, and outpatient follow-up visits. Methods: Population-based retrospective cohort study using health administrative data and survey data. EDs were categorized as having the optimal, other, or no SP for each outcome. Associations were tested with generalized estimating equations. Results: Between 2006/04/14-2009/02/28, 46,510 children with asthma were seen in 146 EDs, with 43 (29.5%) having SPs. Children treated in EDs with the optimal SP compared to no SP had no significant differences in hospital admissions (AOR 1.17; 95% CI 0.91, 1.49) or ED re-visits (AOR 1.09; 95% CI 0.85, 1.40) but were more likely to have follow-up visits (AOR 1.27; 95% CI 1.02, 1.59). Conclusions: SPs for childhood asthma are not common in Ontario EDs and had little impact on outcomes measured.

The variability in caffeine consumption and inconsistencies among studies linking caffeine to heart disease may be explained by genetic variation. Caffeine antagonizes adenosine receptors with downstream effects on dopamine and serotonin. The objectives of this thesis were to determine whether the DRD2 957C>T or HTR2A 102C>T polymorphisms are associated with caffeine consumption or modify the association between coffee consumption and risk of myocardial infarction (MI). DRD2 genotype was associated with caffeine consumption among non-smokers and CYP1A2 -163C allele carriers. HTR2A genotype was associated with caffeine consumption among non-smokers and subjects with the ADORA2A TT genotype. Neither polymorphism modified the association between coffee consumption and risk of MI; however, a significant coffee x HTR2A interaction was seen among subjects with the CYP1A2 -163C allele. The results suggest caffeine’s reinforcing effects may be mediated by the dopamine and serotonin receptors and implicate serotonin in caffeine’s effect on risk of MI.

Objectives: To describe the use of standardized protocols (SPs) in emergency departments (EDs) across Ontario for childhood asthma and analyze the association of SPs with hospital admissions, 7-day ED re-visits, and outpatient follow-up visits. Methods: Population-based retrospective cohort study using health administrative data and survey data. EDs were categorized as having the optimal, other, or no SP for each outcome. Associations were tested with generalized estimating equations. Results: Between 2006/04/14-2009/02/28, 46,510 children with asthma were seen in 146 EDs, with 43 (29.5%) having SPs. Children treated in EDs with the optimal SP compared to no SP had no significant differences in hospital admissions (AOR 1.17; 95% CI 0.91, 1.49) or ED re-visits (AOR 1.09; 95% CI 0.85, 1.40) but were more likely to have follow-up visits (AOR 1.27; 95% CI 1.02, 1.59). Conclusions: SPs for childhood asthma are not common in Ontario EDs and had little impact on outcomes measured.

The variability in caffeine consumption and inconsistencies among studies linking caffeine to heart disease may be explained by genetic variation. Caffeine antagonizes adenosine receptors with downstream effects on dopamine and serotonin. The objectives of this thesis were to determine whether the DRD2 957C>T or HTR2A 102C>T polymorphisms are associated with caffeine consumption or modify the association between coffee consumption and risk of myocardial infarction (MI). DRD2 genotype was associated with caffeine consumption among non-smokers and CYP1A2 -163C allele carriers. HTR2A genotype was associated with caffeine consumption among non-smokers and subjects with the ADORA2A TT genotype. Neither polymorphism modified the association between coffee consumption and risk of MI; however, a significant coffee x HTR2A interaction was seen among subjects with the CYP1A2 -163C allele. The results suggest caffeine’s reinforcing effects may be mediated by the dopamine and serotonin receptors and implicate serotonin in caffeine’s effect on risk of MI.

We first studied factors associated with the rate of colonoscopy by primary care physicians (PCPs) in Ontario between the years 1996 and 2005. Next, we conducted an Instrumental Variable Analysis (IVA) to estimate the effect of colonoscopy on colorectal cancer (CRC) incidence and mortality on average-risk subjects aged 50-74 years. Finally, we explored two study cohorts, one by including subjects who had the outcomes during the exposure period (unselected cohort) and the other cohort by excluding those subjects (restricted cohort). We estimated the absolute risk reduction associated with colonoscopy in preventing CRC incidence and mortality using traditional regression analysis, propensity score analysis and IVA. PCPs who were Canadian medical graduates and with more years of experience were more likely to use colonoscopy. PCPs were more likely to use colonoscopy if their patient populations were predominantly women, older, had more illnesses, and if their patients resided in less marginalized neighborhoods (lower unemployment, fewer immigrants, higher income, higher education, and higher English/French fluency). Using PCP rate of discretionary colonoscopy as an instrumental variable, receipt of colonoscopy was associated with a 0.60% absolute reduction in 7-year CRC incidence and a 0.17% absolute reduction in 5-year risk of death due to CRC. The unselected cohort showed an increase in CRC incidence and mortality associated with colonoscopy, whereas the restricted cohort showed a reduction in CRC incidence and mortality associated with colonoscopy. In the restricted cohort, using different statistical models, the absolute risk reduction varied from 0.52-0.60% for CRC incidence and 0.08-0.17% for CRC mortality. There were social disparities in the use of colonoscopy by PCPs and this disparity increased as the overall use of colonoscopy increased over time. Colonoscopy is effective in reducing incidence and mortality due to CRC. Different methods of subject selection and statistical analysis provided different estimates of colonoscopy effectiveness.

We first studied factors associated with the rate of colonoscopy by primary care physicians (PCPs) in Ontario between the years 1996 and 2005. Next, we conducted an Instrumental Variable Analysis (IVA) to estimate the effect of colonoscopy on colorectal cancer (CRC) incidence and mortality on average-risk subjects aged 50-74 years. Finally, we explored two study cohorts, one by including subjects who had the outcomes during the exposure period (unselected cohort) and the other cohort by excluding those subjects (restricted cohort). We estimated the absolute risk reduction associated with colonoscopy in preventing CRC incidence and mortality using traditional regression analysis, propensity score analysis and IVA. PCPs who were Canadian medical graduates and with more years of experience were more likely to use colonoscopy. PCPs were more likely to use colonoscopy if their patient populations were predominantly women, older, had more illnesses, and if their patients resided in less marginalized neighborhoods (lower unemployment, fewer immigrants, higher income, higher education, and higher English/French fluency). Using PCP rate of discretionary colonoscopy as an instrumental variable, receipt of colonoscopy was associated with a 0.60% absolute reduction in 7-year CRC incidence and a 0.17% absolute reduction in 5-year risk of death due to CRC. The unselected cohort showed an increase in CRC incidence and mortality associated with colonoscopy, whereas the restricted cohort showed a reduction in CRC incidence and mortality associated with colonoscopy. In the restricted cohort, using different statistical models, the absolute risk reduction varied from 0.52-0.60% for CRC incidence and 0.08-0.17% for CRC mortality. There were social disparities in the use of colonoscopy by PCPs and this disparity increased as the overall use of colonoscopy increased over time. Colonoscopy is effective in reducing incidence and mortality due to CRC. Different methods of subject selection and statistical analysis provided different estimates of colonoscopy effectiveness.