Metformin has been associated with a reduction in breast cancer incidence, however its effect on mortality following cancer has not been adequately examined. The purpose of this study was to evaluate the impact of metformin therapy on mortality in women with breast cancer. Using Ontario health databases, this retrospective cohort examined the impact of metformin on mortality among women aged 66 years or older with diabetes and breast cancer. After a mean follow-up of 4.5 years, there was no association between cumulative metformin use and either all-cause or breast cancer-specific mortality (HR 0.97, 95% CI 0.92-1.07; HR 0.91, 95% CI 0.81-1.03 respectively per additional year of cumulative metformin use). Though metformin was not associated with a reduction in mortality in our study of older women with breast cancer, there is still a need to examine whether metformin has an effect on mortality in other breast cancer populations.

Metformin has been associated with a reduction in breast cancer incidence, however its effect on mortality following cancer has not been adequately examined. The purpose of this study was to evaluate the impact of metformin therapy on mortality in women with breast cancer. Using Ontario health databases, this retrospective cohort examined the impact of metformin on mortality among women aged 66 years or older with diabetes and breast cancer. After a mean follow-up of 4.5 years, there was no association between cumulative metformin use and either all-cause or breast cancer-specific mortality (HR 0.97, 95% CI 0.92-1.07; HR 0.91, 95% CI 0.81-1.03 respectively per additional year of cumulative metformin use). Though metformin was not associated with a reduction in mortality in our study of older women with breast cancer, there is still a need to examine whether metformin has an effect on mortality in other breast cancer populations.

Doctor of Philosophy / Department of Electrical and Computer Engineering / Caterina Scoglio / Vector-borne diseases not only cause devastating economic losses, they also significantly impact human health in terms of morbidity and mortality. From an economical and humane point of view, mitigation and control of vector-borne diseases are essential. Studying dynamics of vector-borne disease transmission is a challenging task because vector-borne diseases show complex dynamics impacted by a wide range of ecological factors. Understanding these factors is important for the development of mitigation and control strategies. Mathematical models have been commonly used to translate assumptions concerning biological (medical, demographical, behavioral, immunological) aspects into mathematics, linking biological processes of transmission and dynamics of infection at population level. Mathematical analysis translates results back into biology. Classical deterministic epidemic models do not consider spatial variation, assuming space is homogeneous. Spatial spread of vector-borne diseases observed many times highlights the necessity of incorporating spatial dynamics into mathematical models. Heterogeneous demography, geography, and ecology in various regions may result in different epidemiological characteristics. Network approach is commonly used to study spatial evolution of communicable diseases transmitted among connected populations. In this dissertation, the spread of vector-borne diseases in time and space, is studied to understand factors that contribute to disease evolution. Network-based models have been developed to capture different features of disease transmission in various environments. Network nodes represent geographical locations, and the weights represent the level of contact between regional pairings. Two competent vector populations, Aedes mosquitoes and Culex mosquitoes, and two host populations, cattle and humans were considered. The deterministic model was applied to the 2010 Rift Valley fever outbreak in three provinces of South Africa. Trends and timing of the outbreak in animals and humans were reproduced. The deterministic model with stochastic parameters was applied to hypothetical Rift Valley fever outbreak on a large network in Texas, the United States. The role of starting location and size of initial infection in Rift Valley fever virus spread were studied under various scenarios on a large-scale network. The reproduction number, defined as the number of secondary infections produced by one infected individual in a completely susceptible population, is typically considered an epidemic threshold of determining whether a disease can persist in a population. Extinction thresholds for corresponding Continuous-time Markov chain model is used to predict whether a disease can perish in a stochastic setting. The network level reproduction number for diseases vertically and horizontally transmitted among multiple species on heterogeneous networks was derived to predict whether a disease can invade the whole system in a deterministic setting. The complexity of computing the reproduction number is reduced because the expression of the reproduction number is the spectral radius of a matrix whose size is smaller than the original next generation matrix. The expression of the reproduction number may have a wide range of applications to many vector-borne diseases. Reproduction numbers can vary from below one to above one or from above one to below one by changing movement rates in different scenarios. The observations provide guidelines on executing movement bans in case of an epidemic. To compute the extinction threshold, corresponding Markov chain process is approximated near disease free equilibrium. The extinction threshold for Continuous-time Markov chain model was analytically connected to the reproduction number under some assumptions. Numerical simulation results agree with analytical results without assumptions, proposing a mathematical problem of proving the existence of the relationships in general. The distance of the extinction threshold were shown to be closer to one than the reproduction number. Consistent trends of probability of extinction varying with disease parameters observed through numerical simulations provide novel insights into disease mitigation, control, and elimination.

Doctor of Philosophy / Department of Diagnostic Medicine and Pathobiology / Michael W. Sanderson / The last outbreak for Foot and Mouth Disease (FMD) in the United States (U.S.) was in 1929. Since that time the U.S. has not had any exposure to the disease or vaccination, creating a very susceptible livestock population. The central U.S. has a large susceptible livestock population including cattle, swine, sheep, and goats. The impact of FMD in the U.S. would be devastating. Simulation modeling is the only avenue available to study the potential impacts of an introduction in the U.S. Simulation models are dependent on accurate estimates of the frequency and distance distribution of contacts between livestock operations to provide valid model results for planning and decision making including the relative importance of different control strategies. Due to limited data on livestock movement rates and distance distribution for contacts a survey was conducted of livestock producers in Colorado and Kansas. These data fill a need for region specific contact rates to provide parameters for modeling a foreign animal disease. FMD outbreaks often require quarantine, depopulation and disposal of whole herds in order to prevent the continued spread of the disease. Experts were included in a Delphi survey and round table discussion to critically evaluate the feasibility of depopulating a large feedlot. No clearly acceptable method of rapidly depopulating a large feedlot was identified. Participants agreed that regardless of the method used for depopulation of cattle in a large feedlot, it would be very difficult to complete the task quickly, humanely, and be able to dispose of the carcasses in a timely fashion. Simulation models were developed to assess the impact of livestock herd types and vaccination on FMD outbreaks in the central U.S. using the North American Animal Disease Spread Model (NAADSM), a spatially explicit, stochastic state-transition simulation model. Simulation scenarios with large vaccination zones had decreased outbreak length and number of herds destroyed. Vaccination did not provide additional benefit to control compared to depopulation alone when biosecurity and movement controls were high, however the ability to achieve high levels of biosecurity and movement control may be limited by labor and animal welfare concerns.

Doctor of Philosophy / Department of Electrical and Computer Engineering / Caterina Maria Scoglio / We have analytically discovered the existence of two global epidemic invasion thresholds in a directed meta-population network model of the United States cattle industry. The first threshold describes the outbreak of disease first within the core of the livestock system while the second threshold describes the invasion of the epidemic into a second class of locations where the disease would pose a risk for contamination of meat production. Both thresholds have been verified through extensive numerical simulations. We have further derived the relationship between the pair of thresholds and discovered a unique dependence on the network topology through the fractional compositions and the in-degree distributions of the transit and sink nodes. We then addressed a major challenge for epidemiologists and their efforts to model disease outbreaks in cattle. There is a critical shortfall in the availability of large-scale livestock movement data for the United States. We meet this challenge by developing a method to estimate cattle movement parameters from publicly available data. Across 10 Central States of the US, we formulated a large, convex optimization problem to predict the cattle movement parameters which, having minimal assumptions, provide the best fit to the US Department of Agriculture's Census database and follow constraints defined by scientists and cattle experts. Our estimated parameters can produce distributions of cattle shipments by head which compare well with shipment distributions also provided by the US Department of Agriculture. This dissertation concludes with a brief incorporation of the analytic models and the parameter estimation. We approximated the critical movement rates defined by the global invasion thresholds and compared them with the average estimated cattle movement rates to find a significant opportunity for epidemics to spread through US cattle populations.

Master of Science / Department of Industrial & Manufacturing Systems Engineering / Todd Easton / History has shown that epidemics can occur at random and without warning — devastating the populations which they impact. As a preventative measure, modern medicine has helped to reduce the number of diseases that can instigate such an event, nevertheless natural and man-made disease mutations place us continuously at risk of such an outbreak. As a second line of defense, extensive research has been conducted to better understand spread patterns and the efficacy of various containment and mitigation strategies. However, these simulation models have primarily focused on minimizing the impact to groups of people either from an economic or societal perspective and little study has been focused on determining the utility maximizing strategy for an individual. Therefore, this work explores the decisions of individuals to determine emergent behaviors and characteristics which lead to increased probability of survival during an epidemic. This is done by leveraging linear program optimization techniques and the concept of Agent Based Simulation, to more accurately capture the complexity inherent in most real-world systems via the interactions of individual entities. This research builds on 5 years of study focused on rural epidemic simulation, resulting in the development of a 4,000-line computer code simulation package. This adaptable simulation can accurately model the interactions of individuals to discern the impact of any general disease type, and can be implemented on the population of any contiguous counties within Kansas. Furthermore, a computational study performed on the 17 counties of northwestern Kansas provides game theoretical based insights as to what decisions increase the likelihood of survival. For example, statistically significant findings suggest that an individual is four times more likely to become infected if they rush stores for supplies after a government issued warning instead of remaining at home. This work serves as a meaningful step in understanding emergent phenomena during an epidemic which, subsequently, provides novel insight to an individual’s utility maximizing strategy. Understanding the main findings of this research could save your life.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / H. Morgan Scott / Copper, as copper sulfate, is often used as an alternative to in-feed antibiotics for growth promotion in both swine and cattle diets. Gut bacteria exposed to copper can acquire resistance, which among enterococci is conferred by a plasmid-borne transferable copper resistance gene (tcrB). The plasmid also carries tetracycline [tet(M)] and macrolide [erm(B)] resistance genes. Because of the genetic link between acquired copper (tcrB) and antibiotic resistance in Enterococcus spp., we hypothesized that copper supplementation may exert selection pressure for enterococci to become resistant to macrolides and tetracyclines, and possibly to other antibiotics. We conducted studies in cattle and swine to investigate the relationship between copper supplementation and the fecal prevalence of tcrB-positive enterococci, as well as its potential co-selection for macrolide and tetracycline resistance. The prevalence was higher in animals fed diets supplemented with elevated level of copper compared to normal level (P < 0.05). The tcrB-positive isolates belonged to either E. faecium or E. faecalis; the majority was E. faecium. All tcrB-positive isolates also contained both erm(B) and tet(M) genes; however, none of them harbored the vanA gene. Median minimum inhibitory concentrations (MIC) of copper for tcrB-positive and tcrB-negative enterococci were 22 mM and 4 mM, respectively (P < 0.0001). The overall prevalence of erm(B) and tet(M) genes among enterococcal isolates of cattle were 46.8 % and 57.5%, respectively; in contrast,100% of the swine isolates were positive for both erm(B) and tet(M) genes. The transferability of the tcrB gene was demonstrated by filter mating assay. Multi-locus variable number tandem repeat analysis revealed a genetically diverse population of enterococci. The finding of a strong association between the copper resistance gene and other antibiotic (tetracycline and tylosin) resistance determinants is significant because enterococci are potential pathogens and have the propensity to transfer resistance genes to other bacteria in the gut. The occurrence of vancomycin resistant enterococci in swine in the US is very rare. Strains of E. faecium positive for vanA, that confers resistance to vancomycin, were isolated and characterized from swine feces. The swine strains belonged to clonal complex 17, a well-adapted hospital clone throughout the world.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Wenjun Ma / Influenza A virus (IAV) is an enveloped, segmented, negative-sense RNA virus that infects avian species and mammals. Its segmented feature enables antigenic shift which can generate novel IAVs that pose a threat to animal and public health due to lack of immunity to these viruses. Pigs have been considered the “mixing vessels” of influenza A viruses to generate novel reassortant viruses that may threaten animal and public health. Therefore, it is necessary to understand the pathogenicity and transmissibility of newly emerged reassortant viruses in swine. Adding to this complexity is the newly identified bat influenza A-like viruses which have roused interest in understanding the evolutionary history and pandemic potential of bat influenza. At least 10 different genotypes of novel reassortant H3N2 IAVs with gene(s) from 2009 pandemic H1N1 [A(H1N1)pdm09] have been identified in pigs in the United States. To date, only three genotypes of these viruses have been evaluated in animal models leaving the pathogenicity and transmissibility of the other seven genotype viruses unknown. We showed that reassortant viruses with genes from A(H1N1)pdm09 are pathogenic and transmissible in pigs. Further studies showed that avian-like glycine at position 228 of the HA receptor binding site is responsible for inefficient transmission of the reassortant H3N2 IAV with five A(H1N1)pdm09 genes. Studying the recently discovered IAV-like sequences from bats has been hindered by the lack of live virus isolation or culturing. Using synthetic genomics, we successfully rescued modified bat influenza viruses that had the HA and NA coding regions replaced with two classical IAVs. Additional studies were performed with truncations on NS1 protein and substitution of a putative virulence mutation in bat influenza PB2. Virus reassortment experiments demonstrated that bat influenza has limited genetic and protein compatibility with other influenza viruses; however, it readily reassorts with another divergent bat influenza virus. Taken together, our results provide insights into the pathogenicity and transmissibility of novel reassortant H3N2 IAVs in pigs. It also indicates that the bat influenza viruses recently identified are viable viruses that pose little pandemic threat to humans. Moreover, they provide new insights into the evolution and basic biology of influenza viruses.

Doctor of Philosophy / Department of Plant Pathology / William W. Bockus / James P. Stack / Wheat blast, caused by the Triticum pathotype of Magnaporthe oryzae (MoT), is a serious disease of wheat causing yield failures and significant economic losses during epidemic years in Brazil, Paraguay, and Bolivia. Although outbreaks occur only sporadically, wheat blast is considered a major disease affecting wheat production in South America and may be a threat to the wheat crop in the United States. Wheat is a major crop in the U.S. and wheat exports from the U.S. are important to food security of several countries around the World. Thus, it is important to understand the potential for MoT entry and establishment into the U.S. and to test U.S. wheat cultivars for susceptibility to MoT. The hypotheses of this research project were a) importing wheat grain from Brazil does not pose a risk for MoT establishment in the U.S., and b) resistance to MoT head infection does not exist in U.S. hard red winter wheat elite cultivars. Quantitative pathway analysis models were used to estimate the risk of MoT entry and establishment, in the coterminous U.S. and in a more targeted area within southeast North Carolina, via the importation of wheat grain from Brazil. The pathway model predicted that significant risk for MoT entry and establishment exists in some areas of the U.S. However, in approximately 60% of the coterminous U.S. winter wheat production areas the risk of MoT establishment was estimated to be zero. With respect to winter wheat growing areas in the U.S., conditions for MoT establishment and wheat blast outbreak occur only in small, restricted geographic areas. A higher resolution pathway analysis based on a ground transportation corridor in North Carolina indicated that conditions for MoT establishment exist seven out of ten years. Among U.S. cultivars tested, a continuum in severity to head blast was observed; cultivars Everest and Karl 92 were highly susceptible with more than 90% disease severity, while cultivars PostRock, Jackpot, Overley, Jagalene, Jagger, and Santa Fe showed less than 3% infection.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Harvey Morgan Scott / A randomized controlled field trial was designed to evaluate the effects of two treatment strategies on ceftiofur and tetracycline resistances in feedlot cattle. The two strategies consisted of administering ceftiofur crystalline-free acid administration (CCFA) at either one or else all of the steers within a pen, and subsequent feeding/not feeding of therapeutic doses of chlortetracycline. Both strategies were hypothesized to reduce ceftiofur resistance. The effects of treatment strategies were evaluated via metagenome-based and culture-based assays. In this 26-day study, 176 steers were allocated to 16 pens of 11 steers each. The two strategies were randomly assigned to the pens in a two-way full-factorial manner resulting in four treatment groups. The blaCMY-2, blaCTX-M, tet(A), tet(B), and 16S rRNA gene copies/g feces were quantified using qRT-PCR from fecal community DNA. Antimicrobial susceptibility profiles were determined using microbroth dilution technique from the non-type-specific (NTS) E. coli isolates (n=1,050). The NTS E. coli DNA was screened for the presence of blaCMY-2, tet(A), and tet(B) genes. Pens in which all the steers received CCFA treatment showed an increase in blaCMY-2 and blaCTX-M log10 gene copies/g feces and in the proportion of ceftiofur-resistant and blaCMY-2 positive NTS E. coli. This was in contrast to the pens where only one animal received CCFA treatment. There was a significant decrease in quantities of tetracycline genes in community DNA in pens where all animals received CCFA treatment. In contrast to metagenome-based assay results, culture-based assays indicated an increase in the proportion of tetracycline resistant NTS E. coli upon CCFA treatment. Thereafter, chlortetracycline administration led to rapid expansion both of ceftiofur (blaCMY-2, blaCTX-M) and tetracycline [tet(A) and tet(B)] log10 gene copies/g feces. Chlortetracycline treatment delayed the return of the ceftiofur resistance prevalence to baseline among NTS E. coli and thus did not lead to the hypothesized decrease in ceftiofur resistance. Our data suggest that chlortetracycline use is contraindicated when attempting to avoid expansion of resistance to critically important 3rd generation cephalosporins in feedlot cattle. Further studies are required to better establish the animal-level effects of co-housing antimicrobial-treated and non-treated animals together at varying ratios on the levels of antimicrobial resistance.