Developing and implementing techniques to harvest surveillance information from existing veterinary diagnostic laboratory data

Syndromic surveillance is a tool for continuous, automated extraction of surveillance information from health data sources. The research documented in this dissertation aimed at exploring informatics and data mining tools in order to develop and implement techniques to harvest additional surveillance information from existing diagnostic laboratory data. Data concerning laboratory test requests for diagnosis in cattle were provided by the Animal Health Laboratory (AHL), at the University of Guelph, Ontario. A thorough review of the initiatives of syndromic surveillance in animal health was conducted. Documented difficulties regarding the acquisition of clinical data, and especially sustainability of systems based on voluntary participation of veterinarians or data providers in scattered locations, resulted in the choice of using laboratory data in this research. Automated methods to classify laboratory submission data into clinical syndromes were investigated. One of the challenges of working with laboratory data was determining how to transform diagnostic data into epidemiological information. The most time-consuming step of class between these words, their co-occurrences and the target syndromic group. Once deAfter classidata for the algorithms implemented in the next stages. Lastly, the prospective phases of system development were carried out, that is, the analyses which scan the time series in an on-line process, one day at a time, in order to detect temporal aberrations in comparison to a baseline of historical data. Several aberration detection algorithms were evaluated. Upon the conclusion that no single algorithm was superior in all outbreak scenarios, a scoring system to combine algorithms was developed. All steps were set up using open source software, and delivered to the data provider as a simple desktop application scheduled to run daily in an automated manner. Fast development and simple maintenance is expected to lead to incorporation of this system into the routine of the data, becoming an indispensable tool for diagnosticians and epidemiologists, and encouraging further technical development

Eastern oyster, Crassostrea virginica: Productivity and physiology under varying temperature and salinity conditions

In the early 1990s, the introduction of suspended culture methods and the development of a market for cocktail oysters (65–75 mm) propelled the oyster aquaculture industry in New Brunswick forward, now producing over 140,000,000 oysters (337,000 floating bags) on 2,649 hectares of private shellfish leases. Recently, the industry has been threatened by an oyster disease outbreak, known as MSX in the Bras D’Or Lakes region (Nova Scotia). The possibility of the MSX parasite spreading into New Brunswick waters, as well as an increasing number of aquatic invasive species in the area, is a real concern for the industry and has prompted an investigation on possible mitigation strategies. The benefits of incorporating an upriver site into the production cycle of oyster aquaculture operations were evaluated. Seed (~ 26 mm shell height) and adult (~ 66 mm shell height) oysters were taken from downriver (salinity ~ 20–30‰) aquaculture sites and transferred upriver (salinity ~ 5–20‰) and monitored for shell and meat growth (May-October). At the same time, the impact of the relay fishery (harvest of oyster in closed marginally contaminated areas for relay to tenures in open areas) on oyster productivity was evaluated; wild upriver oysters were transferred downriver and monitored. Productivity data revealed that seed transferred upriver grew and survived as well as seed that remained downriver, while the mortality rates of adult oysters were lower at the upriver site. Meat content was unaffected in adult oysters transferred upriver. However, adult oysters transferred upriver had a gain in shell height (least squares means ± standard error) over the oysters that remained downriver (2.7 ± 0.5 mm vs. 1.8 ± 0.5 mm) and, in shell width (Median [95% CI]; 2.8 mm [1.9, 3.6] vs. 1.0 mm [0.3, 1.2]). Final organic meat content were approximately 35% less in adult oysters transferred downriver compared to those that remained upriver, confirming anecdotal reports from fishers of the relay fishery. Stress response of adult oysters was also assessed (80 and 150 days post transfer). Stress response measured revealed that regardless of their origin (upriver, downriver), oysters maintained upriver showed high levels of lysosomal destabilization and tissue atrophy. By contrast, the transfer downriver had the opposite effect, i.e. low lysosomal destabilization and low tubule atrophy. Results suggest that there exists no association between productivity parameters and the level of stress response measured by the biomarkers. The field investigation prompted further exploration on the impact of hemolymph fluid osmolality on neutral red retention assay (NRA) outcome. The prescribed saline solution for the assay assumes animals are isosmotic to surrounding water; however oysters sampled were hyperosmotic. Hemolymph osmolality was manipulated under laboratory conditions by subjecting adult oysters to temperature (0, 5, 10, 15, 20ºC) and salinity (6, 27‰) regimes. At 10–20ºC, oysters remained isosmotic to ambient waters, while hyperosmotic at 0–5ºC. When mimicking spring freshets (salinity 6‰), hyperosmotic condition was observed in all temperature groups, and was inversely proportional to temperature. Monitoring of valve activity confirmed a restricted exchange at 6‰ salinity (e.g. spring freshet). With these laboratory results, use of filtered hemolymph fluid (NRAMOD) is recommended instead of the prescribed standard solution (standard NRA) adjusted to ambient seawater

L’éducation postsecondaire chez un groupe de finissants de la région Évangéline: deux voies

Cette étude qualitative comporte deux objectifs: 1) examiner les raisons qui motivent le choix d’un établissement postsecondaire chez sept finissants d’une école de langue française dans la région Évangéline à l’Île-du-Prince-Édouard; et 2) explorer l’expérience vécue par ces jeunes lors de cette période de transition qu’est l’entrée au collège ou à l’université. Les données ont été recueillies à l’aide d’entretiens semi-dirigés effectués à deux moments précis: à la fin de la 12e année et à la fin du premier semestre universitaire/collégial. Des courriels ont aussi été échangés durant le semestre. L’analyse des données s’appuie sur quatre concepts fondamentaux qui constituent le cadre théorique de l’étude : la vitalité ethnolinguistique, l’hybridité identitaire, l’insécurité linguistique et la valeur marchande de la langue. L’analyse pertinente au premier objectif de l’étude se présente sous forme de comparaison entre les propos tenus par les participants ayant opté pour un établissement anglophone et ceux ayant choisi une institution francophone. L’analyse révèle que les raisons identifiées par les participants pour justifier leur choix d’établissement postsecondaire confirment les mêmes tendances que celles citées par d’autres chercheurs et vont aussi de pair avec celles mentionnées par les finissants franco-ontariens de l’étude de Lamoureux (2007) ; la réputation perçue du programme ou de l’institution et les raisons d’ordre financier (proximité géographique et bourses d’études) sont des facteurs omniprésents. L’analyse de l’expérience vécue par les participants s’organise principalement autour du facteur linguistique dans deux contextes essentiels de l’expérience postsecondaire : la vie académique et la vie sociale. L’étude révèle que globalement, les sept participants ont vécu une expérience positive lors de leur premier semestre au niveau postsecondaire. Aucune difficulté ou problème majeur n’a été décelé, autre que la période d’adaptation nécessaire et normale qui accompagne le processus de transition école secondaire-université/collège

Evaluation of a 3M Petrifilm on-farm milk culture system for use in selective dry cow therapy

As an alternative to blanket dry cow therapy (BDCT), selective dry cow therapy (SDCT) is considered a more judicious approach to antimicrobial use for the purpose of mastitis control during the non-lactating period. The purpose of this research was to evaluate the utility of a 3M Petrifilm-based on-farm milk culture system (OFCS) for use in a SDCT program. A randomized clinical trial was conducted using 16 low bulk tank somatic cell count (<250,000 cells/mL) dairy herds from Prince Edward Island (n = 10) and Quebec (n = 6), Canada. When used to detect intramammary infection (IMI) in cows at drying off, the OFCS performed well with a sensitivity of 85% and specificity of 73%. By comparing producer-derived Petrifilm results to those obtained using an accurate automated reader, it was determined that producers were able to correctly interpret Petrifilm results with an observed agreement of 91% and kappa value of 0.82. The study groups comprising the clinical trial were a positive control group consisting of cows receiving blanket application of dry cow therapy (DCT) with the addition of an internal teat sealant (ITS), and the OFCS group consisting of cows selectively treated at drying off based on OFCS results with ITS alone (Petrifilm negative) or DCT + ITS (Petrifilm positive). No significant differences in postcalving IMI risk and risk of clinical mastitis in the first 120 days of the subsequent lactation were detected between the study groups. Furthermore, no significant differences were observed between study groups regarding test day milk yield and somatic cell count in the first 180 days of the subsequent lactation. Petrifilm-OFCS-based SDCT enabled a reduction in DCT of 21% as compared to BDCT. The effect of ITS on the interdependence of quarters towards the acquisition of new IMI (NIMI) with coagulase negative staphylococci (CNS) over the dry period was also investigated. It was demonstrated that in cows that were infused with ITS, the presence of CNS in another quarter at drying off was a risk factor for CNS NIMI, but this association was absent in cows without ITS infusion. This unexpected finding may have resulted from inadvertent introduction of CNS during ITS infusion. In quarters of cows without a CNS IMI at drying off (i.e. without a source of contagious CNS), ITS was protective against CNS NIMI suggesting that CNS infection over the non-lactating period can be partly attributed to CNS species located within the environment. According to economic analyses, OFCS-based SDCT resulted in a marginally higher total cost per cow than BDCT. However, OFCS-based SDCT provided the combined benefits of lowering DCT treatment risk without increasing the risk of postcalving IMI, and was superior economically to a SDCT program based on somatic cell count and clinical mastitis history. Overall, the Petrifilm OFCS was an accurate diagnostic tool that was effective in reducing DCT use without compromising the health, welfare, and future milk production of the cow

Health and productivity monitoring of cage-cultured Atlantic halibut (Hippoglossus hippoglossus)

The Atlantic Canadian aquaculture industry is dominated by Atlantic salmon production. In recent years, infectious disease, parasitic infestations, and price fluctuations from international competition have caused disruptions to the industry. Diversification of the industry away from Atlantic salmon production is a potential strategy to insulate the industry from these fish health and market challenges. Atlantic halibut has long been a primary candidate for this diversification. However, the early commercialization of the species over the last 15 years has failed to reach its potential, owning primarily to a lack of information on the biology of the species, best management practices and proven economic feasibility. To address this information gap, a multi-objective Randomized Controlled Trial (RCT) was conducted at a commercial farm on the Bay of Fundy in New Brunswick. The study collected detailed information on the growth and survival of 5000 Atlantic halibut individually identified with Passive Integrated Transponder (PIT) tags and followed over a four year grow-out period. The main objectives of this research were: (1) to evaluate the impact of individual fish characteristics on growth, survival and farm economics, (2) to determine the effects of oil-adjuvanted vaccines on growth performance, survival and vaccine associated lesions, (3) to evaluate the suitability of FT4 Lock-on tags as an external tagging method for individual identification of Atlantic halibut, and (4) to test a Stratified Transport System (STS) as a means of improving fish welfare and the economics of overland halibut transport. A variety of fish level characteristics were found to be important predictors of productivity. Identifying and culling fish with these specific characteristics prior to grow-out was identified as a method to improve overall farm productivity. The side-effects of oil-adjuvanted vaccines were found to be mild in Atlantic halibut, thereby identifying oil-adjuvants as an available tool for future vaccine development. FT4 Lock-on tags were found to be suitable for identifying cage-cultured halibut with the exception of substantial impacts on growth. The STS was demonstrated to reduce post-transport mortality, establishing it as a cost-effective transport solution over currently practiced methods. In conclusion, this research allows producers to make evidence-based management decisions, to strengthen and facilitate the continued development of the Atlantic halibut aquaculture sector in Atlantic Canada

Bridging ‘Islands Of Medicine’: Balancing medical pluralism on La Isla De Chiloe

This thesis brings together the study of islands, anthropology, and postcolonialism; it discusses (1) how global assemblages, such as colonial interactions and neoliberal economies influence individual well-being and local health care ontologies as practice on islands, and (2) the space and place of medical plurality on islands. Ethnographic research took place over four months on Chiloé Island, Chile. The research included interviews with members of the Williche Council of Chief’s health program, medical practitioners in the public health system, and health service employees with the government. An examination of the integration between the Council’s health program and public health care clinics in the archipelago is central to this thesis. This intercultural approach to health care is compared to that of the institutionalization of indigenous medicines within the South Pacific. The relationship among health, economies, and ecosystems on islands, serves as a framework for gaining a different perspective on how medical pluralism occurs on islands

Mitochondrial bioenergetics: An integrated platform to study interactions of multiple stressors

Animals must expend energy to deal with a wide array of stressors associated with environmental change. Because mitochondria produce >90% of the energy requirement of the cell, they are likely the fundamental drivers of responses to environmental change. The primary goal of my thesis was to explore the interactions of three common stressors in aquatic systems – temperature, metals (copper: Cu) and hypoxia– on mitochondrial bioenergetics. To achieve this, I first performed a series of in vitro experiments using rainbow trout, Oncorhynchus mykiss liver mitochondria energized with complex I and II substrates to characterize the acute interactive responses of temperature and Cu on mitochondrial function. These studies revealed that Cu altered the basal and maximal mitochondrial oxidation rates differently depending on the metal dose and temperature. Mechanistically, I showed that Cu impairs oxidative phosphorylation in part by inhibiting the electron transport system (ETS) enzymes, stimulating proton leak, inducing mitochondrial permeability transition pore and dissipating inner membrane potential. Importantly, temperature exacerbated the effects of Cu suggesting that environmental warming, e.g., due to climate change, may sensitize fish to Cu toxicity. The next study combined in vitro and in vivo approaches to shed light on how persistent elevated temperature (warm acclimation) modulates the effects of acute temperature increase, hypoxiareoxygenation (HRO) and/or Cu on mitochondrial function. Sequential inhibition and activation of mitochondrial ETS enzyme complexes permitted the measurement of respiratory activities supported by ETS complexes I-IV in one run and allowed me to identify segments/components of the ETS that are resilient or susceptible to single and combined effects of temperature, Cu and HRO. This study also revealed that warm acclimation blunted the sensitivity of the ETS to acute temperature rise and, together with HRO, sensitized the ETS to Cu. My fourth study examined how warm acclimation influences the ability of fish to handle individual and joint effects of subsequent acute temperature shifts, hypoxia and Cu stress by exposing fish in vivo to the three stressors. Here I measured mitochondrial oxidation and apical endpoints indicative of stress and organismal energy status to assess the relevance of energy metabolism endpoints in vivo. I showed that warm acclimation reduced fish condition, promoted anaerobic metabolism, decelerated the ETS and altered the responses of fish to acute temperature shifts, hypoxia and Cu. Moreover, Cu and hypoxia showed reciprocal antagonistic interaction on the ETS and plasma metabolites, with modest additive actions limited to proton leak. The final study highlighted the functional-biochemical and transcriptional responses of fish to warm acclimation and short-term exposures to Cu and hypoxia. In this in vivo study, activities of ETS enzyme complexes and targeted analyses of transcripts encoding for proteins involved in mitochondrial oxidation, metals detoxification/stress response and energy sensing were done in isolated liver mitochondria and in whole liver and gill tissues by RT-qPCR. Warm acclimation inhibited activities of ETS enzymes while effects of Cu and hypoxia depended on the enzyme and thermal acclimation status. The genes encoding for proteins involved in mitochondrial oxidation, metals detoxification/stress response and energy sensing were all strongly regulated by warm acclimation while Cu and hypoxia clearly increased transcript levels of genes encoding for proteins involved in metals detoxification/stress response. Overall, the studies I carried out not only provided the mechanistic underpinnings of responses of fish to thermal stress, hypoxia and Cu, but unveiled novel interactive effects of multiple stressors. Importantly, I showed that mitochondria are a viable platform for integrating effects of multiple stressors

Welfare of horses transported to slaughter in Canada and Iceland: Assessment of welfare issues and associated risk factors

The welfare of horses transported for slaughter is a growing concern in several countries, including Canada, Iceland and the United States of America (USA). Slaughter of horses involves transportation of horses to a regulated facility and slaughter procedures such as lairage and stunning. The main objective of this study was to identify welfare issues and associated risk factors, particularly those associated with transportation. A welfare assessment protocol was developed to identify pertinent welfare issues, such as injuries, dehydration and fitness for transportation. Prevalence of horses with injuries, a pre-existing clinical condition, a body condition score of less than 3 (on a scale of 5) and those in a non-ambulatory state were calculated. Skin temperature, respiration rate, blood lactate concentration, blood glucose concentration, plasma osmolality, plasma total protein concentration and packed cell volume were also measured. Welfare assessment of horses in Iceland was undertaken before and after transportation to the slaughter plant and at slaughter. Forty six journeys lasting up to 3 hours were studied. Welfare issues identified were the prevalence of bruising and dehydration. Adults were more prone to bruising and dehydration than foals. Some horses showed signs of consciousness after stunning (1.6%) indicating ineffective stunning. In Canada, a prospective study observed 150 truckloads of horses after transportation to a Canadian slaughter plant. Associations between risk factors and welfare outcomes were evaluated using linear regression models. Welfare issues identified were prevalence of injuries, pre-existing clinical conditions, low body condition scores, and the presence of some non-ambulatory horses. There was a significant association between journey duration and the number of horses per truckload with injuries. Signs of dehydration were identified and were associated with journey duration and season. Blood lactate concentration at slaughter indicated increased anaerobic metabolic activity, which was affected by season (summer or winter) and lairage duration. A retrospective study was performed by collating data from all shipper certificates obtained from USDA for journeys in 2009 from the USA to equine slaughter plants in Canada. This study identified journey durations range from one hour to 105 hours. Some injuries in horses transported for slaughter were visible at ante-mortem inspection, whereas other injuries, such as bruises were not visible until post-mortem examination. Digital infrared thermography (DT) was evaluated as a potential tool to detect bruising ante-mortem. A preliminary study to evaluate factors affecting skin temperature (as measured by DT) indicated that an outdoor environment significantly affected skin temperature measured on different regions of interest (ROI) compared with an indoor environment. However, thermal symmetry between ROIs was maintained in outdoor conditions. Using these findings, a second study was performed to evaluate the methodology to detect bruising ante-mortem. Sensitivity to detect bruising was low, possibly due to selection of horses that did not spend time in lairage (i.e. there was no equilibrium time for skin temperature to stabilise after transport). In conclusion, in Canada, injuries and dehydration were mainly associated with journey duration, aggressive behaviour between horses and season. In Iceland, injuries and dehydration were mainly associated with age (adult or foal)

Simulation models for between farm transmission of PRRS virus in Canadian swine herds

Porcine reproductive and respiratory syndrome (PRRS) is a viral disease of pigs, which affects all production stages and has severe economic consequences for the swine industry. The virus is primarily spread between farms through direct and indirect contacts. A limited number of studies have been carried out to understand the between-farm transmission dynamics of the virus. The objectives of this thesis were to explore the contact structures among swine farms in Canada and to use these contact structures to better understand the pattern and dynamics of between-farm spread of PRRS virus among Canadian swine herds. Four different studies were designed and implemented to achieve these objectives. The first study used network analysis tools to analyse pig movement data which revealed characteristics of contact patterns between swine herds and suggested a hierarchical structure within the Canadian swine industry, where pigs typically move in a unidirectional manner from one production stage to another. The median in-degree and out-degree for farms in this study was 1 and ranged between 0-26 and 0-10 respectively for the overall network. The degree distributions demonstrated characteristics of a power-law distribution, suggesting the presence of scale-free structure while the size of clustering coefficient suggested presence of small-world structure in the swine movement network. Additionally, high levels of truck sharing between farms were noted in this study, with a typical truck, during the study period, being shared among four different farms. The second and third studies simulated the between farm spread of the PRRS based on the movement of pigs and the sharing of trucks among swine farms, using the North American Animal Disease Spread Model and the network-based models respectively. These studies provided a means to assess the relative importance of direct and indirect contact via truck sharing on between farm spread of PRRS virus. By including the transmission by trucks in the model, the median number of infected farms increased by 18% and the median epidemic size increased by 44% in the spatial model. Furthermore, with the addition of trucks in the model, the hierarchical structure of the industry was significantly altered and multidirectional disease spread was observed. On the other hand, the network-based models assessed the impact of scale-free, small-world and random network structures on the between farm spread of PRRS virus and demonstrated the influence these network structures can have on the spread of the virus. The spread on scale-free networks resulted in the smallest stochastic die-out percentage with highest epidemic sizes compared to spread on small-world or random networks. Similarly, the incorporation of transmission by trucks in the model had the highest impact on small-world and random networks, where the epidemic size doubled, compared to scale-free networks, where it increased by 20-29%. Given the importance of transmission of the virus via truck (e.g. indirect contacts) identified in the previous studies, the last chapter aims at (i) quantifying the likelihood that a pig transport truck shared among farms could remain contaminated with PRRS virus at the end of Day 1 and to (ii) evaluate the efficacy of commonly used cleaning and disinfection protocols in eliminating the virus from these trucks. The results of this study suggested, when no cleaning and disinfection protocol is applied, that it is moderately likely that the truck could become contaminated and remain infected with the PRRS virus (mean probability ranged between 0.338-0.352, when the truck was shared between two farms), and that this risk marginally increased with an increase in the number of farms the truck was shared among. This final study also suggested that once contaminated, most of the contaminated trucks would likely remain infected for more than one day. The studies presented in this thesis have not only provided a clearer insight into the pattern of contacts between farms, and the impact these contacts can have on PRRS virus spread, but have also highlighted the importance of including data on the sharing of trucks among farms, since trucks will tend to connect farms which would otherwise share no connection. Moreover, the studies in this thesis have reinforced the importance of the proper cleaning and disinfection of trucks between successive shipments, as the findings presented here suggest that with an increasing level of truck sharing between farms, shared trucks are likely to remain contaminated with the virus and sharing of trucks significantly increased the risk of between farm spread of PRRS virus. Not only do the shared trucks have a high probability of becoming contaminated with the virus, but once contaminated, they are likely to remain infected for a comparatively long period particularly in the absence of adequate disinfection. It should be noted that the pig movement data used in this study was not very recent and consisted of movements reported for only four months time period. Additionally, the described models could not be validated due to unavailability of data is another noteworthy limitation of the studies described in this thesis

From Maine to Chiloé: the effects of social enterprises on marginalized experiences: a comparative study of Penobscot Bay Islands, Maine and Chiloe Islands, Chile

Although the notion of islands contains a strong association or undertone of isolation and closure, islands are never closed environments. None the less, Islands are susceptible to exogenous factors and often exposed to development processes that can lead to inequality and inequity in society and space. Global change and the ongoing progression of globalization and processes of deregulation may deepen regional disparities and thus increase or position areas in a state of marginalization. Furthermore, on islands, while size itself matters in economic terms, topography and geographic location relative to major economic centers can also position them in a state of marginalization. Over recent decades, some islands have experienced improvements in terms of their infrastructure, transportation and communication systems. Yet they still struggle with certain aspects such as the cost for daily operation of services, and the overall aspects of development and decision making processes that affect their day to day livelihoods. This research revealed a series of day to day challenges that people on remote islands face. A social enterprise (SE) is a distinctive form of entity that is rapidly gaining recognition from policy makers worldwide. The SEs are seen as unique entities that are changing relationships among those engaged in the market place, civil society and public institutions. They are able to do this through the pursuit of goals that go beyond mere profit acquisition. V This study compares SEs located on islands in the Penobscot Bay, off the coast of Maine on the United States’ eastern sea board, and the Islands of Chiloé, off the southwest coast of Chile. This study of SEs offers an opportunity to understand people’s experiences with SEs and whether, how, and under what circumstances SEs affect the lives of those experiencing marginalization. Furthermore, it explores the effect on the level of inclusion of individuals within island society and their communities and how SEs aid their members in improving their quality of life