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Foot and mouth disease (FMD) costs over $20bn annually in large part due to control costs and production losses. Endemic regions such as sub-Saharan Africa (SSA) are particularly badly affected. Pastoral livestock keepers experience near yearly outbreaks, but the factors which contribute to persistence remain poorly understood. While epidemiological studies in endemic settings have identified risk factors such as transhumance (the seasonal movement of livestock to find better grazing), and enable understanding of the contemporary state of the system they have yet to explain how infection persists in these regions. Key aspects of a system can be explored relatively quickly and cheaply using modelling. However, modelling of FMD is more common for disease-free settings focusing specifically on disease control – starting with and returning to a system free of disease. While disease control in endemic settings is the ultimate aim, this first requires a better understanding of the mechanisms underlying persistence. For this, models specific to endemic settings are required and must account for key differences compared to disease-free settings. In this project a suite of stochastic models was developed to explore dynamics of a highly infectious, directly transmitted pathogen such as FMD. The models developed explore persistence and infection dynamics across local and regional scales investigating the impact of different factors in pastoralist systems and the perceived persistence of disease from field observations. A within-herd model shows that infection cannot persist for longer than 3 months without reintroduction. Including persistently infectious individuals in the model has little impact on the overall infection of individuals within the herd. This strongly supports the idea reintroduction of the disease is required to give the repeated outbreaks that are characteristic of endemic settings. Although exploring persistence likely requires models that account for transmission between herds, understanding of herd-level infection characteristics can be gained from this within-herd model. In endemic settings natural immunity in animals following infection can result in herd immunity and protection against reinfection. The model indicates the mean duration of herd immunity following a large outbreak in a naïve population is 2 years. The duration of herd immunity depends on the susceptibility of the herd prior to the outbreak, the size of the outbreak and the turnover of the population. Accurately predicting the dynamics of heterogeneous real-world systems requires parameterisations that characterise not only the broad behaviour but also its variation (e.g. between herds and regions). Data from outbreaks can be useful in developing suitable parameterisations. Using R0 as an example, values were estimated using a number of standard methods and compared to values calculated from the underlying epidemiological characteristics of simulated outbreaks. Both epidemiological characteristics and the method used to estimate R0 affect whether R0 is over- or under-estimated. These results do not suggest a universally preferred method for estimating R0 but highlight that an understanding of the underlying epidemiology of a system is required prior to method selection. Inaccurate estimation of R0 can have consequences for vaccine control - where R0 estimates are lower than the true value the population will be under-vaccinated. This is costly and result in ineffective control that allows some infection to remain. The infectious period and post outbreak immune period (POIP) of herds in endemic settings is unknown. These are likely different from disease-free settings where control measures are expected; for example, in FMD-free settings there is no herd-level POIP as infected herds are removed from the population. Mixture distributions were fitted to outputs from simulated outbreaks to give herd-level estimates for the infectious period and POIP. It is shown that, in the absence of intervention, there is a period of herd immunity following 65% of simulated outbreaks. Furthermore, analysis suggests a mean herd-level infectious period of 21.5 days – longer than previously used in the modelling of FMD transmission between herds. This work highlights the importance of obtaining and using herd-level estimates which are appropriate for endemic settings. Poor herd-level estimates of epidemiological characteristics can result in inadequate appreciation of transmission dynamics and key factors in the persistence of infection at regional scales. In turn this will compromise the design and implementation of control measures. As persistence was not observed at the herd level, a metapopulation model framework to explore endemic persistence in pastoral systems was developed. A population of 13000 herds (representative of Cameroon’s Adamawa region) was modelled allowing for local and transhumant contact. Although it was not possible to identify FMD specific parameters characterising between-herd disease spread, persistence and dynamics were explored for a limited range of contact and transmission parameters. The results indicate that seasonal transhumance can contribute to the persistence of infection at a regional level. The observed dynamics of infection and immunity are seasonal with immunity during the period of endemic stability greater than 60%. Timing of peak infection is dependent on seasonal variation in both contact between herds and vaccination. Short-term vaccine-derived immunity was modelled and is characteristic of the protection offered by FMD vaccines. The modelled seasonality of vaccination, and subsequent loss of vaccine-derived immunity, results in an increase in susceptible herds following the transhumant period. It is likely that this seasonal increase in susceptibility helps the persistence of infection as has been observed with other diseases such as measles. There is still much that needs to be understood about the dynamics of FMD transmission in endemic regions. Modelling can work well alongside targeted data collection to understand persistence, infection dynamics and assess control measures (particularly over long time scales) that are difficult to undertake in the field. Exploration of models, like that presented in this work, can highlight areas where data from the field would be beneficial to improve model parameterisation and better reflect the system of interest. Although long-term longitudinal tracking of infection at herd level over a range of scales is likely to be costly to collect and challenging to analyse, data of this nature would help inform both within-herd and between-herd models of transmission.

With the recent advances in sequencing technology it is increasingly common to find freely available large genomic datasets composed of thousands of genetic samples of viral or bacterial origin. Because Bayesian approaches possess multiple advantages against more traditional phylogenetic methods, such methods are considered as a standard tool to study the evolution and circulation of fast-evolving pathogens such as viruses. With those Bayesian phylogenetic approaches, the evolutionary and transmission parameters of fast evolving infectious diseases can be estimated to inform their control of in both epidemic and endemic contexts. Zoonoses are diseases that have passed from a non-human animal to a human population. The emergence of such diseases in human populations can be caused by environmental changes bringing wild and domestic animals closer to each other facilitating the transmission to humans. Phylogenetic approaches can help us to understand how disease can be transmitted between wild and domestic animal populations. Using recently developed Bayesian phylogenetic methods the first aim of this thesis was to understand and study the transmission of infectious disease amongst wild and domestic animal populations. Therefore, I performed those epidemiological analysis in an endemic context, using both Eurasian avian influenza sequences and African foot-and-mouth disease virus (FMDV). The second aim was to develop a software capable of reducing potential sampling bias between multiple populations while analysing large genetic datasets in a short running time compared to currently available phylogenetic methods. I first studied the transmission and reassortment pattern of avian influenza within Europe and Asia using internal segments sequences (PB2) originated from wild and domestic birds. Using both a non-structured and structured coalescent approach I determined that the two continents constitute distinct demes that are sporadically connected. Most of the reassortment pattern observed occurred within western Europe and Eastern China. I also determined that while wild Anseriformes are responsible for most of the of the virus circulation in Europe, domestic Anseriformes birds are responsible for the virus movements in Asia. The circulation of the virus between Asia and Europe being mostly done by both domestic and wild Anseriformes birds. Secondly, to understand the patterns of FMDV, I compared the transmission patterns of four FMDV (FMDO, FMDA, FMD SAT1, FMD SAT2) serotypes and estimated the factors influencing the circulation of these viruses in Africa using a discrete and a continuous phylogeographic approach. One conclusion of this chapter is that FMDV strains currently circulating in African livestock were probably introduced in the early 18th century trough livestock movements for the serotype A/O and reintroduced from wild Buffalo population after the African rinderpest epidemic for the SAT serotypes. I also show that movements of domestic cattle were responsible of the FMDV propagation and circulation in Africa with a small role played by wild animal populations. Thirdly, using advanced Bayesian structured coalescent model approximations, I studied the role played by antelope in the transmission of FMDV SAT1 and SAT2 in Africa. I found that for both serotypes antelopes seem to act as an intermediate host between buffalo and cattle. In the last part of the thesis I present a new software “Epitree-sim” that allows the fast estimation of phylogenetic trees and transmission patterns between demes using a fast dating algorithm and repeated subsampling of the sequence analysed.

Bovine tuberculosis (bTB) is one of the most complex, persistent and controversial problems facing the British cattle industry. It is also potentially zoonotic and so has public health implications. The incidence of the disease has been increasing in Great Britain for more than 20 years and is now endemic in southwest regions of the country and occurs sporadically elsewhere. Scotland records very few incidences of bTB and was declared as an Officially bTB free (OTF) region in 2009 for the purposes of cattle trading. However, in order to retain its OTF status Scotland must continue to demonstrate the ability to report low level of disease prevalence whilst maintaining its vigilance to potential new outbreaks. This thesis uses a variety of epidemiological and statistical models to evaluate the ongoing control strategies for bTB in Scottish cattle herds and highlight potential limitations to the current surveillance programmes. In the absence of an established wildlife reservoir, livestock movements are considered the primary mechanism for introduction of bTB into cattle herds. I use movement and bTB data to estimate the within-herd incidence rate for each infected farm in Scotland. The results suggest that this rate varies across farms, and is dependent on the herd size and length of disease exposure. These incidence rates are then used to parameterise a multi-herd dynamic model using stochastic simulations that incorporate multiple disease transmission pathways. With this approach I evaluate the impact of different routine test protocols on the overall simulated epidemics. Based on the model outcome, abattoir surveillance alone is not sufficient to maintain infection at a low constant level. Whilst adapting to more frequent routine testing regime can reduce disease incidence, the sensitivity of the surveillance methods can also have a big impact on the long term stability of the disease prevalence and can act as the main barrier to eradicating the disease from low incidence regions. The single intra-dermal comparative cervical tuberculin (SICCT) test used in the current routine herd surveillance relies on stimulating an immune response and observing delayed hypersensitivity reactions in infected animals. The test suffers highly variable, and often poor, sensitivity with current estimates ranging from 50% to 80%. The lower sensitivities may be associated with early stages of infection, concurrent illness, and farm management conditions as well as the presence of sub-clinically infected carriers that can potentially escape detection. In addition, there was evidence that physiological stress can have a marked effect on the immune responses in animals affected with bTB. I conducted two different types of case-control analyses to investigate the potential effect of stress related events on the outcome of the SICCT test. In the first analysis, a matched design is implemented to examine the effect of recent calving on reactivity to the SICCT. SICCT test positive cattle (cases) were matched with test negative (control) animals within the same farm. By selecting herd-mates (i.e. animals within the same herd at the same time), the study aims to control for space and time. Furthermore, animal age and breed were used as additional selection criteria to control for previous exposure period and potential genetic variation to the reaction of SICCT test outcome. Results from a conditional logistic regression model indicated that animals calved within 60 days prior to test were less likely to respond to the SICCT test in comparison to non-recently calved animals, and that this effect was strongest in the first 2 weeks of the post-partum period. In the second analysis, animals identified with gross pathology at post-mortem (TB-like lesion and/or bacteria culture) and that were SICCT test negative within 60 days prior to slaughter (representing false negative) were compared with confirmed test positives (true positives). Results from multivariable logistic regression model suggested that the probability of missed infection by SICCT test increases with age and male cattle have higher odds of being a false negative compared to females. Repeated skin tests within 60 and 120 days, as well as recent movement and parturition, were all statistically associated with false negative test outcome. Under future surveillance systems, these results could be used to adjust the timings of testing relative to calving, movements and previous test occasions in order to minimise the risks of false negative test results. Alternatively, increasing the threshold for reactor definition in animals under these categories could be considered to complement the poor test sensitivity.

Introduction In sub-Saharan Africa, rapid urbanisation and per capita consumption of animal source foods are expected to accelerate in the short-medium term and to increase the movements of live animals and animal products in the region. In Cameroon, where the livelihood of most of the rural population depends on the agricultural and livestock sector, a wide range of endemic transboundary infectious diseases (TADs) affect livestock production and trade, and have direct detrimental effects on animal, human and environmental health. Livestock mobility represents a central economic activity in the livestock value chain of the country as well as a central strategy of seasonal adaptation to the ecosystem. Livestock movements, however, are also a central driver of infectious diseases dynamics and contacts between livestock populations are major risk factors for disease introduction and circulation. In countries where financial and technical resources are constrained, such as Cameroon, strategic interventions aiming at the surveillance and control of multiple infectious diseases simultaneously are essential for optimising their cost-effectiveness. The overall aim of this study was to apply a methodological framework to contribute to the understanding of cattle movements in Cameroon and of their implications for disease circulation. Methods This project used a variety of epidemiological and statistical methods to characterise cattle movements in the country across different scales. The collection of primary data and information targeted both the formal cattle trade system, across the country, and the informal seasonal transhumance, across the main livestock production areas. Between September 2014 and May 2015 diverse strategies were applied for collecting empirical data and various data sources from multiple Regions of the country were combined. Cattle trade in Cameroon mainly occurs via multiple trading points owned and managed either by the veterinary authorities or the municipalities. A total of 62 livestock markets, and the relevant offices of the Ministry of Livestock, Fisheries and Animal Products (MINEPIA), were targeted for collecting official data on cattle trade referring to a 12-month period ranging between September 2013 and August 2014. Additionally, a questionnaire-based survey with the various livestock markets stakeholders (herders, traders, butchers and veterinary officials) was carried out to collect a variety of information on the cattle market system. During this 9-month period of field work, data on cattle seasonal transhumance were simultaneously collected using a combination of GPS-tracking technology and questionnaire-based survey. Results Volumes of cattle trade, the type of traded animals and their commercial values varied over the year and across the Regions of the country included in this study. Nevertheless, the market supply of live cattle showed similar temporal trends over the year and across the Regions. Although for almost the entire study area the peak of traded animals in the market system was in December 2013, the trade volume was consistently higher during the rainy season (May to September). On the contrary, the reduction in the trade volume during the dry season was accompanied by an opposite trend in the cattle price, with their commercial value being higher during the dry season. Furthermore, a cattle price differential was highlighted between production Regions and high consumption Regions of the country. The highest volume of cattle trade was recorded in the Adamawa Region, which was the main source of cattle for the country while also receiving animals from neighbouring countries, such as Chad and Central African Republic. In contrast, major urban markets in the Littoral and Central Regions were the main receivers of cattle originating from almost all the other areas of the country. Interestingly, the North-West Region appeared to be more independent and isolated within the cattle trade network of Cameroon, particularly receiving few animals from other Regions. Importantly, there was little variation in the structural characteristics of the cattle trade network as well as in its properties across seasons, showing that, despite the seasonality in traded numbers, the network of cattle moving between markets in Cameroon is very stable. This consistent structure of the network over the year increases the robustness of strategic targeted interventions. We found that targeting the top 20% of the most connected markets would significantly reduce the network cohesiveness providing opportunities for strategic disease surveillance, communication and risk mitigation interventions. The centrality of the market within the trading network was also found to be positively associated with the price of live cattle, which tended to be heavily affected by phenotypic characteristics of the traded cattle. The seasonal cattle transhumance has been found as a common and widespread practice for herders attending the market system across whole the study area, highlighting the close relation between formal trading movements and informal pastoral movements across the country. Transhumant herds were observed to undertake migrations across multiple Regions for period exceeding 6 months and showing the potential for multiple types of interactions with domestic and wild animals. Discussion Multiple livestock infectious diseases were identified as being related to the cattle trade system. As neighbouring and non-neighbouring countries were found to be epidemiologically connected it is clear that national strategies for surveillance and control are likely to have limited effectiveness. Regional coordination for designing and implementing prevention and mitigation strategies against infectious diseases is essential to improve animal health also at national level. This study highlights the opportunity for strategic surveillance, control and communication interventions targeting key livestock markets and Regions of Cameroon. Live cattle price and centrality of markets, represented by their connectedness within the trading network, highlights the need to further investigate the links between economic factors and drivers of disease dynamics, such as livestock movements. The complexity of cattle movements in this context was further evidenced by the seasonal transhumance representing an established common mechanism for managing livestock, and closely interacting with the formal trading system as well as with other domestic and wild animal populations. Better data collection and analysis of livestock movements is required for improving the effectiveness of surveillance and control of infectious diseases. Although animal identification and registration systems would represent an ideal step for increasing traceability of cattle movements, enhancing animal health management and the overall competitiveness of the livestock industry, in the short-term a cost-effective intervention should aim at further developing the current data recording and management systems. Pastoralism, for long seen as an economic and environmental activity with little future, also needs to be acknowledged as a key component of the livestock production system in the country and to be considered accordingly in the management of infectious diseases.

Despite Africa accounting for ~20% of the global cattle population, prevalence estimates and related risk factors of bovine tuberculosis (bTB), caused by Mycobacterium bovis, are still poorly quantified in many countries across the continent. Control of bTB in Africa is difficult due to poor monitoring of cattle movements and limited abattoir surveillance. Also M. bovis is zoonotic and risk factors for transmission include living in close contact with cattle and consumption of unpasteurised milk. Cattle keeping is integral to some rural populations in Cameroon and understanding the epidemiology of bTB in cattle populations is important both to bovine and public health. Detection of bTB in cattle is difficult due to variability of immune responses to M. bovis infection. The interferon-γ (IFN-γ) assay maybe useful to estimate bTB prevalence and identify bTB risk factors in Cameroon. However its performance can vary at different stages of bTB pathogenesis and in different cattle populations. Recently Fasciola hepatica co-infections have been reported to suppress IFN-γ responses in M. bovis infected cattle but the potential effect with F. gigantica co-infections on bTB prevalence estimates in Cameroon is unknown. An abattoir study was conducted in Cameroon to assess the performance of the IFN-γ assay. In 2012-13; 2064 slaughtered cattle were sampled from Bamenda abattoir (North West Region; NWR) and Ngaoundere abattoir (Vina Division; VD). Individual animal data was collected from routine meat inspection including identification of bTB and Fasciola pathology. Cattle were also tested for bTB using the IFN-γ assay and an M. bovis antibody ELISA. In the absence of a gold-standard diagnostic, the IFN-γ assay was compared to other diagnostic tests to assess agreement and identify factors that affected performance of the assay. Agreement between IFN-γ assay, TB lesion identification and an M. bovis antibody ELISA was poor-moderate, probably partly related to differences in immune response detected. A presence of Fasciola gigantica also increased the odds of false negative IFN-γ assay results. On further investigation co-infected cattle had increased odds of TB lesions and reduced IFN-γ responses that potentially could lead to ~20% reduction in test sensitivity. In an attempt to take into account the potential impact of F. gigantica, when estimating bTB prevalence, an antibody ELISA was developed to detect the exposure in live cattle. To highlight the awareness of disease in cattle-rearing communities, estimate prevalence and identify risk factors of bTB in cattle populations; two cross-sectional studies were conducted in 2013. A stratified clustered cross-sectional study of pastoral cattle herds, in the NWR and the VD, sampled 1448 pastoral cattle reared by 100 pastoralists. A smaller cross-sectional study sampled 60 dairy cattle from 46 small-holder co-operative dairy farmers. Individual animal data and herd-level data were collected and animals were screened by both the single comparative intradermal skin test (SCITT) and IFN-γ assay. Awareness of zoonotic TB was low yet consumption of raw milk was high in cattle-keeping communities highlighting the need for accurate bTB prevalence estimates. Despite the high awareness of the clinical presentation of bTB, clinical signs identified by pastoral herdsmen were not associated with cattle being bTB positive. The SCITT was used to compare two manufacturers cut offs for the IFN-γ assay, ≥0.05 and ≥0.1, and highlighted that these two diagnostics may detect different populations of bTB positive cattle. Using the IFN-γ assay at ≥0.1, bTB prevalence was highest in dairy cattle (21.67%) and was also present in pastoral cattle in the NWR and VD (11.33% and 6.55% respectively). Importantly, as F. gigantica is endemic in Cameroon and its influence could mean the true prevalence of bTB could be higher. Female pastoral cattle were at lower odds of being IFN-γ assay positive potentially due to immunosuppressive factors had lower odds of disease. Husbandry practices also decreased the odds of being IFN-γ assay positive such as drinking from streams, antelope and contact with herds at grazing. Age increased the odds of pastoral cattle being IFN- assay positive potentially being a confounder to chronicity of bTB and other co-infections may influence IFN-γ responses. Dairy cattle herds had different risk factors for being IFN- positive likely due to differences in husbandry practices. Considering the potential risk to public health of M. bovis this thesis highlights the extent of bTB across two major cattle keeping regions in Cameroon and the public health risk in cattle-rearing communities. Furthermore the relationship between Fasciola co-infection and IFN- responses to M. bovis described has potential implications for bTB diagnosis in cattle populations where the parasite is present across the globe.

Fasciolosis, caused by the trematode parasite Fasciola hepatica, is a multi-host parasitic disease affecting many countries worldwide. It is a well-recognized clinically and economically important disease of food producing animals such as cattle and sheep. In the UK, the incidence and distribution of fasciolosis has been increasing in the last decade while the timing of acute disease is becoming more variable and the season suitable for parasite development outside the mammalian host has been extended. Meanwhile control is proving increasingly difficult due to changing weather conditions, increased animal movements and developing anthelmintic resistance. Forecasting models have been around for a long time to aid health planning related to fasciolosis control, but studies identifying management related risk factors are limited. Moreover, the lack of information on the accuracy of meat inspection and available liver fluke diagnostic tests hinders effective monitoring of disease prevalence and treatment. So far, the evaluation of tests available for the diagnosis of the infection in cattle has mainly been carried out using gold standard approaches or under experimental settings, the limitations of which are well known. In cattle, the infection mainly manifests as a sub-clinical disease, resulting in indirect production losses, which are difficult to estimate. The lack of obvious clinical signs results in these losses commonly being attributed to other causes such as poor weather conditions or bad quality forage. This further undermines establishment of appropriate control strategies, as it is difficult to convince farmers to treat without demonstrating clear economic losses of sub-clinical disease. This project explores the value of slaughterhouse data in understanding the changing epidemiology of fasciolosis, identifying sustainable control measures and estimating the effect of infection on production parameters using data collected at one of the largest cattle and sheep abattoirs in Scotland. Data used in this study include; a) abattoir data routinely collected during 2013 and 2014, b) data collected during 3 periods of abattoir based sampling, c) data collected through administration of a management questionnaire and d) climatic and environmental data from various online sources. A Bayesian extension of the Hui Walter no gold standard model was used to estimate the diagnostic sensitivity and specificity of five diagnostic tests for fasciolosis in cattle, which were applied on 619 samples collected from the abattoir during three sampling periods; summer 2013, winter 2014 and autumn 2014. The results provided novel information on the performance of these tests in a naturally infected cattle population at different times of the year. Meat inspection was estimated to have a sensitivity of 0.68 (95% BCI 0.61-0.75) and a specificity of 0.88 (95% BCI 0.85-0.91). Accurate estimates of sensitivity and specificity will allow for routine abattoir liver inspection to be used as a tool for monitoring the epidemiology of F. hepatica as well as evaluating herd health planning. Linear regression modelling was used to estimate the delay in reaching slaughter weight in beef cattle infected with F. hepatica, accounting for other important factors such as weight, age, sex, breed and farm as a random effect. The model estimated that cattle classified as having fluke based on routine liver inspection had on average 10 (95% CI 9-12) days greater slaughter age, assuming an average carcass weight of 345 kg. Furthermore, estimates from a second model indicated that the increase in age at slaughter was more severe for higher fibrosis scores. More precisely, the increase in slaughter age was 34 (95% CI 11-57) days for fibrosis score of 1, 93 (95% CI 57-128) days for fibrosis score 2 and 78 (95% CI 30-125) days for fibrosis score 3. Similarly, in a third model comparing different burden categories with animals with no fluke burden, there was a 31 (95% CI 7-56) days increase in slaughter age for animals with 1 to 10 parasites and 77 (95% CI 32-124) days increase in animals with more than 10 parasites found in their livers. Lastly, a multi-variable mixed effects logistic regression model was built to estimate the association between climate, environmental, management and animal specific factors and the risk of an animal being infected by F. hepatica. Multiple imputation methodology was employed to deal with missing data arising from skipped questions in the questionnaire. Results of the regression model confirmed the importance of temperature, rainfall and cattle movements in increasing the risk for fasciolosis, while it indicated that the presence of deer can increase the risk of infection and that male cattle have a reduced risk of infection. Overall, this project has used slaughterhouse data to fill important knowledge gaps regarding F. hepatica infection in cattle. It has provided valuable information on the accuracy of routine abattoir meat inspection, as well as other diagnostic tests. It has also provided estimates of the effect of infection on the time cattle take to reach slaughter weight at different levels of infection and identified relevant risk factors related to the infection. In conclusion, knowledge of the effect of infection on slaughter age, as well as regional risk factors for F. hepatica infection, along with an improved use of abattoir inspection results in the evaluation of treatment strategies, can provide farmers and veterinarians with better incentives and tools to improve their herd health strategies and in the longer term help reduce the incidence of liver fluke in cattle.

Dogslife is the first large-scale, longitudinal cohort study of canine lifestyle, morphology and health. The project involves recruiting the owners of UK-based, Kennel Club registered Labrador Retrievers and asking them to submit data about their dogs via an online questionnaire repeatedly as the dogs age. In this thesis, I have analysed Dogslife data regarding the lifestyle, morphology and health of Labrador Retrievers up to four years of age. A validation study was initially undertaken in order to understand the quality of the Dogslife data because this would underlie all future investigations. Owners were visited and veterinary records scrutinised. It was determined that Dogslife illness reports were subject to recall decay and that minor changes would improve the usability of the questionnaire. Accelerometers were subsequently sent to a subset of the cohort and aspects of the Dogslife exercise questionnaire were found to be correlated to accelerometer readings indicative of sedentary, light and moderate to vigorous exercise. Overall, Dogslife dogs were exercised for over two hours each day with the time spent being dominated by time off lead and on other activities. Dogs in England spent less time exercising than those in Scotland and Wales and dogs in family households spent less time exercising than those in single adult households or households comprising more than one adult. Despite being pedigree animals, the males in the cohort were 2-3cm taller than the breed standard. On average, the females met the breed standard but there was wide variation for both sexes. Working dogs in the cohort were over 2kg lighter than household pets and chocolate coloured dogs were 1.4kg heavier than their black and yellow counterparts. Dogs in multi-dog households were 0.5kg lighter than those in households with no other dog. Heavier dogs spent less time fetching, chasing and retrieving and on other exercise. Over 6,000 signs of illness were reported to Dogslife in the first three and half years and approximately half of them did not involve a veterinary visit. Reported signs were dominated by vomiting and diarrhoea, both of which peaked when the dogs were between 3-6 months of age. For the first time, rates of diarrhoea were shown to be positively associated with human population density in the UK. Limber tail was found to be associated with swimming in the cohort and working dogs were more likely to develop the condition than pets. Genetic analyses identified regions of interest that might predispose the dogs to limber tail on chromosomes 6 and 30. Data from the Dogslife project provide a unique resource for investigating the epidemiology of Labrador Retrievers. This thesis creates a platform for all such future investigations.

Slaughterhouses are places where animals are slaughtered for food. In developing countries a lack of appropriate facilities and limited resources mean the slaughter industry is poorly regulated. Poor hygiene practices in slaughterhouses can result in the transmission of diseases from animals to people called zoonoses. Slaughterhouse workers are generally considered at increased risk of being exposed to such diseases due to their close contact with animals and animal products. The aims of this study were: to assess the current conditions in slaughterhouses and the knowledge, attitudes and practices of workers in ruminant and pig slaughterhouses in western Kenya; to determine the exposure of slaughterhouse workers to different zoonotic pathogens; to investigate the risk factors associated with exposure to these pathogens and to quantify the risk of zoonotic disease exposure for slaughterhouse workers compared to the general population. Slaughterhouses in western Kenya were visited between May 2011 and October 2012. Seven hundred and thirty-eight workers were recruited from 142 slaughterhouses. Overall, the slaughterhouses lacked facilities, with 65% (95% CI 63–67%) of slaughterhouses having a roof, cement floor and solid sides, 60% (95% CI 57–62%) had a toilet and 20% (95% CI 18–22%) hand-washing facilities. Less than half of workers 32% (95% CI 29–34%) wore personal protective clothing. Antemortem inspection was practiced at 7% (95% CI 6–8%) of slaughterhouses and 18% (95% CI 16–19%) of workers reported slaughtering sick animals. Slaughterhouse workers were screened for five zoonotic diseases. The unadjusted seroprevalence of the zoonotic diseases were: brucellosis 0.1% (95% CI 0.007– 0.8%); leptospirosis 13.4% (95% CI 11.1–16.1%); Q fever 4.5% (95% CI 3.2–6.2%); Rift Valley fever (RVF) 1.2% (95% CI 0.6–2.3%); taeniasis 1.8% (95% CI 1.0– 3.0%); and cysticercosis 2.6% (95% CI 1.7–4.0%). Risk factors for leptospirosis and Q fever were examined by multivariable logistic regression. Risk factors associated with leptospirosis seropositivity included: having wounds (OR 2.7; 95% CI 1.4–5.3); smoking at work (OR 1.8; 95% CI 1.1–3.0); eating at work (OR 2.1; 95% CI 1.2–3.6); and cleaning the intestines (OR 3.8; 95% CI 1.8–8.2). Protective factors were: working at a slaughterhouse where antemortem inspection was performed (OR 0.6; 95% CI 0.4–0.9). The risk factors significantly associated with Q fever seropositivity included: being intoxicated at work (OR 3.2; 95% CI 1.1–9.4). The odds ratio for leptospirosis seropositivity in slaughterhouse workers was determined to be 2.3 (95% CI 1.6–3.4) times that of the community. For Q fever the odds ratio for seropositivity in slaughterhouse workers was 1.9 (95% CI 1.0–3.8) times that of the community. This is the first report of a range of zoonotic pathogens in slaughterhouse workers in Kenya. This study indicated the potential risk factors for zoonotic disease exposure in slaughterhouses. The current working conditions in slaughterhouses in western Kenya are far below the recommended standard. Improvements need to be made to facilities and practices in all slaughterhouses. Training is recommended to improve awareness for workers, managers and inspectors of the risks of zoonotic disease exposure and methods to reduce it.

More than 2 billion people live on less than 2 US dollars per day. People in these conditions often have inadequate access to basic sanitation, safe water, and medical services. These individuals, households and communities may be at high risk for a wide range of preventable and treatable infectious diseases. The aims of this study were to: 1) describe the prevalence of endemic helminth, protozoal, bacterial and viral infections of people in a small-holder farming community in western Kenya; 2) explore the spatial distribution of infection risk; 3) quantify associations between social and environmental conditions and individual- and household-level infection; 4) identify shared risk factors operating on multiple pathogens. All data were collected between July 2010 and July 2012 as part of a cross-sectional survey of 416 households and 2113 people. This sample was considered representative of a population of 1.4 million people living in an area of western Kenya characterised by high levels of poverty. Sampled individuals were tested for exposure to, or infection with, 21 infectious agents using a range of faecal, blood and serological tests. Extensive questionnaire-based data were also collected. Individual- and household-level risk factors for infection with prevalent pathogens were explored using multilevel logistic regression, with a particular focus on examining the impact of socioeconomic position (SEP). Hierarchical zero-inflated binomial (ZIB) regression was used to derive an estimate of household pathogen ‘species richness’ with correction for imperfect detection. This modelling framework allowed assessment of the relationship between household-level infection with each parasite and a range of social and environmental conditions and, uniquely for a single study setting, the average response of the ‘group’ of parasites to these conditions. This study found very high levels of parasitism in the community, particularly with hookworm (36.3% (95% CI 32.8 – 39.9)), Entamoeba histolytica/dispar (30.1% (27.5 – 32.8)), Plasmodium falciparum (29.4% (26.8 – 32.0)), and Taenia spp. (19.7% (16.7 – 22.7)). Some degree of within-household clustering was found for all pathogens, and this was particularly large for the helminth species and HIV. Most pathogens also showed spatial heterogeneity in infection risk, with evidence of spatial clustering in household-level infection, most notably for HIV, Schistosoma mansoni, P. falciparum and the soiltransmitted helminths. A socioeconomic gradient was identified, even in this predominantly poor community. Increasing socioeconomic position (SEP) resulted in significantly reduced risk of individual infection for E. histolytica/dispar, P. falciparum, and hookworm. By contrast, individuals living in the richest households were at significantly elevated risk of infection with Mycobacterium spp.. Individuals living in the poorest households were least likely to report the recent use of medical treatments. The average pathogen species richness (out of 21 species) per household was 4.7 (range: 0 to 13). Following correction for detection error, the predicted average helminth species count (out of 6 species) was 3 (range: 0.94 to 5.96). While socioeconomic position had little effect on the probability that a household was infected with any of the helminth species of interest, domestic (within-household) transmission appeared to be greatest in the poorest households for hookworm, S. mansoni, Ascaris lumbricoides and Strongyloides stercoralis. Household size had a consistent effect on probably of household infection with each helminth species, so that the largest households were also the most pathogen diverse. Household-level helminth species richness was identified as a significant positive predictor of individual risk of HIV infection, raising potentially important questions about helminth-HIV interactions in the study area. This study integrates approaches from epidemiology and ecology to explore infectious disease risk and its determinants at a range of social and geographic scales in a small-holder farming community in western Kenya. Considering risk at both the individual and household level within the same community can contribute to better understanding of the factors that influence disease transmission in both domestic and public domains.

Taenia solium is a zoonotic helminth which is thought to be one of the leading causes of acquired epilepsy in the developing world. T. solium cysticercosis infections in pigs and humans and human taeniasis were diagnosed using antigen-capture ELISAs. The parasite was found to be endemic in the study site, with cysticercosis being detected by HP10 Ag-ELISA in 6.6% of human samples (95% C.I. 5.6-7.8%) and 17.2% (95% C.I. 10.2-26.4%) of porcine samples. Human taeniasis was detected by Copro-Ag ELISA in 19.9% (95% C.I. 18.2-21.8%) of faecal samples. The study site was found to be co-endemic with a large selection of other neglected tropical diseases, including soil transmitted helminthiasis, schistosomiasis, strongyloidiasis and amoebiasis. Potential control measures for this parasite have been modeled and the exclusion of infective pork from the food chain through the use of a pre-slaughter test for pig farmers, traders and slaughtermen was found to have the potential to avoid 72.6% (95% C.I. 62.1-80.9%) of infective meals consumed in the area at an incremental cost-effectiveness ratio (ICER) of $0.25 (0.2-0.35). Such a diagnostic tool is currently under development and its performance was evaluated as part of this thesis. The novel, user-friendly lateral flow assay, utilising the HP10 monoclonal antibody, was evaluated using a Bayesian framework and was estimated to perform with a Sensitivity of 82.7% (95% B.C.I. 72.5-91.9%) and Specificity of 87% (95% B.C.I. 80.2-93.4), results which demonstrate the potential utility of this test in epidemiological studies and in control strategies. Free-ranging pig production has been previously demonstrated to be a key risk factor for porcine cysticercosis and is commonly practised in this study region. A study carried out as part of this thesis found that these pigs have a home range of 15,085m2 which is almost 10 times the average area of a homested. This work indicates that pigs can be exposed to infective eggs from any human T. solium carriers within that homerange area, greatly assisting transmission of this parasite. Western Kenya is a severely deprived region where pig production is becoming hugely popular and is seen as a major tool for economic development, yet the data presented in this thesis indicates an area with endemic status for the harmful parasite T. solium, for which effective control strategies are desperately required.

This thesis takes data from the Infectious Diseases of East African Livestock (IDEAL) project. The project was a longitudinal calf cohort study based in Western Kenya. Indigenous short horn zebu calves were recruited at birth and then visited every 5 weeks through their first year of life. The aim of this thesis was to improve understanding of the epidemiology of Theileria parva, with a particular focus on variation in host response. 362 of the 548 calves in the study cohort were classified as having seroconverted to T. parva, and 381 to T. mutans before 1 year old. The diagnostic tools used to identify exposure in the calf were compared, and environmental and calf level risk factors associated with the age at seroconversion were sought. Decreased elevation of the homestead and increased size of the herd were found to be significantly associated with an increased hazard of seroconversion to T. parva. There was little variation in hazard of T. mutans captured across the study site. The outcome ‘clinical episode’ was used to classify whether the calf was ill at each routine visit. A large number of calves passed through their first year of life without clinical disease being observed, and a minority of calves experienced the majority of clinical episodes. Multiple clinical episodes were apparently related in time, suggesting that they were due either to the same or connected pathogenic processes. A low birth weight, larger herds, and older farmers were all risk factors for being a sick calf. Both high helminth burden and T. parva were found to be significantly associated with clinical disease at a population level. A lot of variation was seen in the clinical presentation of disease. The clinical signs associated with fatal East Coast Fever (ECF), the clinical disease associated with T. parva infection, were found to be very variable. Although this may have been partly due to the varying times in the disease process that calves were observed prior to death, the complication of the clinical picture was also suggested to be due to co-infections. 71% of the cohort was infected with T. parva in their first year of life, but only a fraction (8.7%) went on to die from that infection. Unmatched and matched nested case control study formats were used to investigate the risk factors associated with death following T. parva infection (ECF death) in these calves. It was found that being infected young was a risk factor for death. Calves owned by older farmers were also at higher risk of death following infection. Going out grazing was found to be protective, and equivocal evidence was found for an association between prior T. mutans exposure and reduced odds of ECF death. If these initial findings from this work are correct, it is likely that T. mutans is influencing the clinical presentation of T. parva in endemic regions.

In any host population, individuals may be infected with multiple pathogens concurrently or in sequence. The direction and strength of pathogen-pathogen interactions are often unknown and dependent on the mechanism of interaction. This thesis is concerned with the epidemiology of infections and coinfections in zebu cattle during their first year of life, and the consequences they have for hosts’ survival probabilities and growth rates. Specifically, the study aims to: a) identify the many different pathogen infections occurring in zebu cattle under one year old, b) identify the main causes of mortality and reduced growth rates, c) test for evidence of effects of pathogen-pathogen interactions on mortality and growth, and d) determine the risk factors for infections with pathogens associated with increased mortality and reduced growth rates in zebu calves. To achieve these aims data collected from an epidemiological follow-up study of a cohort of 548 indigenous zebu cattle, recruited at birth and followed for the entire first year of life was used. Growth rates were enormously variable (52 to 704% of birth-weight) and 88 (16%) of the calves died during the first year, most from infectious disease. In total, 25,104 calf weeks of observation and data from 5,337 individual calf visits were analysed. Over 50 different pathogens were identified in the cohort. The thesis begins by providing an overview of zebu cattle and the importance of cattle diseases relevant to Sub-Saharan Africa, emphasising the importance of epidemiological studies taking into account co-infections, which are common in the natural populations, as opposed to a single-pathogen focus. A detailed description of the study design, data collection and descriptive analysis of non-infectious factors, including management and environmental factors, and a descriptive analysis of all pathogens screened for in the study are provided. Using Cox proportional models with frailty terms, the study then identifies infectious and non-infectious risk factors associated with mortality. Further, the role co-infections play in decreasing survival probabilities are investigated, revealing that the hazard for death from East Coast Fever (ECF) - the single most important disease associated with 40% of all deaths - increases 10 times in animals co-infected with Trypanosoma species, and 1.3 times for every 1000 eggs per gram faeces increase in strongyle egg count. Mixed-effect models are used to study growth rates and the impact of coinfections, revealing both synergistic interactions (lower host growth rates) of T. parva and A. marginale co-infections, and antagonistic interactions (relatively higher host growth rates) of T. parva and T. mutans co-infections compared to single infections with T. parva. Further, this work shows that helminth infections can have a strong negative effect on the growth rates but this is burden-dependent. These findings provide baseline epidemiological data on the diseases with greatest impact on health and performance of young zebu cattle, information that is valuable in the prioritisation and control of diseases. Additionally, they provide evidence of co-infections affecting host growth and survival, and have important implications on disease control strategies, suggesting benefits of aan integrated approach to control of worm, tick and tsetse-borne diseases.

The capacity of zoonotic pathogens to infect multiple hosts creates surveillance challenges but also provides opportunities to gather data from animal species that can be used to understand risks to human health. This thesis presents a conceptual and practical assessment of the utility of domestic dog serosurveillance for the detection and surveillance of two pathogens, influenza A and Leptospira spp. The first chapter gives a theoretical framework that can be used to explore the attributes of animal sentinels and assess their utility in different contexts. In subsequent chapters, this framework is applied in a practical assessment of the utility of a domestic dog serosurveillance approach for the detection and surveillance influenza A and Leptospira spp. at two sites in Africa. Two cross-sectional surveys of the avian and mammal populations at a site in Northern Cameroon were conducted in early 2006 to determine if H5N1 influenza A viruses had circulated in this area and in which species that presence could be detected. Serological and molecular evidence of extensive H5 virus circulation in the domestic duck population was identified. 47% of domestic ducks at the Maga site were cELISA positive for anti-influenza A antibodies and 20% were HI test positive against an H5N1 antigen. There was also evidence of exposure to H5 subtype viruses in the local dog and pig populations. At the Kibera site in Nairobi, a cohort study was established to carry out surveillance of influenza A and Leptospira spp. in the domestic dog population and cross-sectional surveys of the domestic poultry and rodent populations were completed. There was no indication of influenza A circulation in any of the animal species surveyed, indicating low risk of zoonotic influenza A infection in the human population of Kibera. In contrast, there was extensive molecular and serological evidence of the presence of Leptospira spp. in both the rodent and dog populations. 18% of 236 trapped rodents were PCR positive for kidney carriage of pathogenic leptospires and the estimated seroprevalence of anti- Leptospira antibodies in the dog population ranged from 5-36% during the course of the study, indicating high potential risk of leptospirosis infection in the human population. The results indicate that dog serosurveillance can be used as useful tool for the determination of broad-scale patterns of pathogen presence and relative levels of population exposure. However, there are limitations of the data that can be gathered from animal sentinels and the complexities introduced particularly by incomplete understanding of diagnostic test performance must be recognized. Animal sentinel surveillance may be of most use for addressing fundamental questions of what pathogens are present where. In the developing world particularly where disease burden data are still lacking, dog sentinel serosurveillance can provide essential baseline data that can be used to target future research and resource allocation.