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Item Genetic diversity of microbes and its impacts on host switching : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand(Massey University, 2025-08-25) Dos Anjos Almeida, ValterLand use around forests, leading to habitat overlap, increases the risk of anthroponotic and zoonotic pathogen/microorganism transmission between humans, livestock, and wildlife. This scenario is exemplified by Buhoma, a village where most residents are primarily subsistence farmers who raise livestock and cultivate crops near the Bwindi Impenetrable National Park (BINP) in Southwestern Uganda, creating an ideal interface for understanding these dynamics. Given the significance of this geographic location and the underrepresentation of African populations in global microbiome research, this project aims to characterise the gut microbiome diversity and potential novel bacterial species, as well as microorganism sharing within a multi-host system in a rural area with documented interactions between humans, livestock, and wildlife. For microbial detection, DNA extracted from 553 faecal samples collected from humans, gorillas, and livestock was processed and sequenced to analyse microbial species communities in different hosts using shotgun high-throughput sequencing and bioinformatics tools. The analysis of 2,411 bacterial metagenome-assembled genomes (MAGs) confirmed the presence of numerous putative novel bacterial species in the gut microbiomes of the Ugandan hosts studied in this project. While many species were host-specific, others were detected across multiple host gut microbiomes from Buhoma and BINP, and in different host samples from other geographic locations (by comparing the MAGs generated in this thesis with other publicly available genomes). Among the bacterial MAGs assembled in this project, genera such as Prevotella and Treponema—considered markers of the gut microbiome in individuals with traditional agricultural lifestyles—and Campylobacter—which comprises species that are leading causes of bacterial gastroenteritis globally—were further investigated. These genera were found to contain numerous putative novel species, contributing to our knowledge of the human and animal gut microbiomes and enhancing our understanding of the species associated with them. The results of this study reveal a high diversity of previously unknown microbes recovered from human, gorilla, and livestock gut microbiomes collected simultaneously at the same wild rural interface. The Treponema genus includes species that inhabit a wide range of hosts and types of microbiotas. In the Ugandan host samples, 75 Treponema MAGs were reconstructed, enabling the identification of sixteen intestinal species, including thirteen putative novel species. Three of the detected species were found in human samples from this study, as well as in publicly available Treponema genomes recovered from animals such as pigs, cattle, wild boars, roe deer, and goats. This detection underscores the potential for interspecies transmission and the establishment of these bacteria in different hosts. Overall, these findings highlight the complex interplay between humans, animals, and their gut microbiomes, emphasising the need for further research to elucidate the implications for public health. Prevotella species are prevalent and abundant components of microbial communities associated with mammals. This bacterial genus influences individual clinical and metabolic responses to dietary changes and overall health conditions. In humans, Prevotella species have been identified in various body sites such as the skin, oral cavity, vagina, and gastrointestinal tract. In the gut microbiome, they are commonly linked with diets abundant in plant-based foods and are particularly prevalent among agriculturalist populations, where they tend to dominate the microbiota. In the investigation of this genus, 37 MAGs were assembled, all belonging to yet-to-be-described species. Phylogenetic analysis revealed that they represented fifteen putative novel intestinal Prevotella species. The nimJ gene, which confers resistance to metronidazole (a nitroimidazole-class drug), was detected in one of the human intestinal Prevotella species. Given the widespread use of antibiotics like metronidazole for treating both humans and animals in regions of Uganda, including Buhoma, the presence of this gene provides evidence that Prevotella species can acquire resistance to commonly used nitroimidazole-class drugs in areas where their use is prevalent. Of the seven putative novel species identified in human gut microbiomes, two were also present in publicly available genomes in the gut microbiomes from pigs and rhesus macaques living in different geographic locations, providing evidence that the same Prevotella intestinal species can inhabit multiple hosts. Overall, these findings expand knowledge of intestinal Prevotella by introducing numerous previously unknown species, offering a species-level perspective for future studies on Prevotella’s impact on health. Campylobacter species are leading causes of bacterial gastroenteritis worldwide, yet their diversity and transmission dynamics at wildlife–livestock–human interfaces remain poorly characterised. I investigated Campylobacter diversity among sympatric mountain gorillas, livestock, and humans in Uganda, assembling 44 Campylobacter MAGs representing seven species—including five putative novel taxa. Three novel species were found in mountain gorillas, livestock harboured C. vicugnae (goats) and C. sp017646085 (cattle), while human gut microbiomes revealed Candidatus Campylobacter infans (not associated with disease) and C. sp900539255, which was significantly enriched in clinical samples (p=0.001) and displayed unique sulfur and nitrogen metabolic pathways. Antimicrobial resistance genes, including blaOXA-471_1, were detected in Ca. C. infans MAGs. Overall, our findings demonstrate high Campylobacter diversity at the human–animal interface in Buhoma and highlight the importance of expanding reference databases for accurate surveillance and effective public health interventions. In summary, this thesis introduces a substantial amount of new information on gut microbiome bacterial species in gorillas, livestock, and humans living at a wild-livestock-human interface. It also provides detailed insights into three bacterial genera present in the gut microbiomes of human populations, as well as other mammals such as gorillas, cattle, and goats.Item Optimising the use of new data streams for making epidemiological inferences in veterinary epidemiology : a thesis presented in partial fulfilment of the requirements for the degree of PhD in Veterinary Epidemiology at Massey University, Manawatu, New Zealand(Massey University, 2018) Hidano, ArataMany ‘big data’ streams have recently become available in animal health disciplines. While these data may be able to provide valuable epidemiological information, researchers are at risk of making erroneous inferences if limitations in these data are overlooked. This thesis focused on understanding the better use of two data streams—livestock movement records and genetic sequence data. The first study analysed national dairy cattle movement data in New Zealand to explore whether regionalisation of the country based on bovine tuberculosis risk influenced trade decisions. The results suggested that the observed livestock movement patterns could be explained by the majority of, but not all, farmers avoiding purchasing cattle from high disease risk areas. The second study took an alternative approach—qualitative interviews—to understanding farmers’ livestock purchasing practices. This study suggested that farmers are not necessarily concerned with disease status of source farms and that it may be the reliance on stock agents to facilitate trade that creates the observed livestock movement patterns in New Zealand. The findings from this study also implied that various demographic and production characteristics of animals may influence farmers’ livestock selling practices, which were quantitatively verified in the third study analysing livestock movement data and animal production data. These studies not only showed that analyses based solely on ‘big data’ can be misleading but also provided useful information necessary to predict future livestock movement patterns. The final study evaluated the performance of various genetic sequence sampling strategies in making phylodynamic inferences. We showed that using all available genetic samples can be not only computationally expensive, but also may lead to erroneous inferences. The results also suggested that strategies for sampling genetic sequences for phylodynamic analyses may need to be tailored based on epidemiological characteristics of each epidemic.Item Epidemiological, pathological and metabolomic characterisation of an acquired myopathy of dogs in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Manawatū, New Zealand(Massey University, 2018) Hunt, Hayley‘Go Slow’ myopathy (GSM) is an idiopathic myopathy in dogs in New Zealand, characterised by an acute onset of trembling, weakness and collapse, followed by a prolonged period of exercise intolerance. In the first part of this thesis, the epidemiology of the disease was investigated using a telephone survey to obtain information regarding the diet, exercise, and health of affected dogs. Eighty-six confirmed cases were included in this study, and ingestion of wild pig in the week prior to the onset of clinical signs was a consistent finding (76/86 dogs; 88%; 95% confidence interval = 82 – 95%). Cases occurred most commonly in the upper North Island, particularly in Northland. The aim of the second part of this thesis was to characterise the pathology of GSM in the same 86 dogs included in the epidemiological study, using serum biochemistry (78 dogs), histology (20 dogs), and electron microscopy (4 dogs). Acutely, affected dogs had increased serum creatine kinase and aspartate aminotransferase activities, corresponding with the histological finding of skeletal muscle degeneration in the absence of inflammation. Ultrastructural changes in skeletal muscle included mitochondrial hypertrophy, intramitochondrial inclusions and increased sarcoplasmic glycogen. Similar lesions were observed in the skeletal muscle of wild pigs from areas where GSM occurred in dogs. Affected dogs also had increased serum alanine aminotransferase activities due to accumulation of lipid and glycogen in hepatocytes. Overall, the microscopic findings were consistent with a toxic myopathy. To further investigate the pathogenesis of the disease, liver samples were collected from 15 affected dogs and 24 clinically normal dogs for untargeted metabolic profiling using liquid chromatography-mass spectrometry. Comparison of spectra between affected and normal dogs revealed a widespread decrease in phospholipids, and increases in selected dicarboxylic acids and N-acetylated branch chain amino acids in affected dogs. No causative compounds were identified although several candidate mass spectrometric features were identified for future investigation. Taken together, the results of these studies suggest that ‘Go Slow’ myopathy is a toxic mitochondrial myopathy in dogs that is associated with the ingestion of wild pork. The findings reported aid in the prevention, diagnosis, and management of cases, with the primary suggestion being that owners avoid feeding wild pork in areas where the myopathy occurs. Further work is required to elucidate the cause of this disease.Item Model applications of decision support systems in meat hygiene programs : a thesis presented in partial fulfilment of the requirements for the degree of Master of Veterinary Science at Massey University(Massey University, 1996) Logt, Petrus Bernardus van derCurrent systems to ensure safety of meat are to a large degree based on a "procedural" approach which specifies what inspection actions will be taken to protect human health. Both knowledge and disease priorities have changed substantially over recent decades, and moreover the scale of the problems created by any breakdowns in protection has escalated greatly, as food trading and consumption patterns have changed. It is now recognized that meat hygiene needs to focus primarily on ways by which the risk that product will represent a hazard to human health can be effectively reduced, rather than merely ensuring compliance with a defined set of procedures. In addition to human food safety, meat inspection has the potential to contribute information to improve animal health on a national and a local scale. This thesis examines example issues in order to identify possible approaches to the development of decision support systems which assist in protecting meat consumers and improving the health of livestock on farms. The main areas which were explored for this purpose were respiratory disease in lambs and chemical residues in slaughter animals. A literature review of pneumonia and pleurisy in lambs showed that numerous factors have been proposed as predisposing causes for these diseases, but there was surprisingly little valid experimental or observational research evidence to support such statements. A hazard analysis was performed for the micro-organisms which have been isolated from pneumonic lungs. The major commonly detected organisms did not appear to cause a risk to healthy people. However there were a number of micro-organisms which are isolated on occasion from pneumonic and sometimes from healthy sheep lungs that might cause human disease. A case-control study was carried out as an exploratory means to identify risk factors and to generate hypotheses about causal processes. A number of risk factors were initially identified at univariate level. At the second stage the importance of some of these risk factors was quantified in a logistic regression model. Finally a third stage analysis showed the interactions between the factors in a logistic path model, which consisted of three clusters. One cluster included characteristics of the farm and paddocks, one cluster included the yards and practices in the yards, and a third cluster included the types and number of animals on the farm. Two intervention studies were subsequently carried out to evaluate the effect of making various management modifications on the prevalence of pneumonia and pleurisy at slaughter. One intervention study evaluated the time lambs spent in the yards after weaning and the use or oral or injectable drenches. The second intervention study evaluated the use of oral versus injectable drenches and the use of a shower dip versus a wand. The intervention studies showed an effect of time in the yards on pneumonia. There was some association between time in the yards and acute localised pleurisy but none between the other measures tested and respiratory disease. The studies showed clear temporal patterns with regard to pleurisy and pneumonia and enabled comparisons to be made between farms. A study of inspection for pleurisy at slaughterhouses was analysed. The analysis identified the temporal patterns of certain types of pleurisy. Comparisons were made between four participating premises. The sensitivity and specificity of meat inspection for the various types of pleurisy was analysed. The pleurisy data over an eleven year period of the entire country were analysed. Differences were shown between islands and regions. The potential for development of components of a decision support system for pneumonia and pleurisy was illustrated with a number of examples. An important component was to determine how farmers could be assisted in improving the health of their lambs with regard to pleurisy. Ideas to improve farmer involvement were developed. The principles of a decision support system which evaluated the issue of cross-contamination due to handling of product by the inspector were developed. Epidemiological principles of chemical residues in slaughter animals were investigated. A number of statistical quality control tests were applied to known data sets to evaluate what sample sizes would be required to detect changing trends or spatial paterns. Temporal simulations were performed to determine how well clusters in time could be detected. The Moving Average approach was used and it appeared that with the given data set sample sizes well beyond those feasible to achieve would be required. Spatial analyses with a number of different statistics were performed. In this case also, large sample sizes were required for reliable results. It was concluded that use of a risk analysis model to define a risk-reduction strategy targeted to avoid any significant risk to the consumer offered a much more effective tool than a fixed sampling system. This model combines a range of possible risk reduction measures in various mixes, and determines whether or not each of the tested strategies achieves the goal of making it very improbable that a consumer would be exposed to sufficient levels of chemical residues in food to even constitute some minimal public health risk.Item Epidemiological investigation into abortion in farmed red deer in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Sciences at Massey University, Palmerston North, New Zealand(Massey University, 2016) Patel, Kandarp KhodidasReproductive performance in rising two-year-old (R2) and mixed-aged (MA) adult hinds is suboptimal in farmed red deer in New Zealand due to failure to conceive, fetal loss, and perinatal and postnatal mortality. Reproductive efficiency (calves weaned/hinds mated) in the last decade has averaged 75% (Statistics New Zealand 2016). Previous studies have identified risk factors for conception/pregnancy. However, while abortions are considered rare, they have been reported at low levels in a few earlier studies, but more recently a clinical investigation reported up to 10% mid-term abortion in four herds. Hence, abortion may be going unobserved on deer farms. This epidemiological study was designed to investigate fetal wastage in farmed deer in New Zealand. The work presented in this thesis includes estimation of incidence and prevalence along with putative investigation into infectious causes based on blood, uteri and aborted fetal tissue, and analysis of farm and management risk factors based on data collected by questionnaire. It also includes the validation of an ELISA for Toxoplasma gondii which, based on recent clinical observations, was considered a likely contributor to abortion. Gold standard and Bayesian methodology showed this test to be 78.9% and 98.8% sensitive and 97.5% and 92.8% specific, respectively. Eighty-five deer farms were recruited over two-years, comprising 87 R2 and 71 MA herds and 22,130 R2 and 36,223MA hinds. The mean pregnancy rate at usual scan (Scan-1) was 82.0% (range: 7.0 - 100%) in R2 hinds and 92.6% (range: 39.8 - 100%) in MA hinds. Observations of aborting fetuses at scanning, along with a pilot study of early abortion confirms that sub-optimum pregnancy scan results are not attributable to sub-optimum conception rate alone as conventionally believed. A second pregnancy scan (Scan-2) was performed after a mean interval of 90 and 87 days from Scan-1 in a subsample of 11,005 R2 and 7,374 MA hinds, respectively, to determine fetal wastage in the 90-day between-scan (mid-term) period. Abortions were recorded in 73% and 61% of R2 and MA herds, respectively. The mean mid-term abortion rate, in herds with abortion, of 3.9% (range: 0.4 - 19.1%) in R2 was significantly higher than 2.2% (range: 0.6 - 9.1%) in MA hinds (Chisq. p=0.009). Repeatability of abortions investigated in 15 R2 (Student’s t-test p=0.15) and seven MA (Student’s t-test p=0.75) herds was poor demonstrating unpredictability between years. In a supplementary pilot study, abortions earlier than usual Scan-1 were detected in 2/3 R2 and 1/1 MA herd indicating that abortions do occur prior to mid-term. The abortion rates detected were higher than reported earlier and economically significant for many deer farmers, justifying investigation of causation. Serology and/or PCR for T. gondii, Leptospira spp., Neospora caninum, Bovine Virus Diarrhoea virus (BVD), and Cervid Herpesvirus type -1 (CvHV-1) were performed on selected samples from hinds pregnant, non-pregnant and aborting at Scan-1, aborted between scans, and aborting and pregnant at Scan-2, and fetal material as appropriate. Toxoplasma gondii sero-positive R2 hinds at Scan-2 were 1.6 times more likely to have aborted than sero-negative hinds (Chisq. p=0.03). Toxoplasma gondii sero-prevalence was positively related to herd-level abortion rates in R2 hinds (T-test p=0.02). In addition, T. gondii DNA was detected in aborting fetal tissues at Scan-1 and Scan-2 and from uteri of non-pregnant and aborting hinds at Scan-1 and aborted hinds at Scan-2. Combined, these data provide evidence that approximately 8% of abortions in R2 hinds are likely to be attributed to T. gondii. There was no evidence for Leptospira spp., N. caninum, BVD, or CvHV-1 infection played a significant role in abortion. Serology for those pathogens was not associated with mid-term abortion or non-pregnancy at Scan-1 (Leptospira spp. only). No Leptospira spp. DNA was detected in aborted fetal tissue or aborted hind uteri. N. caninum sero-prevalence was 0.6% in 348 samples analysed. Hence, further investigation was not justified. Sero-prevalence to BVD was 12.5%, and while not related to abortion, suggests a possibility of a persistently infected (PI) deer. The sero-prevalence of CvHV-1 was higher in MA than R2 hinds but unrelated to abortion (Chisq. p<0.001). The significance of Cervid Rhadinovirus type-2 (CRhV-2) DNA detected in maternal tissues is unknown. Farm, management, health, and environment autumn and winter risk factors, analysed for pregnancy (Scan-1) and having aborted by Scan-2 showed that winter hay feeding, presence of dairy cattle on farm and co-grazing of hinds with beef cattle were associated with abortion. This risk factor analysis suggests that attention to good nutrition and health, and effective grazing management reduces the risk of abortion. The observed abortion rates were higher than estimates used for power analysis at the study design stage. Therefore, despite that the number of farms able to be recruited was slightly below target, the abortion rates reported are robust. A potential limitation of this study was that the recruitment of farms could not be achieved by random selection, hence results may have been affected by volunteer bias. Further, it was necessary to adopt a cross-sectional blood sampling methodology since a longitudinal study design involving repeat sampling, while preferable, was not possible for logistical reasons due to the scale of this study on commercial farms. Overall, while a major proportion of abortions remained unexplained, this study showed that abortions, sometimes in high numbers, are occurring on deer farms. The mid-term abortion rate observed, if consistent across the industry, would result in losses of $2.10 million. If that rate was consistent throughout gestation, the loss could be up to $5.58 million. Given the magnitude of abortion rates on many properties, further research into causation is justified. However, the poor repeatability or predictability of abortion will make such research using the epidemiological approach adopted here difficult. Due to T. gondii being implicated as a cause of abortion in R2 hinds, research into developing an effective vaccine may be warranted. The research undertaken in this study effectively contributes to knowledge on reproductive inefficiency in farmed deer, providing data on the prevalence, incidence, and causation of abortion, and helping explain sub-optimum pregnancy scan results. These data contribute to understanding of BVD, N. caninum and CvHV-1 which have been little studied in farmed deer and will guide further studies to help the deer industry plan and implement measures to enhance reproductive efficiency.Item Multi-criteria decision analysis (MCDA) for control of transboundary livestock diseases using the example of the 2010/11 foot-and-mouth disease (FMD) outbreak in the Republic of Korea : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Manawatū(Massey University, 2015) Kim, EuTteumDecisions regarding transboundary livestock disease control strategies differ from personal decisions, such as buying groceries, in important ways: the stakes are high and the outcome of a decision will affect people in different fields. Decision making for transboundary livestock disease control strategies requires consideration of a number of factors including the epidemiology of the disease, economic cost of control, and environmental and social impact. For example, when applying pre-emptive slaughtering as a control measure for FMD, decision makers need to consider the epidemiologic effectiveness of the control measure, financial loss to farmers, the operational cost of slaughtering, negative impacts on the environment due to burning or burial of culled animals, and the public’s concerns for the welfare of slaughtered animals. Therefore, it can be challenging for decision makers to choose the best control strategy among alternative strategies. The study presented in the thesis describes the application of multi-criteria decision analysis (MCDA) process as a decision support tool for decision making about transboundary livestock disease control strategies using an example of a simulated FMD outbreak. The first research chapter (Chapter 3) investigates the preferences of chief veterinary officers (CVOs) for the criteria of FMD-control strategies in the Asia-Oceania region, which comprises countries free from or having experienced FMD. Criteria were grouped into epidemiologic, economic, and social-environmental. The CVOs in the Asia-Oceania region considered the epidemiologic criterion more important than the economic or the social-environmental criterion. The importance of the economic criterion differed with FMD status of a country: specifically, those countries considered free of FMD ranked the economic criterion as more important than those without. Among the criteria comprising the epidemiologic criterion, the most important was the size of the FMD-infected area, defined as the geographical size of FMD outbreak area. Within the economic criterion, the operational cost of the FMD-control strategy was considered the most important, and within the social-environmental criterion, the mental health of FMD-affected farmers was the most important criterion. Chapter 4 describes the construction of an epidemiologic model of the spread of the 2010/11 FMD outbreak in the city of Andong, Republic of Korea, to measure the epidemiologic effectiveness of FMD-control strategies. According to the simulation results, the model accurately represented the FMD outbreak in two ways: 1) the median number of simulated FMD-detected farms was the same as the number of detected farms during the actual FMD epidemic, and 2) the simulated epidemic curve was similar to the actual epidemic curve for the 2010/11 FMD epidemic. Thus, the constructed model could be used as a reference for evaluating the effectiveness of alternative FMD-control strategies. The control strategy applied during the 2010/11 FMD epidemic consisted of a pre-emptive slaughter area with a radius of three kilometres, 100 day movement restriction, and vaccination of all FMD-susceptible animals in the country. This was used as a baseline strategy in the study. Alternative levels of these control measures for the FMD-control strategy were simulated to evaluate the effect of alternative strategies. Changes in control measures were: 1) pre-emptive slaughtering within a radius of 0.5, one, and five kilometres of FMD-infected farms; 2) movement restriction of 30 days and 60 days; 3) ring vaccination in a band three to five kilometres from FMD-infected farms. According to the simulation results, the five kilometres slaughtering strategy resulted in the fewest FMD-infected farms. Cost-effectiveness (CE) analysis was applied to evaluate the economic effectiveness of FMD-control strategies using the results of epidemiologic simulation model (Chapter 5). This showed that ring vaccination in a band three to five kilometres from FMD-infected farms was the most cost efficient among alternative FMD-control strategies. The other FMD-control strategies, in decreasing order of economic efficiency, were five kilometre slaughtering, 30 day stop movement, and 60 day stop movement. The 0.5 kilometre and one kilometre slaughtering strategy were excluded in the analysis because these strategies did not control FMD spread during the simulations. Chapter 6 describes the MCDA process for choosing the optimal FMD-control strategy based on the results from Chapters 3, 4 and 5. The measurements of the criteria were merged with the weight of criteria to calculate the overall score of each FMD-control strategy. In the Asia-Oceania region, CVOs preferred ring vaccination over alternative FMD-control strategies, with 30 day stop movement being the least preferred of the FMD-control strategies. The findings presented in each of these chapters have broadened our knowledge of the decision making process regarding FMD-control strategies. The processes were reliable, transparent, and reproducible and can be applied not only to FMD but also to other transboundary livestock diseases such as classical swine fever or highly pathogenic avian influenza.Item Management of facial eczema : a thesis presented in partial fulfilment of the requirements for the degree of Master of Veterinary Studies in Epidemiology at Massey University, Manawatu, New Zealand(Massey University, 2016) Boyd, EmmaFacial eczema is a hepatogenous photosensitisation of ruminants caused by sporidesmin produced by the saprophytic fungus Pithomyces chartarum. It is of large concern to the dairy industry, both with its effects on production and the significant animal welfare implications of affected stock. In 2011 DairyNZ and Sustainable Farming Fund invested in research initially aimed at trying to get a better understanding behind the natural spore count variability in paddocks, between paddocks and between farms and to try and find alternative ways of managing facial eczema without zinc. After this research was completed in 2013 it was deemed necessary to try and understand to what extent management of facial eczema was breaking down and possible reasons for these breakdowns. The overall aim of this research was to try and help farmers improve their management of this disease and reduce incidence of facial eczema. A study comparing the spore counts from paddocks containing varying quantities of herbs, clovers and tall fescue showed that the addition of chicory, plantain, lucerne and white clover into a ryegrass pasture did not provide any reduction in spore counts. Tall fescue paddocks showed lower spore counts over time than pure swards of ryegrass. A study comparing the application of lime and nitrogen in comparison to control paddocks showed that application of lime before the risk period for facial eczema (in November), application of lime after a spore count rise, (in March) or urea application (in December) did not affect the number of spores produced by Pithomyces chartarum. A study investigating the variability of spore counts within farm, paddock, grass sample and water aliquot showed that if spore counts are to be used for monitoring purposes to identify when to start and finish facial eczema(FE) prevention programmes, at least three aliquots per wash water should be selected. Finally, a study looking at the different types of management of FE used and their effectiveness highlighted that FE management on dairy farms in New Zealand could be substantially improved; principally through farmers getting more information on the success of their FE management programs and responding when tests show that FE management is not effective.Item Statistical tools for spatio-temporal epidemiology, with application to veterinary diseases : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Statistics at Massey University, Palmerston North(Massey University, 2015) Richards, KateIn epidemiology we are concerned with disease occurrence and its associated explanatory factors. Through analysis of the patterns in disease spread, in space and/or time, we are able to obtain information about possible risk factors and transmission mechanisms. The main focus in spatial epidemiology has been human health. However, economic costs and the concern about zoonoses has fuelled a growing field of veterinary epidemiology. Veterinary epidemiology has the added complication of the `human effect'. For a disease to be recorded we require humans to detect and report the disease, and once reported human intervention is generally applied. This can lead to the true level of disease being under-represented with the loss of information impeding modelling and model predictions. The reliability of statistical analyses depends on the quality of the underlying data. Anomalies could introduce significant bias and lead to inappropriate decision making. Residual analysis is often used to detect anomalous data, but with hierarchical models (common within epidemiology) the highly exible representation of variation can mask outliers. We propose the use of exceedance probabilities as a tool for identifying and assessing anomalous data in spatio-temporal models for routinely collected areal disease count data. We illustrate this methodology through a case study on outbreaks of foot-and-mouth disease (FMD) in Viet Nam for the time period 2006 to 2008. The exceedance probabilities identify several provinces where the number of infected communes was unexpectedly low. These findings are particularly interesting as these provinces are located along major cattle movement pathways within Viet Nam. With epidemic data, the primary interest is the understanding of the transmission of the disease and the effectiveness of intervention strategies. While epidemic curves provide an excellent representation of the temporal patterns, we propose the additional use of a new graphical tool, the `cluster curve' to summarise the changes in spatial clustering through time. The cluster curve is based on the inhomogeneous K-function, and provides a means for summarizing the progression of clustering in infectious disease outbreak data taking into consideration spatial variation in the underlying population. We look at the application of the cluster curve to two outbreaks of FMD in England (2001) and Japan (2010) and to the 2007 epidemic of Equine Influenza (EI) in Australia. By comparing our knowledge of the actual course of the outbreak with the insight provided by the cluster curve we are able to showcase the effectiveness of our tool. Throughout the progression of the outbreak several time windows obtained small sample sizes. Therefore, we also look at the inclusion of significance indicators to definitively differentiate between true clustering and noise due to these small sample sizes. The epidemic outbreaks studied all had intervention methods applied. The impact of intervention strategies was investigated through the simulation (via InterspreadPlus) of five intervention methods on outbreaks of FMD in two geographical regions. Using the cluster curve, we found that intervention methods that created buffer zones were found to have particular characteristics of spatial spread. We found that non-buffer methods were less effective in controlling local spread. This is most likely due to infection transmission prior to clinical signs. This kind of analysis demonstrates the practical importance of having effective tools for describing changes in the spatial patterns of disease during an epidemic outbreak.Item Spatial data requirements for animal disease management in New Zealand : a dissertation in partial fulfilment of the requirements for the degree of Master of Veterinary Studies (Epidemiology) at Massey University(Massey University, 1998) Mackereth, GrahamThe science of geology has given rise to techniques for managing and analysiing spatial data. The techniques often deal with samples that represent a continuum, such as mineral samples taken from various locations. Some animal health data is similar in nature to geo-statistical data, such as climate data or soil samples from various points on a farm. Animal health data is commonly discrete rather than continuous in space. Farms are represented as point or area features and attributes of the farm are attached to the features. Spatial analysistechniques were reviewed and comment made about their usefulness and validity in disease management. The spatial data available in New Zealand for managing diseases was examined. Spatial data at a farm level is available in the national database management system Agribase, which records details of rural enterprises. The level of data completeness in Agribase was determined. The number of farms without spatial references varied from 10 to 18 percent, depending on the method used to update Agribase. Spatial data is available for cattle and deer herds in the National Livestock Database (NLDB). The number of herds without spatial data varied from 8 to 15 percent. Changes in the management of land information in New Zealand are resulting in an improvement in the quality and completeness of spatial data. In summary for the management of endemic and exotic diseases, farms should be represented as area features. Point coverage's can be generated from these area features and used in some applications, such as simulation models, and for labelling purposes. To function acceptable the applications tested required that 85% of farms or herds were represented spatially.Item Geographical reporting and analysis of infectious animal disease occurrence in Thailand and New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Master of Veterinary Science at Massey University(Massey University, 1999) Teekayuwat, TippawonA comprehensive geographical study and reporting system is presented. Animal disease data from both Thailand and New Zealand were explored and analysed using spatial analysis methods. The particular technique useddepended on the form of the data, aim of the investigation and the epidemiology of the diseaseof interest. Results and methods from some of these analyses were then included in the development of a simple geographical disease reporting and analysis system for Thailand. A number of methods were used to investigate the presence of temporal clustering, spatial clustering and spatio-temporal clustering of foot and mouth disease (FMD) reporting data in Thailand during January 1995 to May 1997. Temporal clustering in the time series of individual districts and individual provinces was found in many districts and provinces. Some of these provinces also showed the evidence of unimodal patterns. Spatial clustering was detected both at the district and province level. Space-time clustering was found at the district level. An exploratory analytical approach was used to investigate spatial clustering of bovine leukaemia virus (BLV) infection in New Zealand dairy herds. Two spatial clusters of BLV positive herds were detected in the Bay of Plenty area (p =0.001) and in the northern part of the South Island (p =0.082). We recommend that further investigations be conducted to define possible reasons for the presence of these observed clusters. The geographical patterns of FMD were described and risk maps of FMD outbreak occurrence in Thailand were developed using logistic regression and classification tree models (CART). The potential impact of spatial autocorrelation on the logistic regression models was assessed. CART models incorporating cost-sensitivity were constructed to develop sets of decision rules for the likelihood of FMD outbreak occurrence. Receiver-operating characteristic (ROC) curves were used to quantify and compare the value of the different models for production of risk maps and to provide a method for decision makers allowing them to optimise sensitivity and specificity of binary decision criteria. A simple geographical disease reporting and analysis system for Thailand was developed using the GIS software ArcView 3.1®, the database management software Microsoft Access 97® and the spatial cluster analysis software SaTScan® version 2.1.3. The programming language AvenueTM which is part of Arc View 3.1 was used bind the different components using a common user interface. The system allows quick and easy production of custom maps for routine reporting as the system is largely automated and requires only basic computer skills from the operator.