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Item Development of evidence-based strategies to control Brucella spp. in dairy herds in Henan Province, China : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Epidemiology at Massey University, Manawatu, New Zealand(Massey University, 2025-03-25) Wang, YuBrucella spp. remains a significant challenge in China, affecting the dairy industry and public health despite decades of voluntary control measures. This thesis aims to address key knowledge gaps in diagnosis, epidemiology, and disease impact of Brucella spp. in dairy herds to inform evidence-based control strategies in Henan Province, China. A scoping review of 61 studies (2004-2022) characterized the epidemiological landscape, revealing that B. abortus biovar 3 predominated 85.8% of Brucella spp. isolates recovered from dairy cattle in China. Considerable heterogeneity was observed in prevalence estimates and Brucella spp. isolation across provinces. These findings guided subsequent investigations into diagnostic accuracy, biosecurity practices, disease impact, and financial analyses. To enhance diagnostic accuracy, a cross-sectional study evaluated the diagnostic performance of four serological tests in Henan dairy herds. Using a novel Bayesian latent class model, optimal cut-off values were established for fluorescence polarization assay and competitive ELISA, estimating test sensitivity (69.7%-89.9%) and specificity (97.1%-99.6%). These findings provide a foundation for improving brucellosis diagnostic strategies. Beyond diagnosis, an assessment of farm biosecurity practices and stakeholder motivations was conducted using a structured questionnaire. Two distinct clusters of dairy herds were identified. Cluster 1, characterized by medium (400-1000) to large (>1000) herd sizes and higher educational levels, showed better adherence to proper biosecurity practices than Cluster 2. Stakeholders prioritized disease impacts and economic losses, highlighting the need for integrating these into the brucellosis control programs. To address this knowledge gap about disease impact, a longitudinal study estimated the effects of Brucella seroconversion on key production indicators. The annual incidence of seroconversion of brucellosis was 13.1% (95% CI: 10.9, 15.6) at the cow level. Seroconverted cows exhibited a reduction in daily milk yield (3.2 kg/day, 95% CI: 2.4, 4.0), elevated somatic cell counts, and increased pregnancy loss (relative risk: 4.26, 95% CI: 3.17, 5.73), compared to that of consistently negative cows. These findings provided essential epidemiological insights into the seroconversion of Brucella spp. and its implications on three essential dairy productivity outcomes. Building on these epidemiological insights, a financial analysis estimated the direct annual costs of Brucella infection at 78.9 Chinese Yuan (CNY) per animal and 4,019 CNY per infected cow. Among the three evaluated interventions (vaccination, test-and-culling, and test-and-culling plus vaccination), vaccination was the most cost-effective, yielding a benefit-cost ratio of 5.84 (95% CI: 4.34 – 7.42) and a net present value of 408.2 thousand CNY over ten years. Overall, this thesis integrates epidemiological, diagnostic, biosecurity, and financial analyses to inform evidence-based brucellosis control in Henan dairy herds. These findings could support farm stakeholders and policymakers in improving the control of Brucella spp. in Henan dairy herds, contributing to broader brucellosis control efforts in China.Item Changing epidemiology of Leptospirosis in New Zealand, with a focus on the novel strain of Leptospira borgpetersenii : 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, 2024-12-25) Sokolova, MarynaIn New Zealand, leptospirosis has been a common disease in dairy cattle since the 1940s. Six pathogenic Leptospira serovars from two species have been identified as endemic to New Zealand: Leptospira borgpetersenii serovars (sv.) Hardjobovis (Hardjo), Tarassovi, Ballum, Balcanica, and Leptospira interrogans sv. Pomona and Copenhageni. From these, sv. Pomona and Hardjo are the most commonly reported in cattle, and sv. Ballum, Tarassovi, and Copenhageni are less common. The estimated 99% of the national dairy herd is vaccinated against leptospirosis by vaccines containing antigens to Pomona and Hardjobovis and sometimes vaccines also include Copenhageni antigen. Vaccines for protecting dairy cows against Tarassovi were unavailable in New Zealand before December 2023. Historically, leptospirosis due to Tarassovi infection in New Zealand cattle was considered accidental and clinically unimportant. Serosurveys of apparently healthy cattle in New Zealand showed that over the past fifty years, Tarassovi seroprevalence increased from 6% (50/300) at MAT ≥ 50 to 18% (698/3878) at MAT ≥ 48. More recently, a serology and urine shedding study from 2015- 2016 evaluated the status of 4,000 dairy cows from 200 randomly selected farms, stratified by New Zealand's geographical location and herd size. The study found that on the animal level, 17% of the study animals showed evidence of past infection with Tarassovi, as defined by at least one sample reacting at MAT ≥ 48 for the study's purposes. Moreover, 96% (90/94) of PCR-positive urine samples were sequenced, and 68% (54/80) of those were found to have a novel allele in the sequenced region at the glmU loci. Thus, the use of molecular diagnostic tools, specifically molecular typing targeting a partial region of the glmU gene, allowed New Zealand researchers to identify a novel L. borgpetersenii strain, informally called strain (str.) Pacifica, in the urine of these cows. The 2015-2016 survey reported that dairy cows with Tarassovi titres were associated with urinary shedding, as determined by microscopic agglutination test (MAT) and polymerase chain reaction (PCR) testing, respectively. Because of this association, str. Pacifica is thought to belong to the serogroup Tarassovi. Additionally, the DNA of str. Pacifica has been retrospectively detected in cattle and deer samples dating back as early as 2007. Moreover, the 19-year (1999-2007) average annual incidence of notified human cases of Tarassovi leptospirosis was estimated at 12.59/100,000 in dairy farmers, compared to an overall annual average incidence of 2.01/100,000. These coincidental findings raised public health concerns. Therefore, at least some cases of Tarassovi seropositivity, as identified by MAT and reported before 2021, could partially be attributed to str. Pacifica. To confirm str. Pacifica's serogroup, isolation by culture and complete genetic characterisation of an isolate are required. Since str. Pacifica was only recently detected, its epidemiology, morphology, maintenance, and pathogenicity in the host population, as well as its impact on animal and human health, were not well understood. In this study, we investigated the possibility of isolating str. Pacifica from cow's urine by running a series of laboratory experiments where laboratory-adapted strains were used as a proxy for L. borgpetersenii str. Pacifica in the absence of an isolate to better understand its growth requirements. Laboratory-adapted Leptospira borgpetersenii strains were seeded into different types of media, and Leptospira growth rates were evaluated (Chapter 3). As a result, we ruled out unsuitable media and growth conditions, and this work helped to select the best media and growth conditions for a follow-up field investigation, where freshly collected cow's urine was seeded into selected media. Str. Pacifica was isolated from the urine of a shedding cow using HAN medium at 37°C and 5% CO2. However, this medium failed to sustain str. Pacifica and the culture was lost (Chapter 4). In addition, over the 2020-2021-2022 milking seasons, we collected and tested blood and urine samples from dairy farms, identified as str. Pacifica positive from the 2016 survey. Our results revealed that str. Pacifica was still maintained in the same dairy herds six years after initial detection. Moreover, we reported an estimated prevalence ratio (PR) of 7, indicating that the prevalence of shedders was seven times as high at the beginning than at the end of lactation in primiparous cows (Chapter 4). These findings provide evidence that str. Pacifica is adapted to dairy cows in New Zealand, and the peak shedding in primiparous heifers occurs in early lactation. Since the highest levels of str. Pacifica shedding were detected at the start of the milking season during peak milk production, which also coincides with a relatively short 3-month mating period, the associations between str. Pacifica and milk production and reproductive performance of milking cows were also investigated using herd test data and serological and PCR test results of the 2016 survey. Statistical models, including linear, logistic, and generalised mixed models with fixed and random effects, as well as a shared frailty survival model, were used to evaluate the associations between str. Pacifica positivity and reproduction (Chapter 5) and milk reproduction (Chapter 6) in dairy cows. Results of the statistical analysis of the association between str. Pacifica positivity and reproduction (Chapter 5) of dairy herds showed that str. Pacifica delayed the time from calving to conception (HR = 0.84; 95%: CI 0.74-0.96), although there was no effect on the pregnancy rate (Chapter 5). An analysis of milk production data did not reveal any associations with str. Pacifica at either animal or herd level (Chapter 6). The absence of clinical signs and the lack of association with milk production and reproduction at both the animal and herd levels provides further evidence towards str. Pacifica being well adapted to dairy cows. Therefore, evidence from this thesis suggests that dairy cattle are the maintenance host for str. Pacifica in New Zealand. It is also important to note that str. Pacifica shedders can infect people, especially dairy farmers, milkers, and farm workers who are in regular contact with str. Pacifica-shedding animals. Therefore, the prevention of str. Pacifica transmission via vaccination or the use of appropriate personal protective gear should be prioritised.Item Molecular epidemiology of chlamydiae at shorebird-human interface 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, 2024) Soon, Xue QiChlamydiae (plural form of the bacteria, Chlamydia) can infect a broad range of avian hosts. The well-recognised Chlamydia, Chlamydia psittaci can cause avian chlamydiosis; a respiratory, ocular, and enteric disease. C. psittaci is also a zoonotic agent causing psittacosis in humans. Worldwide, migratory shorebirds are one of the principal hosts of C. psittaci. New Zealand has two Ramsar sites (internationally important wetlands) that serve as significant stopovers for migratory shorebirds using the East Asian-Australasian Flyway. However, there has been no prior surveillance conducted for chlamydiae in migratory shorebirds in New Zealand. The aim of this study was to perform a chlamydiae survey at four estuarine sites in New Zealand, in both shorebirds and the people that handle them. Molecular methods are currently the most sensitive and rapid tests to detect C. psittaci in birds. Most laboratories have designed an in-house molecular assay or applied published protocols, sometimes with slight changes to the original procedure, for their studies with different purposes. Systematic review of 120 articles revealed that the sensitivity and specificity of a molecular test is dependent on the target genes, primer sequences, type of molecular test (quantitative PCR, conventional PCR), DNA extraction methods, and sampling methods. Of the currently available ten genomic targets to detect C. psittaci in birds, the ompA gene was the most widely used target gene. A testing strategy using a hierarchical approach that includes molecular tests of genus- and species-specific targets is recommended to facilitate detecting the well-recognised C. psittaci as well as other avian chlamydial species. In this study, DNA extracted from choanal and cloacal swabs of 320 live shorebirds of 7 species from New Zealand was screened for chlamydiae by High-Resolution DNA Melt quantitative PCR (qPCR-HRM) analysis. Shedding of chlamydiae was detected in 71 out of 320 (22%; 95%CI 18-27%) shorebirds sampled. Due to low pathogen load, molecular characterisation of avian chlamydial at the species level was possible in only 14 out of 73 positive samples by applying a culture-independent sample preparation method – multiple displacement amplification (MDA). ompA (outer membrane protein A gene) sequencing of the MDA products revealed 100% identity with C. psittaci in one pied stilt, and 99.9% identity with the avian C. abortus strain in five bar-tailed godwits, four pied stilts, and four South Island pied oystercatchers. DNA extracted from the nasal swabs of 27 people handling the shorebirds was screened using the same methodologies as above. qPCR-HRM results of the shorebird handlers showed the detection of chlamydiae in 14 out of 27 (52%; 95%CI 33-71%) participants. And the ompA sequencing results of human samples revealed 100% identity with C. psittaci in one sample, and 99.9% identity with the avian C. abortus strain in ten samples. To our knowledge, this is the first report of avian C. abortus strains in both shorebirds and people in New Zealand. The outcome from this study suggests potential transmission of chlamydiae among shorebirds populations, and between shorebirds and people. With this, we can raise awareness and inform disease prevention protocol for targeted people, in addition to conservation management strategies for shorebirds and public health plans.Item Risk factors for reporting bovine tuberculosis-like lesions and confirmation of Mycobacterium bovis from bovine tuberculosis-like lesions from routine carcass inspection in cattle in New Zealand 2019-2021 : a thesis presented in partial fulfilment of the requirements for the degree of Master of Veterinary Studies (Epidemiology) at Massey University, School of Veterinary Science, Massey University, Palmerston North, New Zealand(Massey University, 2022) Wilson, Tammy IsobelAim: In New Zealand, surveillance for bovine tuberculosis (bTB) is changing as the eradication programme matures. The transition from on-farm testing of livestock to predominantly slaughter surveillance for the detection of infection and providing evidence of disease absence has begun. The aim of this research is to provide data to support a critical evaluation of the effectiveness of slaughter surveillance for bTB in New Zealand. Specifically, the thesis explores risk-factors associated with i) bTB-like lesion submissions from cattle at routine carcass inspection and ii) confirmation of Mycobacterium bovis from bTB-like lesions submitted from cattle at routine carcass inspection. Methods: Lifetime and bTB data were extracted from the National Animal Identification and Tracing database and Disease Management System database for cattle slaughtered for human consumption through registered meat processing plants between 1 January 2019 and 30 September 2021. The data sets were combined using the lifetime animal identification number and collated using R Statistical software (v4.1.2; R Core Team 2021). Animal-level data included sex, age, number of lifetime movements between farms, the bTB herd status of the herd where the animal was sent to slaughter from, the disease control area the animal was sent to slaughter from, the season and year of slaughter, and the meat processor identifier. Multivariable logistic modelling was used to identify risk-factors for bTB-like lesion submission from routine carcass inspection, and risk-factors for confirmation of bTB from bTB-like lesions submitted from routine carcass inspection. Results: During the study period, there was one bTB-like lesion submitted for every 6378 cattle carcasses inspected. bTB was confirmed in one bTB-like lesion for every 60 bTB-like lesions submitted. During routine slaughter surveillance a bTB-like lesion was more likely to be submitted from an animal that came from an infected (OR 3.9, 95%CI 2.66 - 5.73) or suspended (OR 2.08, 95%CI 1.4 - 3.1) status herd, moved less than three times prior to slaughter (OR 1.17, 95%CI 1 - 1.27), and came from an area outside of movement control areas (OR 1.37, 95%CI 1.05 - 1.79). bTB was more likely to be confirmed from an animal that came from and infected status herd (OR 8.26, 95%CI 2.09 - 32.59), was female (OR 4.39, 95%CI 1.23 - 15.72), and came from a movement control area (OR 81.47, 95%CI 5.5 - 1192.37). The baseline risk of bTB-like lesion submission and confirmation of bTB differed between meat processing plants. Conclusion: These findings indicate that meat processing plant-specific factors, not just animal-specific factors alone, influence whether a bTB-like lesion is submitted for testing or confirmed as bTB. Better understanding of factors influencing the probability for a meat processing plant to detect and submit bTB-like lesions would enable more tailored policy-making to improve the overall submission rate. Identifying risk-factors for bTB-like lesion submissions and risk-factors for bTB-like lesions confirmed as bTB may identify enhancements to both on-farm surveillance, and a more efficient, risk-based approach to slaughter surveillance. The content of this research represents a first step for the overall evaluation of bTB slaughter surveillance as fit-for-purpose to support bTB eradication. A complete evaluation, based on this research, is warranted to determine required outputs and metrics for effective slaughter surveillance of bTB, and identify key areas for enhancement.Item Molecular epidemiology of Salmonella in the broiler industry of Sri Lanka : thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand(Massey University, 2021) Liyanagunawardena, NilukshiThe increasing occurrence of non-typhoidal Salmonella in poultry is an emerging threat for public health in Sri Lanka, and salmonellosis has incurred massive economic loss for the poultry industry in the country. Thus, the thesis presented encompasses a comprehensive study to understand prevalence and possible risk factors for Salmonella carriage in broiler farms as well as whole-genome sequence-based population structure, phylogenetic relationships and antimicrobial resistance in Salmonella in Sri Lankan poultry. The studies described in this thesis include a cross-sectional survey (i.e., sampling and questionnaire-based study) conducted from July to December 2017 in broiler farms (115) from poultry-dense areas and associated hatcheries (15) as well as an outbreak study (from 2010 to 2018), based on isolates and metadata from poultry salmonellosis outbreaks. After initial identification and PCR confirmation of a total of 164 Salmonella isolates, whole-genome sequencing was performed and antimicrobial resistance profiles of the isolates were determined. Results revealed a Salmonella prevalence of 32.2%, CI 95% [23.6-40.7] in broiler farms and 66.7%, CI 95% [42.8-90.5] in the associated hatcheries. Litter management, rest period between flocks, feed storage, district and farmers’ knowledge of sick birds were identified as risk factors for Salmonella carriage in the broiler farms, through multivariate logistic regression modelling. Eighteen different multi-locus sequence types of Salmonella were identified, including nine which were reported for the first time in Sri Lankan poultry. The most common serovars were S. Kentucky ST314 (26.8%, CI 95% [20.0-33.6]) and S. Enteritidis ST11 (19.5%, CI 95% [13.4-25.6]). A high percentage of quinolone resistance manifesting as resistance to nalidixic acid (41.5%, CI 95% [33.9-49.1]) and intermediate resistance to ciprofloxacin (45.1%, CI 95% [37.5-52.7]) and enrofloxacin (35.4%, CI 95% [28.0-42.7]) was found. The findings of this thesis, especially in the absence of previous comprehensive studies, will enable the design of control strategies to strengthen the national Salmonella control programme in Sri Lanka.Item Fijian bats : interactions between people and bats and a preliminary investigation into zoonotic pathogens : a thesis presented in partial fulfilment of the requirements for the degree of Masters of Veterinary Science in Wildlife and Zoo Animal Health at Massey University, Palmerston North, Manawatū, New Zealand(Massey University, 2021) McCutchan, Jessica LouiseConservation is an increasingly important global crisis, especially for the conservation of keystone species such as bats. In Fiji, five of the six species of bats are considered threatened to critically endangered on the ICUN Red List. Human encroachment in wild places and habitat loss, are invariably leading to increased contact between people and wildlife. Interactions between humans and bats can be both beneficial and detrimental to each species. This pilot study was undertaken to identify and quantify these interactions in Fiji and recognise the Fijian people’s perception of bats. People were interviewed across the three main islands of Fiji; Viti Levu, Vanua Levu and Taveuni. Throughout these islands, bats were generally perceived as positive. The majority of participants consume and come into contact with bats, or with their urine, faeces, blood and saliva. Young adults and men are more likely to come into contact with bats in Fiji than women. Quantifying these interactions and identifying other risk factors for bat exposure is an important step in targeting conservation efforts, community engagement and education. Through understanding these inter-species dynamics, at risk groups for possible zoonotic pathogen exposure have been identified. Education efforts towards bat conservation and public health risks can be more effectively developed when directed to at risk groups. This education material can build upon the positive perceptions surrounding bats and their importance in Fiji biodiversity. A survey was also carried out for selected zoonotic pathogens Leptospira sp., Histoplasma sp., coronaviruses and paramyxoviruses. Pooled urine and faecal samples were analysed for selected potentially zoonotic pathogens. We identified four genetically distinct Leptospira sp. in urine from Pteropus tonganus and samples collected at a Notopteris macdonaldi roost site. These findings contribute new information to the understanding of leptospirosis in Fiji, which is a nationally notifiable disease with a significant disease burden. Developed with a One Health focus, this pilot study provides baseline data for current disease status and up to date advice regarding public health information, guidelines and education.Item Health risks associated with the conservation of kākāpō (Strigops habroptilus) on offshore islands : 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, 2021) Meda Gedara, Chamindani Manjula JayasingheNew Zealand has a long history of using translocations of native fauna for conservation and offshore islands have been regarded as isolated ecosystems for conservation purposes. Maintaining the biosecurity of these islands is a fundamental part of conservation management. Island translocation has protected the endemic New Zealand parrot kākāpō (Strigops habroptilus) from becoming extinct and resulted a viable population in three offshore islands outside its historical range. However, kākāpō have been affected with novel diseases arising in the island sanctuaries. The aim of this research was to investigate the health risk for kākāpō in offshore islands, focusing on two main diseases. Exudative cloacitis is a disease of the cloaca in kākāpō from Whenua Hou for which no aetiology has been identified. An epidemiological study was conducted to identify the factors associated with the initiation of this disease in kākāpō. Results suggested that the disease is unlikely to have an infectious origin and diseased birds were not geographically clustered within Whenua Hou but reflected the kākāpō distribution within the island. Analysing the pH, moisture and ammonium content of kakapo roost materials did not show any evidence for the cause of the disease in the cloaca. Disease incidence has not been affected by the annual maximum temperature and rainfall each year. Erysipelas, an acute infection caused by the bacteria, Erysipelothrix rhusiopathiae, emerged as a small cluster of mortality in translocated kākāpō in 2004, and has subsequently been diagnosed as a sporadic cause of death for kākāpō and other endangered New Zealand fauna. This study reported the presence of E. rhusiopathiae in different seabird species in two islands Whenua Hou and Te Hauturu-o-Toi through a targeted survey. Whole genome sequencing revealed that there was a geographic difference in genomic diversity of E. rhusiopathiae, and phylogenetic evidence suggested seabirds as a possible reservoir of the organism for endangered native land birds. An Erysipelothrix spp. phylogenetically different from E. rhusiopathiae was detected in Cook’s petrels (Pterodroma cookii) and in kākāpō indicating the diversity in the genus Erysipelothrix in these island ecosystems. The investigations in this thesis demonstrate that while island translocations have been instrumental in conserving endangered fauna in New Zealand, this conservation strategy does expose the translocated populations to novel health risks. Disease management should be a priority in managing endangered species and these results should help to guide management actions for new health issues as they arise.Item Extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase (AmpC) producing Escherichia coli in dairy calves from the Canterbury region : a dissertation presented in partial fulfilment of the requirements for the degree of Master of Veterinary Studies in Veterinary Public Health at Massey University, Manawatū Campus Palmerston North, New Zealand(Massey University, 2020) Mwenifumbo, MerningAntimicrobial resistance (AMR) has become a global public health concern threatening current effective prevention and treatment options. Infections caused by antimicrobial resistance strains are costly, often harder to treat and sometimes fatal. One group of bacteria that contributes to AMR are the extended beta lactamase (ESBL) and AmpC beta lactamase (AmpC) producing E. coli. These are on the critical list of important antibiotic-resistant bacteria of human importance compiled by the World Health Organisation and are a public health concern due to their resistance to an extended range of beta lactams. The main driver for the spread of AMR is the use of antimicrobials in both human and animals. One potential spread is by the feeding of waste milk to calves. Waste milk is the milk that contains antibiotics or other drugs. Waste milk is not recommended as feed for calves due to its association with the development of antibiotic resistance bacteria. Using the culture depended methods and whole genome sequencing, this study aimed to determine the prevalence of ESBL and AmpC producing E. coli isolated from recto-anal mucosal swabs (RAMS) from waste milk fed dairy calves, and to phenotypically and genotypically characterise ESBL and AmpC producing isolates. Recto-anal mucosal swabs samples (n = 40) from waste milk fed dairy calves collected from Canterbury region, New Zealand were screened for antimicrobial resistant E. coli. Fifty-eight percent (23/40) of the calves harboured antibiotic resistant E. coli. 25% (10/40) calves were positive for AmpC producing E. coli and none of the calves were positive for ESBL producing E. coli. The highest prevalence of resistance was observed for tetracycline. PCR and Sanger sequencing revealed that all the AmpC positive E. coli were chromosomal mediated with four mutations in the promoter region of the ampC gene. Whole genome sequencing of eight isolates resistant to both tetracycline and streptomycin revealed additional resistance genes that were not tested phenotypically. Using the Clermont phylogrouping method of E. coli, the AmpC positive, the tetracycline and streptomycin resistant E. coli isolates were distributed among phylogroups B1, C and D. In conclusion, this study revealed the presence of AmpC producing E. coli and other resistance genes in E. coli isolated from waste milk fed calves. Further epidemiological studies are required to determine whether these antibiotic resistant E. coli are associated with waste milk.Item Ecology of infectious diseases in wild bats : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Sciences at Massey University, New Zealand(Massey University, 2019) Hranac, Carter ReedEmerging infectious diseases present significant threats to the health of humans and wildlife. The ecology of emerging infectious diseases is a data hungry field in a world of rare events. Bats are both the source of human pathogens globally and the victims of a novel fungal pathogen causing continent-wide population declines in North America. By using the principals of iterative model design and model guided field work I leverage the mechanistic relationships between seasonally limiting biotic and abiotic factors of wild bats to understand spatio-temporal disease emergence dynamics from and within bat populations. I first use a novel ecological niche modeling technique to relate the seasonal availability of resources to predict African bat birthing events. I then use these model results to test hypotheses that Ebola virus disease (EVD) transmission to humans and non-reservoir animal hosts are related to the birthing events of bats through the use of a spatiotemporal Poisson point process model. The results suggest EVD emergence in Africa may be driven in part by the pattern of births among bats, especially fruit bats. Further, the identified temporal lag terms between bat birthing terms and EVD emergence are consistent with hypothesized viral dynamics in bat populations. Out of sample testing on the two most recent EVD outbreaks in the Democratic Republic of the Congo reveal a high predictive model performance and suggest the existence of both strong regional seasonality and locations persistently at risk of EVD outbreaks in humans and susceptible wildlife. Finally, I model North American winter duration and incorporate spatial variation in host traits related to body mass and composition to update survival estimates for hibernating Myotis lucifugus infected with Pseudogymnoascus destructans, the causative agent of the emerging disease white- nose syndrome (WNS) killing bats in Eastern North American populations. Results indicate that hibernating M. lucifugus in the West are likely to suffer populations declines similar to those observed in the East. All my findings will require further ground-truthing to validate the results, yet demonstrate the predictive power of identified mechanistic relationships on complex infectious disease systems.Item Epidemiology of ovine paratuberculosis in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University, New Zealand(Massey University, 2019) Gautam, MilanThe overall goal of this PhD project was to better understand the general epidemiology of ovine paratuberculosis (PTb) and the specific molecular characteristics of the causing organism Mycobacterium avium subspecies paratuberculosis in New Zealand. To begin with, current control measures for clinical PTb in New Zealand’s major pastoral livestock species (dairy cattle, beef cattle, sheep, deer) were reviewed. Infection with Map is common in all these species and control is voluntary for all livestock industries. Control measures aim to reduce the incidence rate of clinical PTb rather than to eradicate Map infection. Dairy and deer industries have developed resources describing best-practice management options that assist farmers and veterinarians to advise their clients about specific control plans. There is no national control programme for sheep and beef cattle. However, unlike for cattle and deer, the use of a commercial vaccine is licensed for sheep. Evidence in this thesis suggests that vaccination may be a cost effective option for flocks that experience a high incidence of clinical disease. For deer, there is a national abattoir surveillance programme that aims to alert farmers of unusually high rates of PTb-like lesions in deer at slaughter. Evaluations of the biological and economic effectiveness of voluntary control still remains to be undertaken for all industries. Work in this thesis estimated the on-farm economic cost of clinical PTb in sheep (ovine Johne’s disease, OJD) in New Zealand. It was based on data about the incidence of clinical PTb and overall mortality from 20 OJD-affected farms. The benefit-cost ratio of vaccination was estimated. Farms were categorized as either fine-wool breed (Merino, Half-bred, Corriedale) or other breeds and calculations were stratified for these two farm categories. The estimated mortality due to OJD was 2.7 times as high in fine-wool as in other breeds with large variation between farms. A stochastic simulation for a hypothetical flock with 2,000 breeding ewes resulted in an average annual cost of OJD-mortality of NZ $13,100 in fine-wool and NZ $4,300 in other breeds. Vaccinating replacement lambs against OJD would be cost-effective in most flocks when the pre-vaccination annual OJD ewe mortality was >1%. Accurate on-farm observation of OJD to establish incidence would help farmers to make better decisions about vaccination. Frozen-stored faecal and serum samples of individual sheep with no signs of clinical disease from 45 commercial flocks from a 2013 study that determined pooled faecal culture (PFC) status were used to determine faecal Map shedding and antibody in serum. A total of 878 faecal samples were tested with direct faecal real-time quantitative PCR (qPCR) to determine Map shedding prevalence and abundance in individual animals. In addition, the qPCR results were compared with Map antibody ELISA results from 837 corresponding sera to correlate the observed shedding prevalence with sero-prevalence. Overall, 13.1% of faecal samples and 5.8% of serum samples tested positive. The median intra-flock prevalence (IFP) of Map shedding in the qPCR positive flocks was 13.5% with a range of 5–95%. The median IFP of Map ELISA antibody positive flocks was 10% with a range of 5–20%. ELISA results and the DNA concentration in qPCR positive samples were positively correlated. Nevertheless, ELISA was a poor predictor of individual shedding. A more robust assessment of the shedding status of flocks can be achieved by using a combination of qPCR and ELISA of individual animals rather than a single PFC of 20 randomly selected sheep per flock, as was used in the 2013 survey. Type S1 Map isolates from New Zealand and the Australian Telford strain were char- acterized based on single nucleotide variant (SNV) analysis of whole genome sequence data (WGS). A Type S1 genome was completely sequenced and closed for using as a reference for the SNV analysis. Besides defining the genetic relationship between Map isolates from New Zealand, Australia and Europe several phenotypic variables used as surrogates for the severity of PTb in individual hosts were investigated. The New Zealand and Australian isolates formed a closely related group. They were distinctly different from the Type S isolates from countries in Europe. Within New Zealand, Map genotypes and region of sheep farm locations were significantly associated (p <0.05). There were no significant associations between genotype and surrogates for severity, observed in the animals which the genotypes were isolated from, such as histopathological scores of intestinal lesions, host serology or the gross-pathological diagnosis by veterinarians at necropsy. These results suggested that the phenotypic variation of PTb may depend on factors other than Map-genotype in Type S strain. Further studies are required to sub-stantiate a hypothesis about varying virulence factors of the Map genome in New Zealand sheep. In summary, PTb control in New Zealand is voluntary in all major ruminant livestock industries including sheep. In clinically affected commercial sheep farms, estimated mortality due to OJD was 2.7 times as high in fine-wool as in other breeds, but large variations were observed between farms. PTb vaccination in commercial sheep flocks may be cost effective if annual incidence of OJD attributable ewe mortality is >1%. In non-clinical commercial flocks, the median IFP of Map shedding and Map ELISA antibody positive prevalence was 13.5% and 10% respectively. Approximately 1% ewes in qPCR positive flocks were supershedders. Based on analysis of WGS data, Type S Map genotypes from New Zealand sheep were similar across the country and not affected by the type of breed or disease outcome in hosts.