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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 Molecular and eco-epidemiology of Leptospira borgpetersenii serovar Ballum in wild invasive mammals in a farming environment 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, Palmerston North, New Zealand(Massey University, 2020) MOINET, MarieLeptospirosis is an important zoonosis in New Zealand where it has historically been associated with livestock. Formerly negligible in human cases notified, Leptospira borgpetersenii serovar Ballum—associated with rodents and hedgehogs (Erinaceus europaeus)—is now preponderant. The role of wild introduced mammals in the epidemiology of leptospirosis has been overlooked in New Zealand but remains a critical question. In this thesis, we determined the prevalence of Leptospira serovars, renal colonisation and seroprevalence in wild mammals and sympatric livestock. During a cross-sectional and a longitudinal survey, house mice (Mus musculus), ship rats (Rattus rattus) and hedgehogs were trapped in farms with a history of leptospirosis to collect sera and kidneys. Urine and sera from livestock (dairy or beef cattle, sheep) and dogs were also collected on the same farms. Sera were tested by microagglutination test to identify serovars/serogroups that circulate in wildlife for comparison with those circulating in livestock. Urine and kidney samples were used to determine prevalence by qPCR, to isolate circulating leptospires by culture and subject them to whole genome sequencing, in order to determine their phylogenetic relationships and compare them to other sequences locally, nationally and internationally. Capture-mark recapture (CMR) methods were used to investigate the population dynamics of mice naturally infected with Ballum. Finally, the level of lesions and bacterial load in kidneys were assessed visually by histopathology and put in perspective with other results to investigate reservoir dynamics. Direct or indirect presence of Ballum was found in all wild and domestic species investigated. Overall apparent prevalence in mice, rats and hedgehogs was respectively 46%, 95% CI [39, 52%], 44% [26, 62%] and 27% [11, 50%]. It varied greatly between seasons in mice, with a spring peak (83 to 86%) and minimum in autumn (31 to 37%). Mice densities reached up to 56 mice/ha and varied seasonally in the opposite way, resulting in a relatively constant density of infected mice, ranging 3-8 infected mice/ha. An extremely low rate of mutations hindered the investigation of transmission pathways using genomics. However, despite little or no lesions in all species, the bacterial load was markedly higher in mice, suggesting rats and hedgehogs are secondary hosts. Control strategies to mitigate exposure to Leptospira in NZ should include wild mammals, and especially mice.Item Integrating host population contact structure and pathogen whole-genome sequence data to understand the epidemiology of infectious diseases : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy, Massey University, Manawatū, New Zealand(Massey University, 2020) Greening, SabrinaWith advances in high-throughput sequencing technologies, computational biology, and evolutionary modelling, pathogen sequence data is increasingly being used to inform infectious disease outbreak investigations; supporting inferences on the timing and directionality of transmission as well as providing insights into pathogen evolutionary dynamics and the development of antimicrobial resistance. This thesis focuses on the application of pathogen whole-genome sequence data in conjunction with social network analysis to investigate the transmission dynamics of two important pathogens; Campylobacter jejuni and Staphylococcus aureus. The first four studies centre around the recent emergence of an antimicrobial-resistant C. jejuni strain that was found to have rapidly spread throughout the New Zealand commercial poultry industry. All four studies build on the results of an industry survey that were not only used to determine the basic farm demographics and biosecurity practices of all poultry producers, but also to construct five contact networks representing the on- and off-farm movement patterns of goods and services. Contact networks were used in study one to investigate the relationship between farm-level contact risk pathways and the reported level of biosecurity. However, despite many farms having a number of contact risk pathways, no relationship was found due to the high level of variability in biosecurity practices between producers. In study two the contact risk between commercial poultry, backyard poultry, and wild birds was investigated by examining the spatial overlap between the commercial contact networks and (i) all poultry transactions made through the online auction website TradeMe® and, (ii) all wild bird observations made through the online citizen science bird monitoring project, eBird, with study results suggesting that the greatest risk is due to the growing number of online trades made over increasingly long distances and shorter timespans. Study three further uses the commercial contact networks to investigate the role of multiple transmission pathways on the genetic relatedness of 167 C. jejuni isolates sampled from across 30 commercial poultry farms. Permutational multivariate analysis of variance and distance-based linear models were used to explore the relative importance of network distances as potential determinants of the pairwise genetic relatedness between the C. jejuni isolates, with study results highlighting the importance of transporting feed vehicles in addition to the geographical proximity of farms and the parent company in the spread of disease. In the last of the four C. jejuni studies, a compartmental disease transmission model was developed to simulate both the spread and sequence mutations across an outbreak within the commercial poultry industry. Simulated sequences were used in an analysis mirroring the methods used in study three in order to validate the approaches examining the contribution of local contacts and network contacts towards disease transmission. An additional analysis is also performed in which the simulated sequence data is used to infer a transmission tree and explore the use of pathogen phylogenies in determining who-infected-whom across different model systems. A further study, motivated by the application of whole-genome sequence data to infer transmission, investigated the spread of S. aureus within the New Zealand dairy industry. This study demonstrated how whole-genome sequence data can be used to investigate pathogen population and evolutionary dynamics at multiple scales: from local to national and international. For this study, the genetic relatedness between 57 bovine-derived S. aureus isolates sampled from across 17 New Zealand dairy herds were compared with 59 S. aureus isolates that had been previously sampled and characterised from humans and domestic pets from across New Zealand and 103 S. aureus isolates extracted from GenBank that included both human and livestock isolates sampled from across 19 countries. Results from this study not only support evidence showing that the movement of live animals is an important risk factor for the spread of S. aureus, but also show that using cattle-tracing data alone may not be enough to fully capture the between farm transmission dynamics of S. aureus. Overall, by using these two pathogen examples, this thesis demonstrates the potential use of pathogen whole-genome sequence data alongside contact network data in an epidemiological investigation, whilst highlighting the limitations and future challenges that must be considered in order to continue to develop robust methods that can be used to reliably infer the transmission and evolutionary dynamics across a range of infectious diseases.