Bethany Jackson

Exploitation of bears via the illegal wildlife trade risks exposing them to pathogens unlikely to be encountered in the wild, through conditions inherent to capture, transit, and ongoing captivity. Tuberculosis (TB), a disease of humans and livestock that requires close contact to spread, is a prime example of this risk, particularly in regions with high human TB endemism alongside the trade in, and rescue of, bears. This thesis aimed to explore the origin/s and epidemiology of an outbreak of TB in a population of sun bears (Helarctos malayanus) and Asiatic black bears (Ursus thibetanus) at a bear rescue centre in Cambodia, and the utility of locally available diagnostic methods for management of such outbreaks. Confirmed TB of human origin had not previously been described in either species. Between 2009 – 2024, Mycobacterium tuberculosis was isolated from 35 cases (31 sun bear, three Asiatic black bear, and one staff member). Using isolates from the first 32 cases (occurring between 2009 and 2019), alignment of antimicrobial susceptibility testing and genotyping of isolates revealed two clusters, which were confirmed and further explored with whole genome sequencing. We combined epidemiolocal data with single nucleotide polymorphism analysis and exploration of mixed base calls to indicate the evolution of each cluster. We established a likely transmission route in one cluster where the human case acted as an intermediatory between bear cases. Results from testing of 344 bears at three regional bear rescue centres were used to build a Bayesian latent class model to explore the accuracy of available tests for diagnosing pulmonary TB in bears. Five tests were included; microscopy, PCR, and culture of respiratory tract samples, thoracic radiography, and a patient-side lateral flow test designed to detect antibodies to key Mycobacterium tuberculosis complex antigens in serum from elephants and cervids. Our model demonstrated the high specificity and suboptimal sensitivity of the microbiological tests, and a need for caution when interpreting the serological test results. Thoracic radiography was the only diagnostic method with both sensitivity and specificity estimated by the Bayesian latent class model to be above 90%. Finally, we explored the use of thoracic radiography as a screening tool for sun bears at risk of TB, using radiographs from a subpopulation of confirmed TB cases and control (apparently healthy) sun bears. Our results supported the high specificity of radiographic changes for TB diagnosis, and highlighted sensitivity challenges when radiographic changes are subtle, extra-pulmonary, or there are concurrent differential diagnoses to explain changes. The results of this thesis drive evidence-based recommendations to support veterinary and husbandry staff managing bears in resource-poor, high human TB settings, where the surveillance for, and response to, TB outbreaks can have significant consequences for animal welfare, public health, and conservation goals.

Wildlife health data can be a powerful contributor to conservation outcomes, disease surveillance, and the broader objectives of One Health – an aim to achieve optimal health for people, animals, and the environment. Collections of wildlife necropsy reports are a common source of such data. However, the nature of these data creates a resource barrier between acquisition and analysis, resulting in sporadic extraction to inform such outcomes. To evaluate challenges and opportunities provided by wildlife health data, necropsy records for all the culturally, economically, and ecologically significant Sphenisciformes within the Wildbase Pathology Register of Aotearoa New Zealand were extracted, validated, and analysed. This manual process highlighted the dominance of a threatened and arguably cryptic species in the database (hoiho or yellow eyed penguin, Megadyptes antipodes), and that infectious/ inflammatory diagnoses were the most frequently encountered across all reviewed reports (35.7%, 523/1463). The free-text nature of many fields complicated analysis through high rates of typographical variance requiring manual resolution. The manual review shed light on threats to Sphenisciformes in Aotearoa, but also highlighted the temporal cost of knowledge extraction. Using these insights, an application was developed to facilitate time sensitive knowledge extraction, via text-mining and a dashboard approach to analyse and display information akin to the manual necropsy review. Simple algorithms were used to derive categorical fields such as species, and sex, while more complex query-based algorithms were used to quantify subjective elements, such as the prevalence of specific clinicopathologic findings. To evaluate the performance of this application nine professionals in wildlife health were recruited to a pilot study, to quantify the occurrence of four clinicopathological findings across two species datasets extracted from the Wildbase Pathology Register. Results from the testers were compared to the manual review (a “gold standard”), to determine the proportion of false negative and false positive records returned by each tester across the four clinicopathological findings that had been assigned to find. Mean F1-scores, which infer the level of agreement between the tester and the manual review, ranged from 0.63-0.93. Agreement was affected by tester, and the clinicopathologic finding being examined. The majority of misclassification (false positive or false negative records) was attributed to inappropriate search term selection and differences in interpretation of records. Further, the linguistically simple clinicopathologic findings (e.g., ‘oiled’) performed more consistently across users and in greater agreement with the manual review when compared to the other findings tested. The value of the application was affirmed in the pilot testing, however highlighted the potential for individual users, and clinicopathological findings with high rates of synonymy (e.g., “Starvation”), to impact performance. Overall, the development and testing of this application demonstrates the under-recognised value of automated methods in the extraction of knowledge from painstakingly acquired wildlife health data. This utility may be improved through the implementation of more sophisticated semantic-based techniques for data extraction as compared to the relatively simple term-based approaches utilised here. With early warning a recognised precursor to the success of any intervention, be it for conservation or infectious disease purposes, approaches that fast-track evidence-based adaptive management are a global priority for wildlife health.

Lumpy jaw is a well-recognised cause of morbidity and mortality in captive macropods (Macropodidae) worldwide. The extent and causes of the disease are largely unknown, although multiple risk factors associated with a captive environment are thought to contribute to the development of clinical disease. Identification of risk factors associated with lumpy jaw would assist with the development of preventive management strategies, potentially reducing mortalities.

A cross-sectional study was undertaken from 2011 to 2015, to determine prevalence and risk factors for this disease through the distribution of a survey to 527 institutions across Australia and Europe; two regions where macropods are popular exhibits. Veterinary and husbandry records from the period 1st January 1995 up to and including 28th November 2016 (the last date when data were extracted from zoo records) were analysed in a retrospective cohort study, examining risk factors for developing disease and treatments used, over time. Computed tomography was used to examine disease occurrence in wild macropods using skulls from population management culls.

The prevalence of lumpy jaw was found to differ between the two regions (p < 0.0002). A review of 6178 records for 2759 macropods housed within eight zoos across the Australian and European regions, found incidence rates and risk of infection differed between geographic regions and individual institutions. Risk of developing lumpy jaw increased with age, particularly for macropods >10 years (Australia IRR 7.63, p < 0.001; Europe IRR 7.38, p < 0.001). Treatment approach varied and prognosis was typically poor with 62.5% mortality for Australian and European regions combined. Lumpy jaw was detected in all captive genera examined, but was absent from the wild populations studied.

Geographic region influenced the incidence of lumpy jaw, the risks associated with developing clinical disease, and preferred treatment approach. Despite advances in antibiotic therapy and surgical techniques, treatment of lumpy jaw is largely unrewarding for the individual and should be approached on an individual basis. This research provides new information about this refractory disease and makes practical recommendations to reduce disease risk. This information may assist institutions in providing optimal long-term health management for captive macropods; such efforts having a positive impact on both welfare and conservation, including but not limited to captive breeding and translocation programs.

The three black cockatoo species endemic to south-west Western Australia – Carnaby’s cockatoo (Calyptorhynchus latirostris), Baudin’s cockatoo (C. baudinii) and forest red-tailed black cockatoo (C. banksii naso) are threatened and have Recovery Plans guiding conservation efforts. Threats include habitat loss due to land clearing for urban, agricultural and industrial development; competition with other species for nest hollows; poaching; disease; vehicle-strike and illegal shooting.

This research built on previous black cockatoo research with an overall aim to develop and validate reliable methods to track all three species, to gain insight into their movement, distribution, habitat use, activity and behaviour.

In an initial proof of concept trial, we attached tail-mounted tags to two Baudin’s cockatoos. Both birds were successfully tracked for several months after release, demonstrating satellite telemetry can be used to locate and track forest species.

We then developed a double-tag mounting protocol to attach a tail-mounted ARGOS PTT satellite tag and back-mounted solar-powered UvA-BiTS GPS tag to captive black cockatoos. The combination of UvA-BiTS back mount and ventral tail mounted Telonics tags was the best tolerated and provided excellent GPS and ARGOS satellite location data with no interference between the two types of tag.

The focus then moved to the development of an automated classifier tool that used accelerometer data from UvA-BiTS GPS tags to remotely identify behaviours and calculate activity budgets. Using accelerometer data from 15 birds post-release, we determined black cockatoos spend most of their time at rest, interspersed with foraging activity through the day and some movement between roost sites and feeding habitat.

To maximise the retention time of tail-mounted tags, the tail feather life span and time of moulting was studied using moulted tail feathers from captive cockatoos and tagged bird post-release. Captive cockatoos had a mean feather lifespan of 410 days, suggesting tail feathers do not always moult annually. Peak tail feather moulting occurs from December to March, the non-breeding period. The optimal time to attach tail mounted tags is from May to September.

The development and optimisation of tracking methodologies for use on black cockatoos has facilitated the tracking of all three species in the wild. This research has provided data which have enabled identification of key roosting, foraging and breeding habitat and determination of flock movement patterns and habitat use at a landscape scale across the species’ distribution ranges. This information is being used to guide black cockatoo conservation management in relation to habitat protection and restoration.