Rebecca J Vaughan-Higgins

The aim of this project was to determine the prevalence of bornavirus, nidovirus, sunshinevirus and Mycoplasma spp. in pythons in Western Australia. Two captive cohorts were screened: snakes which had been confiscated by the Department of Biodiversity Conservation and Attractions (DBCA) (n=38) and snakes from Perth Zoo (n=15), for which longitudinal samples were also available for all 15 individuals for 2015 and 2017. A third cohort comprised free-living pythons captured and sampled from various locations within Western Australia (n=17). The majority of the pythons in the study were Antaresia spp., Morelia spp. and Aspidites spp.

Deep oesophageal, oral and cloacal swabs, and blood samples were collected. The swabs were screened using conventional and/or quantitative Polymerase Chain Reaction (PCR). Where relevant, positive amplicons were sequenced.

Sunshinevirus and bornavirus were not detected in any of the pythons sampled in this study. All pythons from Perth Zoo tested negative for nidovirus. Two pythons from the confiscated cohort (5.3%; 95% CI: 0.6%, 17.7%) were positive for nidovirus. All of the free-living pythons tested negative for nidovirus, with the exception of one individual which had inconclusive results. Sampling confirmed that Mycoplasma spp. were present in all three cohorts. The highest rates of Mycoplasma spp. detection occurred within the Perth Zoo cohort in 2015 (73.3%; 95% CI: 44.9%, 92.2%) and 2017 (86.7%; 95% CI: 58.5%, 98.3%) followed by the confiscated population (52.6%; 95% CI: 35.8%, 69.0%), and finally the free-living population (35.3%; 95% CI:14.2%, 61.7%). Mycoplasma spp. were detected in snakes with a range of clinical examination findings, with the majority in clinically normal individuals. Additional studies are necessary to determine the clinical significance of Mycoplasma spp. in snakes. This research is one of only a few studies reporting virology and bacteriology screening in free-living pythons in Australia, and is the first report of Mycoplasma spp. detection in freeliving Australian python species.

The current state of sea turtle health in the Indian Ocean is largely unknown, especially for the endemic flatback turtle (Natator depressus) which is listed as ‘vulnerable’ in Western Australia (WA) and ‘data deficient’ globally. Anecdotally, the causes of illness, injury, and death in Western Australian turtles are comparable to those in other parts of Australia and the world (e.g., spirorchiidiasis, fibropapillomatosis, and marine debris interaction) but scientific studies to validate these reports are particularly limited in this region. To address these knowledge gaps, causes of both live and dead turtle strandings in WA were investigated through an array of veterinary diagnostic techniques including necropsy, clinical pathology, diagnostic imaging, histopathology, parasitology, microbiology, toxicology, and molecular analyses. Health assessments were conducted on live animals to determine baseline levels of health and disease for specific populations, predominately nesting and foraging flatback turtles.

Through these health and disease investigations, baselines were developed, along with the discovery of new diseases in flatback turtles including a novel haemoparasite, Haemocystidium spp., occurring specifically in the foraging life stage; a potentially emerging zoonotic bacterium, Streptococcus iniae associated with a multi-species mass mortality event involving post-hatchlings; as well as spirorchiidiasis, previously unreported in this species. Other unusual and emerging diseases were also reported in sea turtles in this study, including microsporidial myopathy, salt gland adenitis, gout, and pseudogout.

In this study, natural disease-related causes of mortality occurred more frequently than direct anthropogenic causes, with parasitoses the most frequently occurring natural disease. Spirorchiidiaisis was the most common cause of mortality (32.0%) with a prevalence of 93.2% in turtles susceptible to the disease (i.e., excluding the post-hatchling life stage). The next most common cause of mortality was unknown (17.3%), followed by trauma (13.3%), endoparasitosis (10.7%), infectious disease (6.7%), and pneumonia (6.7%), with the remaining mortality categories each accounting for less than 5% of cases (including systemic inflammation, osmoregulatory disorder, gastrointestinal impaction, gastrointestinal foreign body, fibropapillomatosis, and metabolic disorder).

We developed the first flatback turtle reference intervals (RIs) in Reference Value Advisor (RefVal v2.1) following the American Society of Veterinary Clinical Pathology (ASVCP) guidelines. We found flatback turtle RIs were generally similar to other published sea turtle RIs and reference values (RVs) but detected significant differences in our study for the various boundary conditions including life stage (nesting or foraging), as well for measurement methodology (field or laboratory tests), justifying the establishment of separate RIs/RVs for nesting and foraging flatbacks, and for field and laboratory techniques.

This study was the first sea turtle health and disease investigation in WA and the eastern Indian Ocean to offer broader insights into sea turtle health and disease status on a regional scale. These essential baselines provided a number of crucial functions which include serving as a reference point for future studies to monitor changes in population health and disease levels. Specifically, these baseline data will be useful for future comparative studies of the same population where changes are an indication of a changing environment. The blood RIs can be used for disease diagnosis, monitoring progress and assessing prognosis of clinical flatback turtle cases in rehabilitation. Considering that diseases in the marine environment are predicted to rise with increasing anthropogenic pressures, detection of new and emerging diseases is of significance to the global knowledge of sea turtle diseases; and for understanding and mitigating disease threats to sea turtle populations. Finally, this study provided a framework to integrate health into future conservation management decisions to ensure the long-term survival of sea turtles.

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.