Analysis of Morbidity and Mortality of Wild Koalas in South-East Queensland using Passive Surveillance Data Viviana Gonzalez-Astudillo BVSc, MNR A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2018 School of Veterinary Science 1 Abstract The koala is an iconic marsupial threatened by habitat loss, trauma, droughts, and diseases. The Australian state of Queensland was estimated to hold the largest koala population during the 1990s; however, this number has nearly halved in two decades, with declines of up to 80%, particularly in South-East Queensland (SE QLD). Despite this alarming reduction, the relative contribution of threats causing this decline in SE QLD had not been quantitatively assessed. In addition, information on the spatial- temporal distribution of morbidity and mortality cases is lacking for SE QLD, along with competing injury and disease risks. To address this issue, a retrospective epidemiological study from cases submitted to hospitals (1997-2013) was performed. The analysis included N=20,250 records, highlighting that most koalas arrived dead (48%), followed by other being euthanized (35%), and a smaller number being released (17%). Trauma by motor vehicles, urogenital chlamydiosis and low body conditions were the leading causes of admission and frequently co-occurred. Of concern was that 37% of koalas were injured but otherwise healthy, and that urogenital chlamydiosis, which causes infertility, overwhelmingly affected females. Multinomial logistic regression models identified year of admission, age class, sex and season as risk factors significantly influencing koala outcomes for main clinical syndromes assessed. Exploratory space-time permutation scans detected significant clusters of trauma, chlamydiosis and low body condition in specific local government areas. In this study, passively-acquired data provided insight into the complex interplay of threats impacting koalas in SE QLD. Although hospitals have been providing specialised care to koalas for decades, there is no standard nomenclature to record admissions, complicating the estimation of causes of mortality and the incidence of comorbidities. Additionally, autopsies are frequently not conducted in a systematic manner, hampering the identification of comorbidities and disease interactions in the SE QLD population decline. A literature search for the commonly documented morbidity and mortality causes for koalas was used to categorise standardised nomenclature. This was followed by a large scale autopsy survey (2013-2016) including N=519 koala autopsies from carcasses derived from main SE QLD hospitals. Demographically, there was a higher number of mature koalas of breeding age admitted with infections and trauma compared to young/subadult or senescent koalas. Trauma by motor vehicles, urogenital and ocular 2 chlamydiosis were the leading causes of admission, frequently presenting as comorbidities. About 19% of koalas suffering injuries were otherwise healthy. Of concern was the high numbers of koalas with chronic diseases leading to low body condition and the disproportionate number of females diagnosed with reproductive disease. No observable evidence was found to explain low body condition in 6% of young/subadult males. A low body condition was found to significantly influence the likelihood of animal attacks verses normal body condition injured by motor vehicles or animals (p = 0.007). Novel and rare conditions were characterised grossly and histologically for koalas. Trauma and chlamydiosis have been maintained as main causes of admission to hospitals over two decades of koala population surveys, stressing the relative importance of these conditions in the koala decline. Chronic diseases dominated the study, and there is evidence debilitation increases susceptibility to succumb to other causes. The demographic distribution of admission could reflect population structure and cumulative exposure risk to trauma. The overrepresentation of female koalas with chlamydiosis reflects the surveillance by hospitals to curb the release of permanently infertile carriers. Although there are limitations to the interpretation of hospital-acquired data, both studies present comprehensive and quantifiable evidence that aetiologies are acting jointly as multifactorial elements in the continuing koala decline. Koala disease monitoring is usually based on opportunistic sampling, which may lead to variation in diagnosis for the same koala between clinical and pathological examination. Thus, understanding the accuracy when making a diagnosis is essential to understand the causes for the koala decline. Mixed models were used to estimate the probability of agreement of producing the same diagnosis for the same koalas by veterinary hospitals or pathologists. Almost 80% of the variation in the agreement was explained by the diagnosis effect, highlighting that some diagnoses may be easier to make than others. There was a high probability of agreement for commonly diagnosed conditions, and low probabilities of agreement for historically underdiagnosed conditions, subclinical parasitosis, and resolved tissue injuries. Variation in the agreement on producing the same diagnosis was influenced to a lesser degree by koala-specific characteristics such as carcass preservation. This highlights that clinical 3 examination in wildlife hospitals is accurate for common koala conditions, while autopsies increased detection sensitivity to identify specific aetiologies, diagnoses and comorbidities. Multiple factors can influence the quality of an autopsy. In spite of this, autopsy remains an important method to confirm or overturn a diagnosis, and clarify or correct clinical signs in cases with diagnostic uncertainty, such as with emerging or novel diseases in wildlife. 4 Declaration by Author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from co-authors for any jointly authored works included in the thesis. 5 Publications during Candidature • Peer-reviewed papers Gonzalez-Astudillo V., Leon-Alvarado O.D., Ossa-Lopez, P.A., Rivera-Paez, F.A., Ramirez-Chaves, H.E. 2018. Sarcoptic mange in wild Quichua Porcupines (Coendou quichua Thomas, 1899) in Colombia. International J for Parasitology: Parasites and Wildlife. 7: 95-98. Gonzalez-Astudillo V., Allavena R., McKinnon A., Larkin R., Henning J. 2017. Decline causes of Koalas in South East Queensland, Australia: a 17-year retrospective study of mortality and morbidity. Scientific Reports 7:42587. Gonzalez-Astudillo V., Hernández S.M., Peters V., Yabsley M.J., Keel K.M., Munk B., Ruder M.G., Brown J., Fischer J.R., and Nemeth M.N. 2016. Mortality of passerines and relatives submitted to a wildlife diagnostic laboratory (Southeastern Cooperative Wildlife Disease Study, USA): a 36-year retrospective analysis. Journal of Wildlife Diseases 52: 441-458. Gonzalez-Astudillo V., Bustamante-Rengifo J.A., Bonilla A., Castillo-Giraldo A.O., Lehmicke A.J.J., Astudillo-Hernandez M. 2016. Synanthropic Cockroaches (Blattidae: Periplaneta spp.) Harbor Pathogenic Leptospira in Colombia. Journal of Medical Entomology. 53:177-82. Gonzalez-Astudillo V., Ramirez H.E., Henning J., Gillespie T.R. 2016. Current knowledge of studies of pathogens in Colombian mammals. MANTER: Journal of Parasite Biodiversity. Occasional papers, Number 4, September 1. doi:10.13014/K2057CV6. Nemeth, N.M., Gonzalez-Astudillo V., Oesterle, P., Howerth, E.W. 2016. A 5-Year Retrospective Review of Avian Diseases Diagnosed at the Department of Pathology, University of Georgia. Journal of Comparative Pathology 155:105-120. González Astudillo V., Schaffer-White A., Allavena R., Palmieri C. 2015. Multiple Intra- abdominal Serosal Myxosarcomas in Two Koalas (Phascolarctos cinereus). Journal of Comparative Pathology 152: 283-286. 6 González-Astudillo V., Peña-Stadlin J.E., Bustamante J.A., Astudillo Hernández M. 2015. Terminal leptospirosis in a woolly monkey (Lagothrix lagotricha) in Colombia. Revista MVZ Cordoba 20: 4505-4510.