METHODS AND RESOURCES ARTICLE A non-invasive tool for assessing pathogen prevalence in koala (Phascolarctos cinereus) populations: detection of Chlamydia pecorum and koala retrovirus (KoRV) DNA in genetic material sourced from scats Faye Wedrowicz 1,2 • Tom Saxton 1 • Jennifer Mosse 2 • Wendy Wright 2 • Fiona E. Hogan 2 Received: 1 March 2016 / Accepted: 5 July 2016 Ó Springer Science+Business Media Dordrecht 2016 Abstract Pathogenic diseases may threaten the viability of wild animal populations, especially when already vulner- able. The mitigation of risks associated with pathogenic infections in populations is an important factor in conser- vation strategies. Koalas are of conservation concern across the north of their range and are affected by two main pathogens; Chlamydia pecorum and the koala retrovirus (KoRV). This study tested whether DNA from C. pecorum and KoRV could be detected in genetic material isolated from koala scats. Detection of C. pecorum in scat isolated DNA samples was compared with results obtained from urogenital swabs collected from the same individuals as part of an independent study. The ability to detect KoRV in scats from both northern and southern regions of the koa- la’s range was also assessed. There was a high level of concordance (5/6) between the detection of C. pecorum in DNA isolated from scats and urogenital swabs from the same individual. In positive samples, C. pecorum ompA genotypes were identical between DNA from scats and urogenital swabs in two out of three cases. In samples from the south of the koala’s range, KoRV copy number was higher in DNA isolated from scats compared to DNA isolated from ear tissue, potentially indicating the detection of horizontally acquired infections. Our results demonstrate the ability to detect C. pecorum and KoRV in DNA isolated from koala scats. This method will be useful for studying the prevalence, transmission and impact of these pathogens in wild populations which may subsequently inform con- servation management strategies. Keywords Non-invasive pathogen detection  Faecal samples  Chlamydia pecorum  Koala retrovirus (KoRV)  Wildlife health monitoring  Wildlife conservation  Quantitative PCR Introduction Pathogens infecting wild animal populations can affect the health of individuals and may lead to reduced fitness and mortality. Pathogenic diseases can reduce species viability and have been implicated in wild population declines (Tompkins et al. 2015). Consequently, pathogens may have a negative impact on biodiversity and their role as a potential driver of extinctions is becoming increasingly apparent (Smith et al. 2009). Greater data collection may facilitate characterisation and understanding of pathogen prevalence, transmission and impacts, and has the potential to inform and enhance management and conservation strategies. Endemic to Australia, the koala (Phascolarctos ciner- eus) is an arboreal marsupial inhabiting the country’s east coast, from Queensland to South Australia (Fig. 1), that has suffered dramatic population declines over the past two decades (Department of the Environment 2015). While the causes of decline are likely multifactorial, two pathogens have potential contributory roles: the obligate intracellular bacterium, Chlamydia pecorum, and the koala retrovirus (KoRV), both of which infect koalas throughout their Electronic supplementary material The online version of this article (doi:10.1007/s12686-016-0574-3) contains supplementary material, which is available to authorized users. & Faye Wedrowicz Faye.Wedrowicz@gmail.com 1 Faculty of Science, Monash University, Clayton, VIC, Australia 2 School of Applied and Biomedical Sciences, Federation University Australia, Churchill, VIC 3842, Australia 123 Conservation Genet Resour DOI 10.1007/s12686-016-0574-3