An eDNA toolkit for the surveillance of wildlife pathogens in traded amphibians: Raw Data and Code

Raw data and code associated with the PhD thesis: An eDNA toolkit for the surveillance of wildlife pathogens in traded amphibians, submitted September 2024.

Amphibians are threatened globally, with dramatic declines reported in many species attributed to the deadly pathogens Batrachochytrium dendrobatidis (Bd) and Ranavirus (Rv). Both pathogens have spread through international wildlife trade networks, which remain largely unmonitored, presenting major conservation and welfare challenges despite legal obligations to do so. Environmental (e)DNA methods can provide highly sensitive non-invasive pathogen surveillance for both traded and wild amphibians. To investigate the relationship between eDNA detection and environmental pathogen persistence, pathogen eDNA decay rates were quantified across a range of temperatures (15-25ºC), finding that eDNA decay is rapid for both pathogens. Low levels of pathogen eDNA remained detectable for the duration of the experiment (>28 days). I consider high concentrations of eDNA to represent viable pathogen in the environment, sustained due to active shedding from infected individuals. This demonstrates the usefulness of eDNA for the monitoring immediate population-level infection status. I used eDNA methods to identify Bd infections in a large Xenopusresearch facility (EXRC, Portsmouth, UK) by sampling animals opportunistically in line with 3Rs guidelines. Having identified Bd infections in a subpopulation of Xenopus laevis, I compared detection from 4 types of eDNA and swab data for ~60 animals over 10 days. Positive Bd eDNA signals were consistently detected in tank-water, whereas detection appears more variable from other eDNA sources (i.e. sump/sludge/sock), and swab positives cycled between positive and negative for most individuals. I then used compartmental mathematical disease models to investigate the relationships between environmental detection, prevalence and individual loads. My findings are put into context of captive management, pathogen surveillance of traded amphibians and general animal welfare. Ultimately, an improved knowledge of both the potential and limitations of pathogen eDNA can be transferred to other challenging disease systems for improved pathogen monitoring and safeguarding of amphibian populations worldwide.