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 (<i>Bd</i>) and Ranavirus (<i>Rv</i>). 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 (&gt;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 <i>Bd</i> infections in a large <i>Xenopus</i>research facility (EXRC, Portsmouth, UK) by sampling animals opportunistically in line with 3Rs guidelines. Having identified <i>Bd</i> infections in a subpopulation of <i>Xenopus laevis</i>, 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.

本数据集关联2024年9月提交的博士学位论文《跨境交易两栖动物野生病原体监测的环境DNA（eDNA）工具包》。全球两栖动物正面临生存威胁，诸多物种因致命病原体蛙壶菌（Batrachochytrium dendrobatidis, Bd）和蛙病毒（Ranavirus, Rv）引发种群大幅衰退。上述两种病原体均通过国际野生动物贸易网络扩散，而该贸易网络目前仍基本处于未监管状态，即便存在相关法定监管义务，仍对生物多样性保护与动物福利造成了严峻挑战。环境DNA（eDNA）技术可为交易及野生两栖动物提供高灵敏度的非侵入式病原体监测手段。为探究eDNA检测与环境病原体存留间的关联，本研究在15至25℃的温度梯度下量化了病原体eDNA的降解速率，结果显示两种病原体的eDNA降解均较为迅速，但实验全程（超过28天）仍可检测到低浓度的病原体eDNA。本研究认为，高浓度eDNA可代表环境中具有活性的病原体，此类高浓度病原体源于感染个体的主动释放，这也证实了eDNA技术可用于实时监测种群层面的感染状态。本研究依据3R原则，通过机会性采样，在英国朴茨茅斯大学大型爪蟾（Xenopus）研究设施（EXRC）中利用eDNA技术鉴定Bd感染情况。在鉴定出非洲爪蟾（Xenopus laevis）亚种群的Bd感染情况后，本研究针对约60只实验动物，对比了10天内4种eDNA样本与拭子样本的检测结果。水箱水体中始终可检测到Bd eDNA阳性信号，而其他eDNA样本（即集水坑污泥、过滤袜样本）的检测结果波动较大；多数个体的拭子检测结果则呈阳性与阴性交替出现的周期性变化。随后，本研究利用分区数学疾病模型，探究了环境检测结果、感染率与个体病原体载量之间的关联。本研究结果结合了圈养管理、交易两栖动物的病原体监测以及通用动物福利的相关场景进行阐释。最终，本研究对病原体eDNA技术的应用潜力与局限性的深入认知，可推广至其他复杂疾病系统，以优化全球两栖动物种群的病原体监测工作，并为其种群保护提供支撑。