Data from: Design- and model-based strategies for detecting and quantifying an amphibian pathogen in environmental samples

Accurate pathogen detection is essential for developing management strategies to address emerging infectious diseases, an increasingly prominent threat to wildlife. Sampling for free-living pathogens outside of their hosts has benefits for inference and study efficiency, but is still uncommon. We used a laboratory experiment to evaluate the influences of pathogen concentration, water type, and qPCR inhibitors on the detection and quantification of Batrachochytrium dendrobatidis (Bd) using water filtration. We compared results pre- and post-inhibitor removal, and assessed inferential differences when single versus multiple samples were collected across space or time. We found that qPCR inhibition influenced both Bd detection and quantification in natural water samples, resulting in biased inferences about Bd occurrence and abundance. Biases in occurrence could be mitigated by collecting multiple samples in space or time, but biases in Bd quantification were persistent. Differences in Bd concentration resulted in variation in detection probability, indicating that occupancy modeling could be used to explore factors influencing heterogeneity in Bd abundance among samples, sites, or over time. Our work will influence the design of studies involving amphibian disease dynamics and studies utilizing environmental DNA (eDNA) to understand species distributions.

精准检测病原体，是制定应对新发传染病管理策略的核心前提——此类传染病对野生动物而言，已是愈发严峻的威胁。对宿主外自由存活的病原体进行采样，虽能提升推断准确性与研究效率，但此类采样手段仍较为罕见。本研究通过室内实验，评估了病原体浓度、水体类型与qPCR抑制剂对采用滤水法检测、定量蛙壶菌（Batrachochytrium dendrobatidis，Bd）的影响。我们对比了去除抑制剂前后的检测结果，并评估了在空间或时间维度上采集单份与多份样本时的推断差异。研究发现，qPCR抑制作用会干扰天然水体样本中Bd的检测与定量，进而导致关于Bd检出率与种群丰度的推断出现偏差。可通过在空间或时间维度上采集多份样本，缓解Bd检出率相关的推断偏差，但Bd定量层面的偏差仍持续存在。Bd浓度差异会导致检测概率出现波动，这表明可利用占用模型（occupancy modeling）探究样本、样点间或随时间变化的Bd丰度异质性的影响因素。本研究成果将为两栖动物疾病动态相关研究，以及利用环境DNA（environmental DNA，eDNA）解析物种分布的研究的实验设计提供重要参考。