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Environmental DNA-based detection of Batrachochytrium salamandrivorans in captive settings

Brunner, Jesse1; Yarber, Christian1

Published Sep 11, 2023 on Dryad. https://doi.org/10.5061/dryad.hdr7sqvp5

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Sep 11, 2023 version files 264.49 KB

Abstract

Detecting pathogens in the live animal trade is critical for tracking and preventing their movement, introduction, and spillover into susceptible fauna. However, the scale of the live animal trade makes individually testing animals infeasible for all but the most economically important taxa. For instance, while the fungal pathogen, Batrachochytrium salamandrivorans (Bsal), threatens amphibian, particularly caudate diversity, in Europe and the Americas, screening even a fraction of the millions of live amphibians imported into the United States, alone, is impractically laborious and expensive. A promising alternative to individual-level sampling (e.g., swabbing the skin of salamanders) is to instead collect DNA from the animals’ environment (e.g., housing container or water) which allows us to screen a whole group of animals at a time. 

We used a series of experiments with Bsal-spiked water and substrates and experimentally infected rough-skinned newts (Taricha granulosa) to determine how best to collect Bsal environmental DNA (eDNA) samples, that is, which methods yield the greatest recovery of Bsal eDNA, and evaluate the capacity of these methods to detect Bsal-infected animals in conditions that might be found in captive settings and trade.

We found that filtering water housing infected animals for even an hour can consistently recover detectable levels of Bsal eDNA, that there is little evidence of Bsal eDNA being clumped in housing containers or being swamped or inhibited under realistically dirty conditions, and that eDNA-based methods achieves an equivalent or higher chance of detecting Bsal infections in a group of co-housed newts with fewer samples than traditional methods of individually swabbing.

By sampling the genetic materials shed or produced by a whole group of animals, eDNA-based methods are a powerful means of detecting pathogens, such as Bsal, in shipment and captive population. These methods bring routine pathogen surveillance into reach in many more contexts and can thus be an important tool in conservation and disease control.