Pooled samples and eDNA-based detection can facilitate the “clean trade” of aquatic animals

Abstract

the regional and international trade of live animals facilitates the movement, spillover, and emergence of zoonotic and epizootic pathogens around the world. Detecting pathogens in trade is critical for preventing their continued movement and introduction, but screening a sufficient fraction to ensure rare infections are detected is simply infeasible for many taxa and settings because of the vast numbers of animals involved-hundreds of millions of live animals are imported into the U.S.A. alone every year. Batch processing pools of individual samples or using environmental DnA (eDnA)-the genetic material shed into an organism's environment-collected from whole consignments of animals may substantially reduce the time and cost associated with pathogen surveillance. Both approaches, however, lack a framework with which to determine sampling requirements and interpret results. Here I present formulae for pooled individual samples (e.g,. swabs) and eDNA samples collected from finite populations and discuss key assumptions and considerations for their use with a focus on detecting Batrachochytrium salamandrivorans, an emerging pathogen that threatens global salamander diversity. While empirical validation is key, these formulae illustrate the potential for eDnA-based detection in particular to reduce sample sizes and help bring clean trade into reach for a greater number of taxa, places, and contexts.

Application of Environmental DNA for Monitoring Red Sea Bream Iridovirus at a Fish Farm

“…eDNA has been studied extensively since the 2000s with numerous applications, such as metagenomics, species detection, or biomass estimation ( 1 , 2 ). Aquatic animal pathogens are basically waterborne; therefore, eDNA has been studied as a potential tool for monitoring aquatic animal diseases in aquaculture ( 3 – 5 ) and border control ( 6 , 7 ). Although the term “eDNA” has not been used in fish virus research, eDNA could be applied in monitoring waterborne viruses in combination with virus concentration techniques.…”

Novel chytrid pathogen variants and the global amphibian pet trade

“…Because animals can carry Bd without showing clinical signs of disease, such requirements are unlikely to prevent pathogen transmission. Thus, IHCs need to include the results of PCR-based Bd screening tests, either by swabbing individuals or by pooling samples obtained, for example, by water filtering (e.g., Kolby et al, 2014Kolby et al, , 2015Brunner, 2020).…”

“…Notably, outbreaks of chytridiomycosis have not been reported in Asia, where amphibians may have evolved resistance to the disease (Bataille et al, 2015;Fu & Waldman, 2019). Some globally traded species, including African clawed frogs (Xenopus laevis) and American bullfrogs (Rana catesbeiana), also survive infection without presenting clinical signs of chytridiomycosis (Fisher & Garner, 2007, 2020Weldon et al, 2004). Nonetheless, they can transmit the pathogen to other species (Fisher & Garner, 2020;Reeder et al, 2012).…”

Threats to UK freshwaters under climate change: Commonly traded aquatic ornamental species and their potential pathogens and parasites

“…Traditionally, the testing of host species for PPP presence often requires destructive sampling, which limits the number of specimens and ultimately reduces the probability of PPP detection. However, new methodologies that incorporate molecular techniques at border control posts, such as environmental DNA, may present a good non-lethal option (Trujillo-González et al 2019b;Brunner 2020) for improved PPP detection. Measures such as heat ramping (gradually increasing the water temperature over a minimum period) can be used during quarantine to detect latent infections (Eide et al 2011); however, this may not appropriate for all PPPs, when surveillance aims to target multiple PPPs and where there is a need to adhere to animal welfare laws and guidance.…”