The spread of infection from reservoir host populations is a key mechanism for disease emergence and extinction risk and is a management concern for salmon aquaculture and fisheries. Using a quantitative environmental DNA methodology, we assessed pathogen environmental DNA in relation to salmon farms in coastal British Columbia, Canada, by testing for 39 species of salmon pathogens (viral, bacterial, and eukaryotic) in 134 marine environmental samples at 58 salmon farm sites (both active and inactive) over 3 years. Environmental DNA from 22 pathogen species was detected 496 times and species varied in their occurrence among years and sites, likely reflecting variation in environmental factors, other native host species, and strength of association with domesticated Atlantic salmon. Overall, we found that the probability of detecting pathogen environmental DNA (eDNA) was 2.72 (95% CI: 1.48, 5.02) times higher at active versus inactive salmon farm sites and 1.76 (95% CI: 1.28, 2.42) times higher per standard deviation increase in domesticated Atlantic salmon eDNA concentration at a site. If the distribution of pathogen eDNA accurately reflects the distribution of viable pathogens, our findings suggest that salmon farms serve as a potential reservoir for a number of infectious agents; thereby elevating the risk of exposure for wild salmon and other fish species that share the marine environment.


  • In multi-host infectious disease systems, reservoir host species are those that alone can maintain the parasite and sustain transmission to other host species [1]

  • We modelled the presence of pathogen DNA as a binary variable per site using a generalized linear mixed-effects model (GLMM) with a binomial error distribution, that included fixed effects for farm activity or Atlantic salmon environmental DNA (eDNA), and random effects for site and species

  • Reservoir host populations can increase the risk of disease transmission to, and extinction risk of, nearby host populations [1,3]

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In multi-host infectious disease systems, reservoir host species are those that alone can maintain the parasite and sustain transmission to other host species [1]. Pathogen transmission from domesticated salmon is a concern for the conservation of wild salmon in Canada, including coho (Oncorhynchus kisutch), Chinook (Oncorhynchus tshawytscha), and sockeye (Oncorhynchus nerka) as well as wild populations of Atlantic salmon and sea trout in other regions where salmonid aquaculture encroaches on wild habitat [24,25,26,27,28]. We use eDNA to empirically evaluate the distribution of a diverse assemblage of pathogens in the marine environment in relation to domestic salmon populations in coastal British Columbia (BC), Canada. In this system, transmission among salmonids can occur between five species of wild Pacific salmon and net-pen farmed Atlantic salmon (Salmo salar) via their shared marine environment. Over 3 years (2016–2018), we analysed the occurrence of 39 pathogens, including viral, bacterial, and eukaryotic agents, at subsets of these 58 salmon farm locations, a fraction of which are fallowed at any given time

59. Di Cicco E et al 2018 The same strain of Piscine

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