Environmental DNA/RNA for non-invasive early detection and monitoring of pathogen dynamics in Atlantic salmon (Salmo salar) recirculating aquaculture systems (RAS)

Recirculating Aquaculture Systems (RAS) provide efficient fish production with reduced water use and precise environmental control. However, their closed design facilitates susceptibility to pathogen persistence and disease outbreaks, highlighting the need for effective monitoring and treatments. Over a 12-week study, water samples (purified eDNA/eRNA) were evaluated in two freshwater RAS units at a commercial pre-smolt Atlantic salmon (Salmo salar) farm as a non-lethal and non-invasive alternative to tissue samples for early pathogen detection. A key aim was furthermore to elucidate the infection dynamics by monitoring five pathogens: salmon gill poxvirus (SGPV), non-virulent infectious salmon anaemia virus (ISAV-HPR0), infectious pancreatic necrosis virus (IPNV), piscine orthoreovirus genotype 1 (PRV-1), and the bacterium Flavobacterium psychrophilum. The study revealed similar sequential infection patterns of the four viral pathogens in both RAS units, starting with clinical infection by SGPV, followed by infection with ISAV-HPR0, alongside a concurrent clinical infection with IPNV and sporadic PRV-1 detections. SGPV peaked earlier and caused higher mortality in one system, consistent with elevated SGPV levels detected in water prior to fish transfer. A strong positive correlation was found between gill swabs and water samples for SGPV and ISAV-HPR0. Although high viral loads of IPNV were recorded in fish in one system, with sporadic detections in the other, no consistent correlation could be established between kidney swabs and water samples. No correlation was seen for PRV-1 as well. F. psychrophilum showed minor fluctuations in gill swabs but higher, yet stable, levels in water samples. Our study elucidates the infection dynamics of key Atlantic salmon pathogens in RAS and demonstrates the potential of eDNA/eRNA as a non-invasive tool for the prediction, early detection, and monitoring of SGPV and ISAV-HPR0 in Atlantic salmon RAS.