Integrated approaches for pathogen monitoring and shotgun metagenomic analysis in Atlantic salmon farming

Specific tools for detecting waterborne pathogens are essential for limiting disease spread in aquaculture. We evaluated a field-deployable workflow combining filtration of eDNA/eRNA with targeted (RT-)qPCR and complementary shotgun metagenomics to monitor pathogens and microbial community dynamics across an Atlantic salmon production cycle, from hatchery to offshore cages. The primary aim was to assess workflow feasibility and performance under real farm conditions, while secondarily examining whether metagenomic profiles could contextualise microbial shifts associated with pathogen presence. ISAV was consistently detected in hatchery water at ~ 4×10³–9×10³ copies per litre, whereas PRV1 was detected only inside sea pens from August onward (~ 4×10²–1.5×10⁴ copies per litre) and increased by more than two orders of magnitude after wellboat delousing. Shotgun metagenomics yielded a median of ~ 1.5×10⁵ reads per sample (mean read length ~ 2.5 kb; N50 > 2 kb), enabling broad taxonomic screening. PRV1-positive seawater samples showed modest decreases in richness and shifts in viral taxa, though patterns were subtle and should be interpreted cautiously given low pathogen loads. The workflow was practical for trained farm personnel, and this integrated approach offers a scalable system for routine pathogen surveillance and supports earlier, evidence-based biosecurity actions, providing broader microbial information than qPCR alone.