Samples of dying farmed salmon were made available from the Fisheries and Ocean Canada regulatory farm audit program. These samples are collected to monitor background losses in production populations, to detect ongoing or recent health events within the industry, and to ensure reporting compliance with OIE (World Organization of Animal Health) listed diseases. Farm audit samples are collected on randomized BC farms, with one to six fresh silver (recently dead) fish sampled per farm audit in 2011–13. At the time of collection, clinical and environmental data are noted, and tissue samples are taken for histopathology, bacterial and viral culture and molecular analysis. Veterinary diagnostics were conducted on these samples prior to our application of the VDD, and were based largely on histopathology and clinical data. Our team had already conducted quantitative molecular analyses of 45 infectious agents known or suspected to cause disease in salmon on cDNA/DNA from combined tissues (heart, liver, head and anterior kidney, gill, pyloric caeca, spleen), so the backdrop of known infectious agents was determined for each sample. The VDD biomarkers were applied on this same cDNA from 240 farmed Atlantic salmon and 68 farmed Chinook salmon collected from 2011 to 2013 (Table 1 C). We utilized these data to assess the ability of the VDD to discriminate fish experiencing viral- versus bacterial- or parasite-induced diseases based on tissue pools.
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