Non-Lethal Samples for Detecting Salmonid Pathogens: Potential for Investigations of Wild Fish Populations

Non-lethal sampling methods to test fish for pathogens can reduce the need to sacrifice large numbers of fish to determine infection prevalence. This can be particularly useful for investigating pathogens in fish populations designated as threatened or endangered, such as the listed (threatened) populations of wild Chinook salmon and steelhead in the Snake River (Pacific Northwest, USA). Additionally, non-lethal sampling combined with tagging allows monitoring of performance and survival of fish after testing. Molecular pathogen detection assays such as the polymerase chain reaction (PCR) enable testing of small tissue samples, and real-time quantitative PCR (qPCR) allows rapid quantification of pathogens in samples. Fin clips, gill snips, and surface mucus scrapings were determined to be suitable non-lethal samples in tests with juvenile Chinook salmon (Oncorhynchus tshawytscha) between 2.8 and 15.2 g in weight, but blood and kidney biopsy samples caused ≥5% mortality and may be appropriate only for larger fish. We tested non-lethal sampling methods for detection of the microsporidian parasite Nucleospora salmonis and the bacterial kidney disease (BKD) agent Renibacterium salmoninarum, two salmonid pathogens that cause chronic infections, have immunosuppressive properties, and can be difficult to detect. Non-lethal gill snip samples were demonstrated to be a suitable substitute for lethal kidney tissue samples for detection of N. salmonis in naturally infected juvenile salmonids. Results of laboratory challenge experiments indicated that testing of fin, surface mucus, or gill samples by qPCR was an adequate non-lethal substitute for kidney sample testing to detect R. salmoninarum. We used non-lethal samples of gill tissue for single-sample detection of N. salmonis and R. salmoninarum DNA in out-migrating juvenile wild and hatchery origin Chinook salmon and steelhead (O. mykiss) collected at Lower Granite Dam on the Lower Snake River over a 3-year period. All tested fish were marked with passive integrated transponder (PIT) tags before they were transported by barge to a release site below the lowermost hydroelectric dam (Bonneville Dam) on the Columbia River. The PIT tags from some fish that had been sampled non-lethally at Lower Granite Dam were recovered after the nesting season from colonies of piscivorous birds on East Sand Island in the Columbia River estuary. This research enabled non-lethal comparison of prevalence and levels of two pathogens in wild and hatchery origin salmonids, and investigation of the possible influence of infection with one or both pathogens on fish susceptibility to avian predation.