A Comparison of Nonlethal and Destructive Methods for Broad‐Based Infectious Agent Screening of Chinook Salmon Using High‐Throughput qPCR

Abstract

Molecular tools, such as high-throughput quantitative polymerase chain reaction (HT-qPCR), are useful for monitoring multiple infectious agents in wild animal populations (i.e., broad-based screening). If destructive tissue samples cannot be obtained due to experimental design requirements (e.g., bio-telemetry; holding with repeated biopsy) or the conservation status of host species, then nonlethally sampled tissues can be substituted. However, infection profiles have been found to differ between nonlethally and destructively sampled tissues. We present a comparative analysis of nonlethal (gill and blood) and destructive (pool of internal and external tissue) approaches for broad-based infectious agent screening of adult Chinook Salmon Oncorhynchus tshawytscha. Of a possible 47 agents, 16 were detected overall by nonlethal and destructive methods. Our results indicated moderate differences in infection profiles among tissues, with limitations of each tissue type dependent on the ecology of each agent. The gill was the most comprehensive screening tissue, as more infectious agents were detected overall in gill (n = 16) than in blood (n = 12) or multi-tissue pools (n = 15). The agreement in the estimated agent prevalence between tissue types ranged from poor to excellent, while overall agent community structure (the combined prevalence of all agents) showed low agreement between tissue types. Two agents occurred at 100% prevalence in all tissue types. Nine agents, including types of bacteria and gill parasites, were more prevalent in gill than in blood, while five agents, including one virus and several microparasites, were more prevalent in blood. Future studies should pair microscopy and histopathology with HT-qPCR to better characterize host health and disease development relative to molecular detection of agents across tissue types.

A molecular assessment of infectious agents carried by Atlantic salmon at sea and in three eastern Canadian rivers, including aquaculture escapees and North American and European origin wild stocks

“…St. John fish could only be nonlethally sampled for gill as opposed to gill, heart, and kidney from Restigouche and escapee fish. However, gill has been shown to have equal or greater infectious agent richness than multi-tissue pools (Teffer and Miller 2019). Only one virus, ASCV, was detected (in just one host) in the Restigouche River.…”

“…Gill, heart, and kidney biopsy samples (multi-tissue) were taken from fish in Greenland and at the Magaguadavic and Restigouche rivers in 2017, whereas only kidney samples were taken from Greenland-sampled fish in 2016 and only nonlethal gill biopsies from fish of the threatened St. John River population in 2017. Gill biopsies have been shown to comprise most infectious agents detected in multi-tissue HT-qPCR analyses (Teffer and Miller, 2019).…”

An evaluation of the potential factors affecting lifetime reproductive success in salmonids

“…While lethal sampling has been employed in numerous studies assessing pathogens in salmonids, other studies have employed nonlethal methods (e.g., Elliott et al, 2015 ; Fernández‐Alacid et al, 2018 ; Kittilsen et al, 2009 ; Rees et al, 2015 ). The use of noninvasive and nonlethal sampling across salmonid studies remains a priority for state, federal, and tribal fisheries agencies, and much progress has been made on developing these sampling techniques (Coble et al, 2019 ; Lawrence et al, 2020 ; Teffer & Miller, 2019 ). Therefore, an assessment of the effect of pathogens on reproductive success in salmonids is a tractable area of research and remains an area of high need.…”

Host‐pathogen‐environment interactions predict survival outcomes of adult sockeye salmon (Oncorhynchus nerka) released from fisheries

“…This technology allows for the simultaneous quantification of 96 molecular assays (i.e., targeting either host or infectious agent genes) on 96 tissue samples; the platform has been analytically validated against traditional qPCR for its use in infectious agent screening (Miller et al, 2016), applied in multiple field surveys of wild salmon populations (Bass et al, 2017; Nekouei et al, 2018; Thakur et al, 2018; Tucker et al, 2018), and paired with evaluations of host gene expression (Jeffries et al, 2014; Miller et al, 2014, 2017; Teffer et al, 2017, 2019). Gill has been identified as a representative tissue for nonlethal evaluation of transcriptomics including host infection burdens, which comprise most microorganisms detected in multitissue qPCR surveys of Pacific salmon (Jeffries et al, 2021; Teffer et al, 2017; Teffer & Miller, 2019). Here, we used this tool to characterize the development of multiple infections in gill during a ≥5‐week period simultaneously with the expression of a suite of host stress and immune genes to describe how differences in initial infection burdens, infection development, and host responses in gill contribute to the early mortality of Pacific salmon.…”