Detection and Quantification of the Oomycete Saprolegnia parasitica in Aquaculture Environments

Abstract

Saprolegnia parasitica induces heavy mortality in aquaculture. The detection of S. parasitica is often time consuming and uncertain, making it difficult to manage the disease. We validated a previously published real-time quantitative PCR (qPCR) assay to confirm the presence of S. parasitica in fish and in water using environmental DNA (eDNA) quantification. Analytical sensitivity and specificity of the assay was assessed in silico, in vitro and the qPCR assay was compared with microbiological cultivation methods to detect and quantify S. parasitica in water samples from a controlled fish exposure experiment and from fish farms. Furthermore, we compared the use of an agar cultivation method and the qPCR assay to detect S. parasitica directly from mucus samples taken from the fish surface. The analytical sensitivity and specificity of the qPCR assay were high. The qPCR assay detected 100% of S. parasitica-positive water samples. In a field study, the qPCR assay and a microwell plate (MWP) enumeration method correlated significantly. Furthermore, the qPCR assay could be used to confirm the presence of S. parasitica in skin mucus. Thus, the qPCR assay could complement diagnostic methods in specifically detecting saprolegniosis in fish and used as a surveillance method for S. parasitica pathogen in aquaculture environments.

Identification and genetic characterization of Saprolegnia parasitica, isolated from farmed and wild fish in Finland

“…Such knowledge is important to eventually develop strategies to prevent and control the spreading and transfer of this economically important disease. Also, additional studies on the association between S. parasitica and co‐infective bacterial agents are worth addressing, preferably using qPCR and species‐specific DNA primers based on the results obtained in the present study (Korkea‐aho et al, 2022). The presence of the significant Saprolegnia species in biofilms of fish farm tanks, tubes and equipment might also be necessary to examine in the future, using the results obtained in the present study as a baseline.…”

Environmental DNA as a Tool for Better Understanding the Distribution, Abundance, And Health of Atlantic Salmon and Pacific Salmon

“…For example, qPCR assays were used to detect DNA from Gyrodactylus salaris, a monogenean parasite of Atlantic Salmon and other salmonids, in southern Norway and northwestern Russia, areas where this trematode was inferred to have recently been introduced (Rusch et al 2018;Hansen et al 2022). Other investigations used qPCR to detect eDNA of the oomycete Saprolegnia parasitica or the myxozoan Kudoa thyrsites from water samples collected at salmon aquaculture facilities in Finland and Canada, respectively (Korkea-aho et al 2022;Marshall et al 2022). In another study, researchers collected eDNA samples near both active and fallow Atlantic Salmon farms in British Columbia, and screened them using qPCR for 39 viruses, bacteria, and parasites that may affect fish health (Shea et al 2020).…”

“…The application of eDNA tools also show promise for the early detection of emergent pathogens or invasive species that could negatively impact fish health, with the potential to promote rapid response and effective mitigation and management strategies. For example, diverse eDNA tools have already been developed and applied to assess the presence of viral, bacterial, and parasitic agents associated with salmon aquaculture and fish stocking (Rusch et al 2018;Shea et al 2020;Bettazzi et al 2021;Hansen et al 2022;Korkea-Aho et al 2022;Marshall et al 2022). Quantitative PCR and metabarcoding approaches to detect eDNA of nonnative fish species that compete with, and predate upon salmon within their native range have also been developed and applied in the eastern Canada, the northwestern USA, and Hokkaido, Japan (Dunker et al 2016;Franklin et al 2018;Imamura et al 2020;O'Sullivan et al 2020;Rubenson and Olden 2020).…”

Fisheries Volume 49 Number 4 April 2024

“…For example, qPCR assays were used to detect DNA from Gyrodactylus salaris , a monogenean parasite of Atlantic Salmon and other salmonids, in southern Norway and northwestern Russia, areas where this trematode was inferred to have recently been introduced (Rusch et al 2018 ;Hansen et al 2022 ). Other investigations used qPCR to detect eDNA of the oomycete Saprolegnia parasitica or the myxozoan Kudoa thyrsites from water samples collected at salmon aquaculture facilities in Finland and Canada, respectively (Korkea-aho et al 2022 ;Marshall et al 2022 ). In another study, researchers collected eDNA samples near both active and fallow Atlantic Salmon farms in British Columbia, and screened them using qPCR for 39 viruses, bacteria, and parasites that may affect fi sh health (Shea et al 2020 ).…”

“…The application of eDNA tools also show promise for the early detection of emergent pathogens or invasive species that could negatively impact fi sh health, with the potential to promote rapid response and effective mitigation and management strategies. For example, diverse eDNA tools have already been developed and applied to assess the presence of viral, bacterial, and parasitic agents associated with salmon aquaculture and fi sh stocking (Rusch et al 2018 ;Shea et al 2020 ;Bettazzi et al 2021 ;Hansen et al 2022 ;Korkea-Aho et al 2022 ;Marshall et al 2022 ). Quantitative PCR and metabarcoding approaches to detect eDNA of nonnative fi sh species that compete with, and predate upon salmon within their native range have also been developed and applied in the eastern Canada, the northwestern USA, and Hokkaido, Japan (Dunker et al 2016 ;Franklin et al 2018 ;Imamura et al 2020 ;O ' Sullivan et al 2020 ;Rubenson and Olden 2020 ).…”