Improved 18S rDNA profiling of parasite communities in salmonid tissues using a host blocking primer.

Sensitive screening of eukaryotic communities in aquaculture for research and management is limited by the availability of technologies that can detect invading pathogens in an unbiased manner. Amplicon sequencing of 18S ribosomal DNA (rDNA) provides a potential pan-diagnostic test to overcome these biases; however, this technique is limited by a swamping effect of host DNA on low abundance parasite DNA. In this study, we have adapted a host 18S rDNA blocking assay to amplify eukaryotic DNA from salmonid tissue for amplicon sequencing. We demonstrate that effective salmonid 18S rDNA blocking enables sensitive detection of parasite genera in salmonid gill swabs. Furthermore, 18S rDNA amplicon sequencing with host blocking identified enriched pathogen communities in gill swabs from Atlantic salmon suffering from severe clinical gill infections compared to those exhibiting no clinical signs of gill infection. Application of host 18S rDNA blocking in salmonid samples led to improved detection of the amoebic parasite Neoparamoeba perurans, a parasite of significant threat to the Atlantic salmon aquaculture industry. These results reveal host 18S rDNA blocking as an effective strategy to improve the profiling and detection of parasitic communities in aquaculture species. This assay can be readily adapted to any animal species for improved eukaryotic profiling across agricultural and veterinary industries.

Dead reckoning of protist viability with propidium monoazide (PMA)-quantitative PCR; a case study using Neoparamoeba perurans.

The ability to distinguish between viable and non-viable protozoan parasites is central to improved human and animal health management. While conceptually simple, methods to differentiate cell viability in situ remain challenging. Amoebic gill disease, caused by Neoparamoeba perurans is a parasitic disease impacting Atlantic salmon aquaculture globally. Although commercial freshwater treatments alleviate AGD, viable amoebae remain on gills or in used treatment water. Existing PCR-based assays are able to quantify N. perurans abundance but cannot discriminate amoeba viability. We investigated the use of propidium monoazide (PMA) application, prior to real-time PCR, to distinguish between alive and dead cells. We demonstrate that 200 µM PMA can significantly reduce amplification from non-viable (isopropanol treated) cultured amoebae across at least three logs of cell concentrations. Using a serial dilution of viable and non-viable cells, we show that non-PMA PCR amplifies both viable and non-viable amoebae, while PMA exposure suppresses (but does not completely inhibit) amplification from non-viable amoebae. The effect of freshwater treatment on N. perurans viability was assessed using the PMA-PCR. Following PMA exposure, amplification from freshwater treated amoebae was reduced by approximately 94-97 %. Taken together this study demonstrates that PMA combined with traditional real-time PCR can estimate amoeba viability.