Amoebic gill disease (AGD) is a severe infection of farmed Atlantic salmon (Salmo salar L. ) caused by the marine amphizoic amoeba, Neoparamoeba perurans. Since its emergence in the mid-1980 s, the disease has continued to spread and has become a global concern. Currently, we still know little about how N. perurans spread between farms, production cycles, regions, and counties. Such an understanding could aid the aquaculture industry to inform fallowing and control measures for salmonids. The genomic analyse s required to achieve N. perurans molecular epidemiology, however, are frustrated by characteristically high levels of intercellular bacterial contamination. A handful of N. perurans genes have been successfully sequenced (18S rRNA, cytochrome oxidase I, ITS, etc) but with insufficient genetic resolution to be beneficial to either farmer or regulator. A draft genome was developed in the Llewellyn lab enabling the development of hundreds of new sequencing markers. A multiplex PCR was developed using 202 primer pairs within a single PCR reaction to amplify loci across the nuclear, and mitochondrial of N. perurans and kinetoplast genome. These markers were sequenced directly from gill swab samples at low cost to provide epidemiologically relevant information to genotype N. perurans from multiple sites across Norway (n = 9), Scotland (n = 4), and Ireland (n = 1) from 2019, 2021 – 2023 for molecular epidemiological analysis.
To date , there is no effective means of attributing AGD infections to a source or effective prevention of the parasite transmission between farms, production cycles, and the environment. Our work aims to take steps towards achieving this by demonstrating that high-resolution genetic information may be readily derived directly from gill swab samples to inform AGD treatment and control. Further research, aims to relay this information back to individual farm managers of affected sites by developing and implementing a web-based visualisation tool to track genotypes, spread over time to enable targeted and timely approaches to AGD outbreaks.