Molecular epidemiology of Neoparamoeba perurans, causative agent of amoebic gill disease (AGD) in farmed salmonids

The amoeba Neoparamoeba perurans is the causative agent of Amoebic Gill Disease (AGD), one of the most significant health challenges faced by the global marine salmonid aquaculture industry. Treatments for AGD enable salmon producers to improve salmon welfare and reduce mortality, but the disease often returns in the same production cycle to the same fish. Although we are starting to understand more about N. perurans and its interaction with the host, there remains little known about the phylogeographic history and population genetics in relation to its distribution, abundance and evolutionary process that influence its epidemiology. As an important global pathogen, it is important to start understanding its transmission routes and molecular variation. Different variants of the parasite have been suggested to have emerged globally but there have been few studies that have attempted to identify the total number of variants, found within a particular locality nor have there been any attempts to assess the potential movement of such variants within and between farms. This PhD will use elements of both classic epidemiology and molecular epidemiology to assess movement and connectivity between fish farms and provide essential insights into transmission. The project will utilise both archived and contemporary samples to provide insights into the molecular population genetic structure of N. perurans in Scotland. Similarly, phylodynamic analyses will be employed to assess movement between infected sites. To achieve this, we will employ already established nuclear and mitochondrial molecular markers and will also attempt to develop new markers to assess fine scale evolutionary processes which could affect the transmission and epidemiology of the parasite. Within Scotland's salmon aquaculture, field samples will form a basis for answering epidemiological questions, such as what the prevalence of AGD is, and can we quantify and explain infection pressure. Open-source data such as environmental variables obtained from satellite data will be used to complement existing data for meta-analysis. An overall understanding of the molecular epidemiology of N. perurans will enable us to provide better recommendations for health management of AGD. Successful candidates will have the opportunity to work within internationally recognised teams at Epidemiological Research Unit of Scotland's Rural College (SRUC) and Institute of Aquaculture, University of Stirling and to receive training in cutting-edge epidemiological analysis, molecular biology, and parasitological techniques.