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

阿米巴Neoparamoeba perurans是阿米巴鳃病（AGD）的病原体，这是全球海洋鲑鱼水产养殖业面临的最重大的健康挑战之一。AGD的治疗使鲑鱼生产者能够改善鲑鱼的福利并降低死亡率，但这种疾病通常会在同一生产周期内返回到同一种鱼。虽然我们开始了解更多关于N。秘鲁人及其与宿主的相互作用，仍然很少有人知道的地理历史和人口遗传学的分布，丰度和进化过程，影响其流行病学。作为一种重要的全球性病原体，重要的是要开始了解其传播途径和分子变异。已经提出寄生虫的不同变体在全球范围内出现，但很少有研究试图确定在特定地区发现的变体总数，也没有任何尝试评估这些变体在农场内和农场之间的潜在移动。该博士将使用经典流行病学和分子流行病学的元素来评估养鱼场之间的运动和连通性，并提供对传播的重要见解。该项目将利用存档和当代样本，以提供深入了解N。秘鲁人在苏格兰同样，将采用动态分析来评估感染部位之间的移动。为了实现这一目标，我们将采用已经建立的核和线粒体分子标记，并将尝试开发新的标记，以评估精细尺度的进化过程，这可能会影响寄生虫的传播和流行病学。在苏格兰的鲑鱼养殖中，现场样本将成为回答流行病学问题的基础，例如AGD的流行程度，以及我们能否量化和解释感染压力。从卫星数据获得的环境变量等公开来源数据将用于补充现有数据，以进行元分析。全面了解N.秘鲁人将使我们能够为年龄、性别和多元性健康管理提供更好的建议。成功的候选人将有机会在苏格兰农村学院（SRUC）流行病学研究单位和斯特林大学水生生物研究所的国际认可的团队中工作，并接受尖端流行病学分析，分子生物学和寄生虫学技术的培训。

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.