Population genetics and genomics of ovine nematode parasites and their application to study the molecular basis of anthelmintic resistance

寄生虫（线虫）是英国和全世界放牧牲畜（绵羊、牛和山羊）最严重的健康问题之一，造成重大的经济损失和动物福利问题。最重要的寄生虫类型生活在动物宿主的胃和肠中。有些会导致严重的腹泻，而另一些则以血液为食，导致内出血和贫血。受影响严重的动物可能会死亡，或者不得不以福利为由被销毁，而受影响较轻微的动物的生长速度则不理想，这可能对农民造成严重的经济影响。事实上，寄生虫是羊身上最重要的经济疾病，据估计每年给羊产业造成8000万英镑的损失。它们对牛也同样重要。这些经济损失与感染的严重程度直接相关，因此，通过减少感染牲畜的寄生虫的数量，我们可以按比例降低该行业的成本，并改善动物福利。这些寄生虫的控制在很大程度上依赖于用药物（驱虫药，通常称为驱虫药）对牲畜进行常规治疗，目前只有三种主要类型可用。在世界许多地方，寄生虫现在对所有这些药物都具有耐药性。在英国，超过60%的羊蠕虫对至少一种药物具有耐药性，而且多重耐药性正在增加。因此，耐药蠕虫的问题对英国羊和牛产业的可持续性构成了重大威胁。耐药性的检测存在问题，目前的方法是老式的、劳动密集型的和非常不敏感的，使得诊断不可靠，不可能早期发现。因此，有必要开发用于常规诊断和监测的现代敏感测试，并作为研究耐药寄生虫出现和传播方式的工具。了解这些问题对于设计既有效又可持续的寄生虫控制制度至关重要，并且对于开发使用这些重要药物的方法而不会加剧耐药性的发展至关重要。该项目旨在开发和应用工具来阐明这些寄生虫的生物学和遗传学的一些关键方面，这将有助于我们了解耐药性是如何发展的以及如何对抗它。绵羊蠕虫将被研究，因为这些寄生虫的耐药性是最先进的，它们适合进行实验工作。该项目还将开发一个基因组序列数据库，不仅使我们能够研究耐药性问题，而且将帮助其他研究人员开发疫苗并确定这些寄生虫的新药物靶点。研究团队将是多学科的，包括具有遗传学、分子生物学、基因组学、流行病学、统计学、寄生虫学和临床兽医学专业知识的兽医和科学家。该项目的第一阶段将是建立所需的工具，包括DNA序列和两种主要寄生虫的遗传标记。在这项工作的同时，将从英国各地的绵羊身上收集寄生虫样本，并进行基于分子的诊断测试，以确定存在的物种。然后，已经开发的遗传标记将被用来为寄生虫种群“指纹”，以调查它们的遗传多样性。将对已知具有耐药性的寄生虫基因进行测序，以调查寄生虫对这些药物产生耐药性的不同途径，并提供信息，为开发基于寄生虫DNA分型的敏感诊断测试铺平道路。最后，将研究一种以前未应用于寄生虫的遗传分析系统，该系统将扫描蠕虫的基因组，以识别含有以前未知的赋予抗性基因的区域。

Parasitic worms (nematodes) represent one of the most serious health problems of grazing livestock (sheep, cattle and goats) in the UK and throughout the world, causing significant economic loss and animal welfare problems. The most important types of parasitic worms live in the stomach and intestine of their animal host. Some cause diarrhoea, which can be severe, whilst others feed on blood and cause internal bleeding and anaemia. Severely affected animals may die, or have to be destroyed on welfare grounds, whilst more mildly affected animals have sub-optimal growth rates which can have serious economic implications for the farmer. Indeed, parasitic worms the most economically important disease of sheep and have been estimated to cost the sheep industry in the region of £80M per annum. They are similarly important in cattle. These economic losses are directly related to the severity of infection and so by reducing the number of parasites infecting livestock, we can proportionally reduce the costs to the industry as well as improving animal welfare. Control of these parasites is heavily dependent upon the routine treatment of livestock with drugs (anthelmintics, commonly called wormers) and there are only three major types available. In many parts of the world, parasitic worms are now resistant to all of these drugs. In the UK, over 60% of sheep worms are resistant to at least one drug class and multiple resistance is increasing. Consequently, the problem of drug resistant worms is a significant threat to the sustainability of the UK sheep and cattle industries. Detection of resistance is problematic and current methods are old fashioned, labour-intensive and very insensitive, making diagnosis unreliable and early detection impossible. Consequently, there is a need to develop modern sensitive tests for routine diagnosis and surveillance and as tools to study the way in which drug resistant parasites appear and spread. An understanding of these issues is critical for the design of parasite control regimes that are both effective and sustainable and to develop ways of using these important drugs that do not exacerbate the development of resistance This project aims to develop and apply tools to elucidate a number of key aspects of the biology and genetics of these parasites that will help us understand how drug resistance develops and how it may be combated. Sheep worms will be studied because drug resistance is the most advanced in these parasites and they are amenable to experimental work. The project will also develop a genome sequence database that will not only enable us to study the problem of resistance but will assist other researchers to develop vaccines and identify new drug targets in these parasites. The research team will be multidisciplinary and include vets and scientists with expertise in genetics, molecular biology, genomics, epidemiology, statistics, parasitology and clinical veterinary medicine. The first stage of the project will be to establish the tools needed, including DNA sequence and genetic markers from the two major parasite species of parasite to be studied. In parallel to this work, parasite samples will be collected from sheep throughout the UK and molecular-based diagnostic tests used to determine the species present. The genetic markers that have been developed will then be used to 'fingerprint' the parasite populations to investigate their genetic diversity. Parasite genes that are already known to confer resistance will be sequenced to investigate the different ways parasites are becoming resistant to these drugs and to provide information that will pave the way for the development sensitive diagnostic tests based on parasite DNA typing. Finally, a system of genetic analysis, not previously applied to parasitic worms, will be investigated that will scan the worm's genome to identify regions containing previously unknown resistance-conferring genes.