The BUG consortium Building Upon the Genome: using H. contortus genomic resources to develop novel interventions to control endemic GI parasites

Most food-producing animals are infected with a variety of different roundworms, or nematodes, many of which live in the digestive tract. These parasites cause a range of disease in their hosts, from diarrhoea and anaemia, to death, in severe cases. They are a major welfare issue and cause significant economic losses to farmers, in terms of reduced production and treatment. It is estimated that these worms cost the UK sheep industry a conservative £84 million per annum. At the present time these parasites are controlled using drugs known as anthelmintics, but many of these chemicals no longer work effectively because the parasites have developed resistance to them, analogous to antibiotic resistance in bacteria. How anthelmintic resistance arises and spreads throughout the worms on a farm is not known. The problem has become so serious in the UK that some sheep-farming enterprises have had to close because the worms can no longer be controlled. Our project will investigate ways of ensuring that the existing drugs are managed to minimise the occurrence and spread of resistance and will also study novel approaches to vaccine development. The current methods for detecting resistant parasites are labour intensive and insensitive, making early detection impossible and analysis of the extent of the problem difficult. This makes it hard to evaluate strategies aimed at reducing the spread of resistance. We need to develop more sensitive methods to detect resistant parasites and so must understand the genetic changes in the parasites that lead to resistance. We have recently sequenced the genome of one of these parasites called Haemonchus contortus (the Barber's pole worm) and found it to be large and complex, containing a similar number of genes to the human genome. Studying this genome will identify novel ways of controlling nematode infections and our research is aimed at using new technologies to ensure that farmers can continue to produce livestock effectively. We plan to use information from the genome to identify markers of drug resistance in Haemonchus and in a closely related worm called Teladorsagia circumcincta, which is the most prevalent parasite found in the UK sheep population. By identifying the genetic changes in worms exposed to anthelmintics, we aim to understand how resistance arises and to develop markers to identify resistant worms on sheep farms. This information will be used to help model how resistance spreads and to investigate how different treatment schedules affect the development of resistance, taking into account climate change scenarios. In the longer term, we would like to develop vaccines against these worms. Although many attempts have been made to do this, most have not been successful, as we have no way of assessing whether the antigens tested to date are the most effective at stimulating a host immune response. However, our project will provide the basis for identifying genes that are under selection by the sheep immune system and therefore likely to be antigenic. We will combine results from this study with knowledge of where and when specific antigens are expressed in the worm to optimise the selection of potential vaccine candidates. Finally, the results from this project will be used to design sustainable control strategies for sheep parasites in the face of anthelmintic resistance and climate change. We have robust plans to engage with the farming community through workshops and publications to ensure that the implications of our work are translated into good farming practice. While this project focuses on parasites of sheep, we anticipate that much of what we learn about anthelmintic resistance will be directly applicable to parasites of cows, horses and pigs where anthelmintic resistance is an emerging problem. Moreover, as the same drugs are increasingly used to control related worms in humans, our work will also impact on human health.

The aim of this project is to provide sustainable control of nematode parasites of sheep based on an improved understanding of AR and the identification of novel vaccine candidates. Nematodes from two sources will be sequenced: H. contortus from a genetic backcross between IVM-sensitive and resistant lines and T. circumcincta and H. contortus from farms with current clinical AR problems. We will use a method of genotyping by sequencing (ddRAD-Seq) that can be applied to large numbers of individuals, and whole genome sequencing of pools of larvae. This population genetics approach will be underpinned by significant improvements in the genomes of both nematodes based upon the construction of a genetic map for H. contortus and high coverage, individual worm sequencing for T. circumcincta. Markers of AR will be validated in a UK-wide bio-bank containing both parasite species, collected from farms with known histories of anthelmintic usage over several years. Analysis of AR-conferring regions of the genome will reveal the underlying mechanisms, which will be tested in a C. elegans transgenic model system. Once identified, AR markers will be used to study the origin and spread of resistance alleles and to model and assess the effects of different anthelmintic regimes on the development of AR. Additional modelling studies will address the impact of climate change on worm survival and effective refugia and will seek to future-proof any new management strategies. Sequencing data will be employed in a population genomics approach to vaccine discovery with the aim of identifying novel candidate antigens for future development. The study will be underpinned by a cost-benefit analysis of new management strategies and a knowledge exchange module that will involve close liaison with the farming industry to identify the optimal means of implementing new strategies.

The beneficiaries of this project include the farming community and their advisors, the pharmaceutical industry and the general public. Our project will identify markers of AR and will improve our understanding of the mechanisms and spread of resistance throughout populations. Although much of the knowledge produced will be fundamental, it has the potential to have significant impact in the UK and internationally where the problems of AR are even more acute. The sLoLa will support innovation in science by applying new technologies and generating novel tools for parasitic nematode research. The project will provide excellent training opportunities for the post-docs in genetic, genomic and quantitative approaches to complex biological problems. We will ensure interactions amongst the post-docs by hosting training periods in each Institute. The group at WTSI contribute to several courses and workshops and so have significant experience of training in genomics and next-generation sequence data analysis. Skills acquired during the course of the project will be applicable to many other organisms and will equip the PDRAs for future careers in academia, the bio-tech or pharmaceutical industries.

We will generate data that are of considerable interest to the pharmaceutical industry, some of whose drugs are now largely ineffectual in various parts of the world. Our work will generate tools to detect and monitor resistance, which will be used to improve strategies to mitigate the development of AR. By shedding new light on the mechanisms of resistance, the results will influence the design and use of future anthelmintics and may identify opportunities to restore efficacy to current drugs. Although much effort has been invested in developing a vaccine for H. contortus, most attempts to protect sheep using these antigens in recombinant format have failed. We currently have no way of determining whether the antigens tested to date are the most effective, as they were not selected based on their association with protection in the field. A population genomics approach allows the identification of antigens under selection by the host immune system. It will also identify genes whose products are essential for survival, information that could be exploited in other ways, such as the design of novel inhibitors.

This project has the potential to impact upon farming practices in the UK and elsewhere. Previous advice such as 'dose and move', appears to result in an increased selection for resistance, but is still widely used. The SCOPS (Sustainable Control Of Parasites of Sheep) initiative provides farmers and vets with valuable up-to-date information and guidelines for parasite control but we still lack a basic understanding of the mechanisms of AR on which to base this advice. The development of effective parasite control strategies would improve animal health and welfare, the quality and safety of British lamb and the economic viability of the UK sheep industry. We will engage with farmers and vets through publications in the farming press, attendance at agricultural meetings, veterinary CPD courses, and workshops to determine how findings from this project can be used to establish the best means to improve farm profitability and animal welfare in both the short and the long term. Worm control in dairy herds was recently estimated to cost the UK economy £281 million per annum and the impact of AR would significantly raise that figure. Thus our work has the potential to contribute to the economy by increasing the efficiency of livestock production and safeguarding the industry against an inevitable future challenge. By helping produce high quality meat with excellent standards of animal welfare we hope to influence the public perception of British farming. We have opportunities to interact with the public at events such as the Royal Highland Show and with school children through engagement activities, such as science clubs.