Improved understanding of species diversity through molecular ecology, provides better management strategies for UK agriculture and helminth diseases

Fasciola hepatica, usually termed "the temperate liver fluke", is a worldwide problem for agriculture. Infections known as fasciolosis, primarily damage ruminant production, and have been reported across many regions of Europe including the UK and Northern Ireland (NI). Fasciolosis as a food-borne disease, results from the consumption of the infective larvae, which greatly reduces global livestock capacity and efficiency. It is estimated that fascioliasis causes annual economic losses in the UK of £110 million, while across Europe the impact is considerably larger, at £524 million.
Despite its importance, there is a lack of basic ecological knowledge associated with liver fluke. This includes the diversity and distribution of their snail intermediate hosts integral to the parasite lifecycle. This lack of knowledge limits efforts to successfully assess and combat threats in order to improve animal welfare and productivity. It is unclear what factors drive increased helminth presence and prevalence, but candidates include climate change, decreased interspecies competition among competitors of the intermediate snail host, changes in anthelmintic usage leading to resistance, and high levels of animal movements.
Understanding the biodiversity of the helminth and their snail host(s) is key for understanding the ecology of disease transmission. This project will investigate the role of species biodiversity for disease transmission by building an interdisciplinary team. This team will increase research capability and capacity focused on helminth parasites important to UK agriculture. Using a molecular ecology approach, this project will bring together expertise in parasitology, molecular biology and computational biology, ecology, and agricultural management; and will receive input from academic, government and industry partners. The School of Biological Sciences at QUB, has a long history of collaboration with farmers. We have already isolated DNA from the environment (soil), which is known as or eDNA, from farms with a history of helminth disease. While specific assays are being used to look for the presence of suspected known helminth and snail species, we will used new technologies to capture the complete picture of biodiversity at these sites.
In this project we will undertake these activities- Use next generation sequencing from eDNA obtained from helminth infected farms in Northern Ireland, to characterise parasite and snail host biodiversity. Determine if helminth and snail biodiversity is correlated with anthelmintic (anti-parasite drug) usage. Lastly, form a research network which uses new sequencing strategies to assess UK agriculture sites for "biodiversity health" as risk factors associated with helminth transmission.
The development of these techniques will lead to actionable data that can be applied to the future management of agriculture. Furthermore we will demonstrate that environmental samples, when analysed by molecular methods to determine species biodiversity can answer ecological questions. In considering parasitological, ecological and biodiversity perspectives, invasive species detection, food/water hygiene and biosecurity (anthelmintics in water or bacterial/viral outbreaks) can be managed.

Fasciola hepatica, is a worldwide problem for agriculture, primarily damaging ruminant production. Understanding the biodiversity of the helminth and their snail host(s) is key for understanding the ecology of disease transmission. This project will investigate this by bringing together expertise in parasitology, molecular biology and computational biology, ecology, and agricultural management; and will receive input from academic, government and industry partners.
Biodiversity through metagenomics using older sequencing protocols produces shorter amplicon sequences, which yield limited phylogenetic resolution. Longer amplicons produce more robust taxonomic assignment and higher phylogenetic utility, which is possible with the Oxford Nanopore platform. eDNA from soil has been already collected, extracted and characterised by qPCR and ddPCR for the presence of well-studied helminth (F. hepatica and C. daubneyi) species and their major snail intermediate host (G. truncatula). eDNA corresponding to farms historically positive or negative will be assessed by nanopore sequencing. To allow both a broader and more focused approach published universal primer sets will be used to enrich eDNA for the following taxonomic ranks, Eukaryota, Metazoa, Gastropoda, Trematoda and Nematode/Platyhelminths.
The presence of anthelmintics in the environment may have unexpected consequences for biodiversity.
To explore this the key anthelmintics will be analysed in matching environmental sources used for biodiversity assessment. By mapping snail and parasite biodiversity to anthelmintic usage we will better gauge the impact these molecules have on biodiversity.
By incorporating sequencing data for species biodiversity and cryptic species identification, with analytical environmental anthelmintic detection, we will be able to better model the flow of materials (chemicals) and pathogens within the environment.