Determining the Population Structure of Parascaris spp. in Kentucky Horses using Next Generation Sequencing

Determining the population structure of Parascaris spp. using next generation sequencing Parascaris spp. are pathogenic nematodes that affect the gastrointestinal system of young horses globally, causing clinical disease and death. Parascaris spp. is also found to be the only ascarid to have anthelmintic resistance to macrocyclic lactones, the only ascarid species to show drug resistance besides Ascaridia spp. in poultry. Population genetic studies are vital tools in providing a foundation for understanding genetic variation and how it associates with genotypic frequency. Despite its clinical significance, very little work has been done on Parascaris spp. to identify its population structure. Population genetic work has been done in trichostrongyle parasite species, such as Haemonchus contortus but since these species are only distantly related to Parascaris spp., their population structures are likely not representative of ascarids and therefore do not allow comparison for mechanisms of resistance, biological adaptation, evolution, pathogenicity, and gene flow. Population genetics studies have been done with ascarid parasites Ascaris lumbricoides and A. suum with a population structure being described between these two closely related species. One population genetic study has been using DNA fingerprinting to characterize the population structure of Parascaris spp. and found all global populations to homogenous, with no apparent geographical barriers to gene flow. This was unexpected given that specimens were collected from three different continents and that collections included two uniquely isolated equine populations. We hypothesize that the DNA fingerprinting technique did not provide sufficient information to fully capture the population genetic structure among the studied specimens. This study will use next generation sequencing (NGS), which has a higher sensitivity to genetic variants and expansive genomic coverage. The study aims to determine the population structure of Parascaris spp. in a hierarchical manner: 1) within a horse, 2) within an isolated herd, 3) within horses in the state of Kentucky and 4) within horses globally. Worms will be collected from the small intestine of foals 2-5 months old, and DNA will be extracted for NGS. Sequencing data will be analyzed for evidence of selection through allelic frequencies and fitness through selection coefficients, for signs of genetic drift by identifying allele frequency changes in the populations and determining if there is gene flow between samples by determining if the populations are in or out of Hardy-Weinberg equilibrium. Specimens will also be modeled to show the genetic distances between individuals, as well as genetic distances between populations. This study will provide new information on the population structure of Parascaris spp., creating a foundation for additional population genetic studies.