title: Determining population structure in Kentucky Parascaris univalens specimens
Creators: name: Constance Finnerty
Publisher: name: University of Kentucky Libraries
Year: 2024
Subjects: classificationCode: 4.3
subject: FOS: Veterinary sciences

description: Parascaris univalens is a highly pathogenic nematode that affects the gastrointestinal system of young horses. When unaddressed, this parasite causes severe intestinal impactions and even death. Parascaris univalens is also found to have an emergence of anthelmintic resistances, causing a concern for horse owners. Despite its clinical significance, very little work has been done on Parascaris univalens to identify its population structure. This study aimed to determine the population structure of Parascaris univalens through Illumina next generation sequencing (NGS) on three hierarchical categorizations: within a horse, within an isolated herd, and within horses in the state of Kentucky. A total of 60 (35 males, 22 females) Parascaris spp. specimens were collected from 11 out of 12 foals necropsied from the Gene Lyons Gluck equine parasitology herd, which has not had anthelmintic intervention since the 1970’s, and 65 parasites (20 males, 26 females, 19 immatures) were collected from 23 of the 32 foals necropsied at the Veterinary Diagnostic Laboratory. To determine population structure within the host, the small intestine of the Gluck foals was separated into 4 equal sized sections 1-4, with section 1 representing the section closest to the stomach, and section 4 representing the section closest to the large intestine. For section 1, 23 parasites were collected, section 2 had the largest amount of collected parasites at 34, 24 collected from section 3, and section 4 was the smallest at 8 Parascaris spp. specimens collected. In addition to separation by sex and stage, a new categorical variable “infection intensity” was created to try and determine if there was an effect of crowded vs. noncrowded living conditions of the parasite on population structure, with 6 horses falling under the ‘Low’ classification (< 25 parasites), 2 falling under ‘Medium’ (25-75 parasites), 2 falling under ‘High’ (75-125 parasites) and 1 foal falling under ‘Very High’ (> 125 parasites) in the Gluck samples. These 125 parasites underwent DNA extraction using the Qiagen DNeasy Blood and Tissue extraction kit, with Gluck parasites yielding higher quantities of DNA. Sequencing was done using an Illumina 2x150 bp short-read platform at 10x depth, and VCF files for statistical analysis generated by utilizing a GATK bioinformatic pipeline. Principal component analyses (PCA) by the three hierarchical levels (intestine, herd, populations) and the additional infection intensity variable were created using the ‘plink’ software, with evidence of population structure within the Gluck versus Kentucky population, and not the intestinal, herd or infection variables. This finding was supported by low fixation indices and negative inbreeding coefficients for these populations, with only the Kentucky versus Gluck level displaying a low level of differentiation (FST = 0.034), and an AMOVA across all for levels of categorization (intestine, herd, populations, infection) only indicated population as a significant factor of variation, with 4.47% of variation being accounted for. Lastly, a STRUCTURE plot was created for 1-10 groups for k repeated by 10 iterations for the population hierarchical level. The Evanno method suggested the best value of k to fit the data was 1, indicating that Gluck and Kentucky parasites are within the same population.

We concluded that while there is no evidence of population differentiation occurring at the intestinal, within herd, and within infection intensity groups, there is evidence of low levels of differentiation between Gluck foals and Kentucky foals. While this differentiation does not give rise to two separate populations, isolation by distance (IBD) due to the intentional isolation of the Gluck herd. These results help to identify the current population structure of Parascaris univalens in Kentucky, and act as a stepping-stone for additional studies to be developed to investigate population structure of this parasite using NGS on a global scale, as well as studies that investigate the potential causes of structure, or lack thereof, as well as identifying potential loci of interest.
description: ©2024 Constance Finnerty