# Characterizing mixed strongyle infections in foals and broodmares using cytochrome c oxidase subunit I deep amplicon sequencing

## TL;DR

This study used sequencing to analyze strongyle infections in foals and mares, finding differences in parasite species and diversity between the two groups.

## Contribution

The study provides new insights into the species composition and diversity of mixed strongyle infections in foals and broodmares using deep sequencing.

## Key findings

- Deep sequencing identified 16 small strongyle species but no large strongyles in equine samples.
- Mares showed higher richness and diversity of strongyle species compared to foals.
- Certain strongyle species were more prevalent in mares or foals, suggesting age-related infection patterns.

## Abstract

Mixed strongyle infections represent the most prevalent equine parasitosis and can result in life-threatening disease, especially in young horses. Species involvement and pathogenesis of this parasitosis are poorly understood, and data on foals and broodmares are notably lacking.

In a longitudinal study undertaken in 2022 in Germany, individual faecal samples (n = 497) and metadata were collected for naturally infected foals and broodmares (n = 48) kept under conventional husbandry conditions. Nematode infections were detected coproscopically via the Mini-FLOTAC method. In a subset of strongyle egg-positive samples (n = 46), species were identified using cytochrome c oxidase subunit I deep amplicon sequencing. Species prevalence, richness, and alpha and beta diversity were compared between foals and mares.

Overall, 22.2% of the foal samples and 10.2% of the mare samples were strongyle egg positive (eggs per gram > 5). Parascaris spp. were only detected in foals (15.1%). Strongyloides westeri was detected in one foal sample. Strongyle egg detection increased in likelihood with each additional sample timepoint (OR = 1.42, P < 0.001) and with ascarid egg detection (OR = 6.49, P < 0.001), while last anthelmintic treatment with pyrantel decreased the odds of detecting eggs (OR = 0.12, P = 0.002). Deep amplicon sequencing detected 16 species of small strongyles but no large strongyle species. Cylicostephanus goldi, Cylicostephanus minutus operational taxonomic unit II and Cylicocyclus ashworthi were significantly more prevalent in mares (P < 0.05), while Cylicostephanus calicatus operational taxonomic unit II was more prevalent in foals (P < 0.01). Mares showed a significantly higher amplicon sequence-variant-based richness (Chao 1 index, P < 0.001) and diversity (inverse Simpson index, P < 0.01) than foals. Group (foals vs. mares) explained some of the variance in beta diversity, according to permutational multivariate ANOVA. Co-infection with Parascaris spp. did not affect strongyle community composition in the foals. Bray–Curtis and Jaccard distance (dissimilarity) plots showed separate clusters for mares and foals, with some overlap and a moderate model fit.

Cytochrome oxidase-based characterization of mixed strongyle infections revealed strongyle community differences between broodmares and foals. Possible age associations were identified for four species of small strongyles, including two cryptic species. Low overall strongyle prevalence and egg-shedding intensity, non-random sampling and differences in anthelmintic treatment schemes limited the statistical power of this study.

The online version contains supplementary material available at 10.1186/s13071-025-07192-1.