Quantitative genetics of gastrointestinal strongyle burden and associated body condition in feral horses

Strongyle faecal egg counts in Swiss horses: A retrospective analysis after the introduction of a selective treatment strategy

The standard parasite management of horses based on regular anthelmintic treatments, now practiced for decades has resulted in a worrying expansion of resistant helminth populations, which may considerably impair control on the farm level. The aim of the present study was to obtain a retrospective (year 2010 - 2016) nationwide analysis of faecal egg count (FEC) data from the Swiss adult horse population, related to horse age and geographic region. Thirteen labs provided a total of 16,387 FEC data of horses aged four to 39 years (average: 13.6 years). The annual number of performed FEC tests increased from 38 to 4,939 within the observation period. Independent of the annual sample size the yearly patterns of the FEC were very similar. Seventy-eight percent (n = 12,840) of the samples were negative and 90 % (n = 14,720) showed a FEC below 200 strongyle eggs per gram (EPG) of faeces. The annual mean strongyle FEC ranged between 60 and 88 EPG with a total mean of 75 EPG. Horses aged 4-7 years showed a significantly (p < 0.00001) higher mean FEC compared with the other age groups, differences were not significant among the older horses. Based on ZIP codes, samples were allocated by 70.0 %, 6.0 % and 0.2 % to the German-, French- and Italian-speaking regions of Switzerland, respectively. With 222 EPG the mean FEC in the French part of Switzerland was significantly higher (p < 0.05) than in the German-speaking region (60 EPG). Eggs of Parascaris spp., anoplocephalids and Strongyloides westeri were found in 0.36 %, 0.32 % and 0.01 % of the samples, respectively. Based on 3,813 questionnaire feedbacks from owners in 2017 covering a total of 12,689 horses, sixty-eight percent (n = 8,476) were dewormed without diagnosis, two percent (n = 240) were not dewormed at all, whereas for 30 % (n = 3,721) the selective anthelmintic treatment (SAT) concept was applied. The SAT implementation rate differed significantly (p < 0.0005) between regions, with 33 %, 20 % and 25 % for the German-, French- and Italian-speaking areas, respectively. The rate of horses spending 16-24 h on pasture per day was significantly higher in the French-speaking region compared to the German-speaking part of Switzerland (p < 0.0001). In addition, pasture hygiene was practiced at a significantly lower rate in the French-speaking part compared to the German- and Italian-speaking regions (both p < 0.0001). Overall, the shift towards the SAT-concept represents a very promising development with respect to mitigating the further spread of anthelmintic resistance.

The cost of host genetic resistance on body condition: Evidence from divergently selected sheep

Trade-offs between host resistance to parasites and host growth or reproduction can occur due to allocation of limited available resources between competing demands. To predict potential trade-offs arising from genetic selection for host resistance, a better understanding of the associated nutritional costs is required. Here, we studied resistance costs by using sheep from lines divergently selected on their resistance to a common blood-feeding gastro-intestinal parasite (Haemonchus contortus). First, we assessed the effects of selection for high or low host resistance on condition traits (body weight, back fat, and muscle thickness) and infection traits (parasite fecal egg excretion and loss in blood haematocrit) at various life stages, in particular during the periparturient period when resource allocation to immunity may limit host resistance. Second, we analysed the condition-infection relationship to detect a possible trade-off, in particular during the periparturient period. We experimentally infected young females in four stages over their first 2 years of life, including twice around parturition (at 1 year and at 2 years of age). Linear mixed-model analyses revealed a large and consistent between-line difference in infection traits during growth and outside of the periparturient period, whereas this difference was strongly attenuated during the periparturient period. Despite their different responses to infection, lines had similar body condition traits. Using covariance decomposition, we then found that the phenotypic relationship between infection and condition was dominated by direct infection costs arising from parasite development within the host. Accounting for these within-individual effects, a cost of resistance on body weight was detected among ewes during their first reproduction. Although this cost and the reproductive constraint on resistance are unlikely to represent a major concern for animal breeding in nutrient-rich environments, this study provides important new insights regarding the nutritional costs of parasite resistance at different lifestages and how these may affect response to selection.

The energetic costs of sub-lethal helminth parasites in mammals: a meta-analysis

Parasites, by definition, have a negative effect on their host. However, in wild mammal health and conservation research, sub-lethal infections are commonly assumed to have negligible health effects unless parasites are present in overwhelming numbers. Here, we propose a definition for host health in mammals that includes sub-lethal effects of parasites on the host's capacity to adapt to the environment and maintain homeostasis. We synthesized the growing number of studies on helminth parasites in mammals to assess evidence for the relative magnitude of sub-lethal effects of infection across mammal taxa based on this expanded definition. Specifically, we develop and apply a framework for organizing disparate metrics of parasite effects on host health and body condition according to their impact on an animal's energetic condition, defined as the energetic burden of pathogens on host physiological and behavioural functions that relate directly to fitness. Applying this framework within a global meta-analysis of helminth parasites in wild, laboratory and domestic mammal hosts produced 142 peer-reviewed studies documenting 599 infection-condition effects. Analysing these data within a multiple working hypotheses framework allowed us to evaluate the relative weighted contribution of methodological (study design, sampling protocol, parasite quantification methods) and biological (phylogenetic relationships and host/parasite life history) moderators to variation in the magnitude of health effects. We found consistently strong negative effects of infection on host energetic condition across taxonomic groups, with unusually low heterogeneity in effect sizes when compared with other ecological meta-analyses. Observed effect size was significantly lower within cross-sectional studies (i.e. observational studies that investigated a sub-set of a population at a single point in time), the most prevalent methodology. Furthermore, opportunistic sampling led to a weaker negative effect compared to proactive sampling. In the model of host taxonomic group, the effect of infection on energetic condition in carnivores was not significant. However, when sampling method was included, it explained substantial inter-study variance; proactive sampling showing a strongly significant negative effect while opportunistic sampling detected only a weak, non-significant effect. This may partly underlie previous assumptions that sub-lethal parasites do not have significant effects on host health. We recommend future studies adopt energetic condition as the framework for assessing parasite effects on wildlife health and provide guidelines for the selection of research protocols, health proxies, and relating infection to fitness.

Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs

The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of single nucleotide polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics’ Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10 ng of host DNA (ATG’s recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 88.8% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.

Genetic × environment variation in sheep lines bred for divergent resistance to strongyle infection

Drug-resistant parasites threaten livestock production. Breeding more resistant hosts could be a sustainable control strategy. Environmental variation linked to animal management practices or to parasite species turnover across farms may however alter the expression of genetic potential. We created sheep lines with high or low resistance to Haemonchus contortus and achieved significant divergence on both phenotypic and genetic scales. We exposed both lines to chronic stress or to the infection by another parasite Trichostrongylus colubriformis, to test for genotype-by-environment and genotype-by-parasite species interactions respectively. Between-line divergence remained significant following chronic stress exposure although between-family variation was found. Significant genotype-by-parasite interaction was found although H. contortus-resistant lambs remained more resistant against T. colubriformis. Growth curves were not altered by the selection process although resistant lambs were lighter after the second round of divergence, before any infection took place. Breeding for resistance is a sustainable strategy but allowance needs to be made for environmental perturbations and worm species.

Integrative biology defines novel biomarkers of resistance to strongylid infection in horses

The widespread failure of anthelmintic drugs against nematodes of veterinary interest requires novel control strategies. Selective treatment of the most susceptible individuals could reduce drug selection pressure but requires appropriate biomarkers of the intrinsic susceptibility potential. To date, this has been missing in livestock species. Here, we selected Welsh ponies with divergent intrinsic susceptibility (measured by their egg excretion levels) to cyathostomin infection and found that their divergence was sustained across a 10-year time window. Using this unique set of individuals, we monitored variations in their blood cell populations, plasma metabolites and faecal microbiota over a grazing season to isolate core differences between their respective responses under worm-free or natural infection conditions. Our analyses identified the concomitant rise in plasma phenylalanine level and faecal Prevotella abundance and the reduction in circulating monocyte counts as biomarkers of the need for drug treatment (egg excretion above 200 eggs/g). This biological signal was replicated in other independent populations. We also unravelled an immunometabolic network encompassing plasma beta-hydroxybutyrate level, short-chain fatty acid producing bacteria and circulating neutrophils that forms the discriminant baseline between susceptible and resistant individuals. Altogether our observations open new perspectives on the susceptibility of equids to strongylid infection and leave scope for both new biomarkers of infection and nutritional intervention.

Long-term storage of feces at -80 °C versus -20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome

The development of next-generation sequencing technologies has spurred a surge of research on bacterial microbiome diversity and function. But despite the rapid growth of the field, many uncertainties remain regarding the impact of differing methodologies on downstream results. Sample storage temperature is conventionally thought to be among the most important factors for ensuring reproducibility across marker gene studies, but to date much of the research on this topic has focused on short-term storage in the context of clinical applications. Consequently, it has remained unclear if storage at −80 °C, widely viewed as the gold standard for long-term archival of feces, is truly required for maintaining sample integrity in amplicon-based studies. A better understanding of the impacts of long-term storage conditions is important given the substantial cost and limited availability of ultra-low temperature freezers. To this end, we compared bacterial microbiome profiles inferred from 16S V3–V4 amplicon sequencing for paired fecal samples obtained from a feral horse population from Sable Island, Nova Scotia, Canada, stored at either −80 °C or −20 °C for 4 years. We found that storage temperature did not significantly affect alpha diversity measures, including amplicon sequence variant (ASV) richness and evenness, and abundance of rare sequence variants, nor presence/absence, relative abundances and phylogenetic diversity weighted measures of beta diversity. These results indicate that storage of equine feces at −20 °C for periods ranging from a few months to a few years is equivalent to storage at −80 °C for amplicon-based microbiome studies, adding to accumulating evidence indicating that standard domestic freezers are both economical and effective for microbiome research.

Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters

Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.

A repeatable and quantitative DNA metabarcoding assay to characterize mixed strongyle infections in horses

Horses are ubiquitously infected by a diversity of gastro-intestinal parasitic helminths. Of particular importance are nematodes of the family Strongylidae, which can significantly impact horse health and performance. However, knowledge about equine strongyles remains limited due to our inability to identify most species non-invasively using traditional morphological techniques. We developed a new internal transcribed spacer 2 (ITS2) DNA metabarcoding 'nemabiome' assay to characterise mixed strongyle infections in horses and assessed its performance by applying it to pools of infective larvae from fecal samples from an experimental herd in Kentucky, USA and two feral horse populations from Sable Island and Alberta, Canada. In addition to reporting the detection of 33 different species with high confidence, we illustrate the assay's repeatability by comparing results generated from aliquots from the same fecal samples and from individual horses sampled repeatedly over multiple days or months. We also validate the quantitative potential of the assay by demonstrating that the proportion of amplicon reads assigned to different species scales linearly with the number of larvae present. This new tool significantly improves equine strongyle diagnostics, presenting opportunities for research on species-specific anthelmintic resistance and the causes and consequences of variation in mixed infections.

Not playing by the rules: Unusual patterns in the epidemiology of parasites in a natural population of feral horses (Equus caballus) on Sable Island, Canada

Sable Island, Nova Scotia, Canada hosts one of few natural populations of feral horses (Equus caballus) never exposed to anthelmintics. Coproculture revealed cyathostomes, Strongylus equinus, S. edentatus, and S. vulgaris, with S. equinus (unusually) dominating in adult horses and cyathostomes dominating in young horses (<3 years of age). We examined 35 horses found dead in the springs of 2017 and 2018, as well as fecal samples from live horses in spring (n = 45) and summer 2018 (n = 236) using McMaster fecal flotation and Baermann larval sedimentation on fresh samples, and modified Wisconsin flotation and sucrose gradient immunofluorescent assay for Giardia and Cryptosporidium on frozen samples. Mean strongyle fecal egg counts were 666 eggs per gram (EPG) in dead horses, 689 EPG in live horses in spring, and 1105 EPG in summer; domestic horses are usually treated at counts exceeding 200 EPG. Adult horses (unusually) had patent infections with the lungworm Dictyocaulus arnfieldi and ascarids (Parascaris spp.), and in spring, dead horses had 5 times higher odds of having patent ascarid infections than live horses, likely due to malnutrition and corresponding immunodeficiency. Fecal prevalence and intensity of D. arnfieldi and Parascaris spp. were significantly higher in young horses, and in spring versus summer. A higher proportion of fecal samples were positive for strongyle and ascarid eggs using a centrifugal flotation technique on previously frozen feces, as compared to a passive flotation method on fresh feces. Eggs of the tapeworm Paranoplocephala mamillana were present in fecal samples from 28% of live, and 42% of dead, horses in spring. This research represents several new geographic records (S. edentatus, D. arnfieldi, and Eimeria leuckarti), provides insight into unusual patterns of parasite epidemiology in a nutrition-limited environment, and has conservation and biosecurity implications for this unique equine population, as well as for parasite management in domestic horses.

Parasites in Horses Kept in A 2.5 Year-Round Grazing System in Nordic Conditions without Supplementary Feeding

Simple Summary

Grazing horses year-round may be a means to increase biodiversity. In this study, parasite occurrence was documented on a monthly basis in 1- to 3-year-old Gotlandsruss stallions grazed year-round for 2.5 years. Horses became infected by several parasites and, when needed (>200 strongyle eggs/gram feces), horses were dewormed with the anthelmintic drug pyrantel, which has low or no ecotoxic impact on soil fauna. This strategy failed to control small strongyle occurrence. Horses excreted larger amounts of small strongyle eggs during summer–autumn than during the rest of the year, and the number of excreted eggs increased year-on-year. High small strongyle egg excretion did not seem to affect the body condition of the horses. Some horses were also infested with chewing louse, but did not scratch more than unaffected horses. We found that to keep egg excretion below 200, pyrantel was not sufficient and a substance known to be toxic to dung fauna and freshwater invertebrates had to be used on some occasions.

Abstract

Horse grazing can be favorable from a biological diversity perspective. This study documented the occurrence of endo- and ectoparasites and sought to reduce parasite egg excretion with the anthelmintic drug pyrantel in 12 Gotlandsruss stallions maintained in a year-round grazing system for 2.5 years. Feces samples were collected monthly and all horses were treated with pyrantel, the anthelmintic drug of choice in biological diversity preservation, at study population mean cyathostomin eggs per gram (EPG) of >200. The relationship between cyathostomin EPG and body condition was studied, as was horse behavioral response to Bovicola equi (chewing louse) infestation. Eggs of cyathostomins (small strongyles), Parascaris spp. (roundworm), Oxyuris equi (pinworm), Anoplocephala perfoliata (tapeworm), and Gasterophilus spp. (botfly) were detected at least once during the trial. Excretion of cyathostomin eggs was highest during summer–autumn and increased year-on-year. No relationship was found between cyathostomin EPG and body condition. Infestation with B. equi did not affect the number of scratching sessions compared with unaffected horses. Therefore, in this year-round grazing system, pyrantel treatment had to be complemented with moxidectin to reduce excretion of cyathostomin eggs, thus compromising biological diversity.