Serosurvey for selected pathogens in Iberian roe deer

Background  

The roe deer is the most abundant and widespread wild Eurasian cervid. Its populations are expanding and increasingly in contact with livestock. This may affect the distribution of infectious diseases shared with other wild and domestic ungulates.     

Influence of livestock,habitat type,and density of roe deer (<Emphasis Type="Italic">Capreolus capreolus</Emphasis>) on parasitic larvae abundance and infection seroprevalence in wild populations of roe deer from central Iberian Peninsula

Livestock farming is a common human activity that not only modifies natural habitat but also may lead to interactions with other wild animal species. We studied whether health status of roe deer (Capreolus capreolus) is influenced by density, livestock, and type of habitat. We analyzed 208 samples (120 fecal and 88 sera) from roe deer populations of central Iberian Peninsula to evaluate both presence and abundance of parasitic oocysts, eggs, and/or larvae, especially of gastrointestinal and bronchopulmonary parasites, as well as the prevalence of five infectious diseases (infectious bovine rhinotracheitis (IBR), pestivirosis (BVD/BD), paratuberculosis (PTB), bluetongue (BT), and brucellosis). Fecal samples were collected in transects in pine and oak forests and endoparasites were detected by means of coprological techniques. Serum samples were obtained from hunted individuals and the serological testing for the infectious pathogens was performed by ELISA and Rose Bengal tests. Livestock and habitat type were associated both with the presence and the number of bronchopulmonary nematode L1-larvae per gram of feces (lpg), which was higher in areas with livestock and in pine forests. However, roe deer density neither influenced parasite presence nor lpg values. Regarding infectious pathogens, only seropositive samples for PTB and pestivirus were obtained indicating a possible transmission between domestic and wild ungulates in the study area. The low prevalence found is consistent with other studies in the Iberian Peninsula suggesting that roe deer have little contact with the infectious agents studied. Our results highlight that both habitat type and livestock significantly mediate abundance of parasitic larvae in roe deer, being higher under competition scenarios and in habitats of lower quality, a valuable aspect to be considered in future management and conservation strategies.     

Patterns of wolfCanis lupus predation on wild and domestic ungulates in the Western Carpathian Mountains (S Poland)

We studied the predator-prey relationships among wolvesCanis lupus Linnaeus, 1758, wild ungulates, and livestock in the managed mountain forests of the Western Carpathians (S Poland). Though roe deerCapreolus capreolus dominated in the community of wild ungulates and livestock was abundant within the study area, the three wolf packs preyed mainly on red deerCervus elaphus (42% of food biomass), and next on the roe deer (33%). In both species of deer, wolves preferred killing females and juveniles more frequently than expected from their respective shares in the populations. Wild boarSus scrofa made up 4% of the food biomass, in accordance with its low share in the ungulates community. Despite the easy access of wolves to numerous unprotected sheep flocks pastured on meadows among woods, livestock constituted only 3% of the wolf food biomass. Wolves preyed mostly on sheep (88%), killing on average 34 per year. Most cases of livestock depredation occurred in August –September, on pastures located most often >50 m apart from buildings. Usually, lack of proper guarding was conducive to wolf attacks.     

Density of Wild Prey Modulates Lynx Kill Rates on Free-Ranging Domestic Sheep

Understanding the factors shaping the dynamics of carnivore–livestock conflicts is vital to facilitate large carnivore conservation in multi-use landscapes. We investigated how the density of their main wild prey, roe deer Capreolus capreolus, modulates individual Eurasian lynx Lynx lynx kill rates on free-ranging domestic sheep Ovis aries across a range of sheep and roe deer densities. Lynx kill rates on free-ranging domestic sheep were collected in south-eastern Norway from 1995 to 2011 along a gradient of different livestock and wild prey densities using VHF and GPS telemetry. We used zero-inflated negative binomial (ZINB) models including lynx sex, sheep density and an index of roe deer density as explanatory variables to model observed kill rates on sheep, and ranked the models based on their AICc values. The model including the effects of lynx sex and sheep density in the zero-inflation model and the effect of lynx sex and roe deer density in the negative binomial part received most support. Irrespective of sheep density and sex, we found the lowest sheep kill rates in areas with high densities of roe deer. As roe deer density decreased, males killed sheep at higher rates, and this pattern held for both high and low sheep densities. Similarly, females killed sheep at higher rates in areas with high densities of sheep and low densities of roe deer. However, when sheep densities were low females rarely killed sheep irrespective of roe deer density. Our quantification of depredation rates can be the first step towards establishing fairer compensation systems based on more accurate and area specific estimation of losses. This study demonstrates how we can use ecological theory to predict where losses of sheep will be greatest, and can be used to identify areas where mitigation measures are most likely to be needed.     

Survey of Pestivirus infection in wild and domestic ungulates from south-western Italian Alps

The transmission of pestiviruses between domestic and wild ruminants has not been documented in communal alpine pastures shared between wildlife and livestock. The aim of this study was to investigate the role of domestic and wild ungulates species from Varaita Valley (SW Italian Alps) in the epidemiology of Pestivirus infections. Sera from free-ranging alpine chamois (Rupicapra rupicapra) and roe deer (Capreolus capreolus) were collected from 1994 to 2009 and 2001 to 2009, respectively. Also, sera from cattle and sheep sampled in 2009 were studied. Sera were tested for the presence of antibodies against pestivirus with an ELISA assay. Sera from positive animals were subsequently tested with a comparative virus neutralisation test using the BVDV-NADL and BDV-137/4 strains. Sera were tested for the presence of pestiviral antigen and the presence of viral RNA with a commercial ELISA assay and RT-PCR. Antibodies against Pestivirus were detected in 132 out of 312 (42%) chamois, in 30 out of 175 (17%) cattle and 6 out of 24 (25%) sheep. No antibodies were found in roe deer. No Pestivirus antigen or RNA was detected in any of the samples. Results indicate circulation of pestiviruses among the studied chamois, cattle and sheep populations. However the role of wild ungulates in the dynamics of Pestivirus infection is still unknown and monitoring the presence of these viruses in wild ungulates would be of importance, especially in the chamois population, where pestiviruses seem to circulate extensively.     

Spatial variability in wolf diet and prey selection in Galicia (NW Spain)

We studied wolf (Canis lupus) diet for three different landscapes in the north-western Iberian Peninsula, differing in land uses and availability of food for wolves. We examined 2740 scats, collected over a period of 4 years, in order to describe wolf diet, its geographic variation, and trophic preferences. The most consumed species were wild pony, roe deer and cattle. We observed differences in wolf diet among the three study sites, related to the availability and accessibility of food resources in each habitat. For the two study sites in northern and central Galicia, wolves showed similar diet, with high occurrence of wild pony (37 vs. 34%) and cattle (20 vs. 23%), but differing in the consumption of wild ungulates (16 vs. 8%) and carrion (7 vs. 14%). Wolf diet in eastern Galicia’s mountain ranges was entirely different, due to the higher consumption of wild ungulates (70%). Wolves showed clear prey selection patterns. Between wild ponies and livestock, wolves positively selected ponies. Among wild ungulates, wolves positively selected roe deer. Wild pony and roe deer are key species for wolf feeding in Galicia. In the Galician wild pony range, ponies are the main food for wolves. Given that the availability of wild ponies may contribute to the decrease in wolf predation on cattle, it is essential to develop innovative administrative decisions in such areas to preserve this traditional equid population. In the same way, the population of roe deer should be strengthened in the livestock areas outside the range of wild pony.     

A new diagnostic approach to fast-track and increase the accessibility of gastrointestinal nematode identification from faeces: FECPAKG2 egg nemabiome metabarcoding

Effective gastrointestinal nematode management in livestock industries is becoming increasingly difficult due to the rise of anthelmintic resistance and changes in the temporal and geographical distribution of major gastrointestinal nematodes. Underpinning the response to these challenges is the need for a fast-tracked diagnostic identification technique, making it easier for livestock producers to make informed gastrointestinal nematode management decisions. The traditional ‘gold-standard’ approach, larval culture followed by morphological differentiation, is laborious and potentially inaccurate. We developed a new diagnostic approach to identify gastrointestinal nematodes that integrates a remote-location digital faecal egg count platform, FECPAK^G2, with internal transcribed spacer 2 (ITS2) nemabiome metabarcoding. The technique involves a quick and simple protocol to harvest concentrated strongyle eggs from the FECPAK^G2 cassette utilising a repurposed pipette tip, followed by DNA isolation and Illumina next generation amplicon sequencing. The gastrointestinal nematode compositions and alpha diversity generated by our FECPAK^G2 egg nemabiome metabarcoding approach was not significantly different to traditional morphological larval differentiation and nemabiome metabarcoding of larval and faecal samples. We demonstrated that storing FECPAK^G2 harvested eggs in either DNA isolation lysis buffer or 80% ethanol (v/v) had no impact on gastrointestinal nematode identification outcomes for at least 60 days; enabling the transport of biological samples from their remote origins to a molecular diagnostic facility for nemabiome metabarcoding, in the absence of a cold chain. We discovered that sustained gastrointestinal nematode egg embryonation in the lysis buffer storage solution lead to higher yields of DNA compared with ethanol-stored gastrointestinal nematode eggs or faeces with gastrointestinal nematode eggs. Taking advantage of an already well-established platform such as FECPAK^G2, and providing the livestock producers that use it with the option to identify gastrointestinal nematodesin their samples and contribute to large-scale gastrointestinal nematode distribution and/or anthelmintic resistance surveys, is an important future direction for the FECPAK^G2 egg nemabiome metabarcoding approach.     

Host Movement and the Genetic Structure of Populations of Parasitic Nematodes

Mitochondrial DNA (mtDNA) sequence data were used to compare the population genetic structures of five species of parasitic nematodes from three different hosts: Ostertagia ostertagi and Haemonchus placei from cattle, H. contortus and Teladorsagia circumcincta from sheep, and Mazamastrongylus odocoilei from white-tailed deer. The parasites of sheep and cattle showed a pattern consistent with high gene flow among populations. The parasite of deer showed a pattern of substantial population subdivision and isolation by distance. It appears that host movement is an important determinant of population genetic structure in these nematodes. High gene flow in the parasites of livestock also indicates great opportunity for the spread of rare alleles that confer resistance to anthelmintic drugs. All species, including the parasite of deer, had unusually high within-population diversities (averages of 0.019-0.027 substitutions per site between pairs of individuals from the same population). Large effective population sizes (Ne), perhaps in combination with rapid mtDNA evolution, appear to be the most likely explanation for these high within-population diversities.     

The feeding habits of wolves in relation to large prey availability in northern Italy

We investigated wolf feeding habits in relation to the abundance of wild and domestic ungulates to test the hypothesis that large prey are preferred and that their abundance affects the use of other food categories and diet breadth. We determined diet composition by scat analysis from December 1987 to December 1992. The research was carried out in three study areas located in northern Italy and characterised by marked differences in wild and domestic ungulate abundance. In study area A (low wild and domestic ungulate availability) fruits, livestock, other vertebrates and wild ungulates made up the bulk of the diet (71% in volume). In area B (high availability of livestock) wolf diet was mainly based on sheep and wild boars (80% in volume). In study area C (high availability of wild ungulates) wild ungulates were the main food of wolves (90% in volume). Significant differences were found among study areas in the mean percentage volume of all food categories and in particular for wild ungulates, livestock, other vertebrates and fruits (p < 0.0001 in all cases). Diet breadth decreased in areas with high availability of large wild and domestic herbivores. The use of livestock species was lower where there was high abundance, richness and diversity of the wild ungulate guild. Selection for wild ungulate species was partially affected by their abundance: however other factors as prey social behaviour, adaptability to the habitat (for introduced species), and body size could have an important role in species selection by wolves. In particular in area C wild boars were selected for, roe and red deers avoided, and fallow deers and mouflons used as available. Livestock species were used in relation to their abundance and accessibility, in particular sheep were selected for and cattle avoided; but if calves bom in the pastures were considered as the only available cattle, they were selected for and sheep were used as available. Large and in particular wild herbivores were found to be of great importance for the wolf population maintenance in northern Italy, one of the most important recovery areas of Mediterranean wolves.     

Faecal egg counts and nemabiome metabarcoding highlight the genomic complexity of equine cyathostomin communities and provide insight into their dynamics in a Scottish native pony herd

Understanding the composition of gastrointestinal nematode communities may help to mitigate or exploit parasite adaptations within their host. We have used nemabiome deep amplicon sequencing of internal transcribed spacer-2 (ITS-2) ribosomal DNA to describe the temporal and host species composition of gastrointestinal nematode communities following sampling of six Scottish ponies across 57 months. In the absence of parasite control, each horse showed seasonal trends of increases and decreases in faecal egg counts, consistent with the epidemiology of equine strongylid parasites, however, the composition of parasites within individuals changed over time. Sixteen presumptive strongylid species were identified in each of the horses, 13 of which were distributed in a complex clade together with small numbers of amplicon sequences which could not be classified beyond the Cyathostominae subfamily level. Egg shedding of seven trichostrongylid species, which had previously been identified in co-grazed Soay sheep, was identified during the early spring. Faecal egg counts and the percentage of amplicon sequences assigned to each gastrointestinal nematode species were combined to describe their relative abundance across both host and time. Significant differences in species diversity between horses and between months were observed, being greatest from March to May and least from October to December. The magnitude of the individual horse effect varied between months and, conversely, the magnitude of the seasonal effect varied between individual horses. The most abundant gastrointestinal nematode in each of the horses was Cylicostephanus longibursatus (46.6% overall), while the abundance of the other strongylid species varied between horses and relative to each other. Patent C. longibursatus infections over the winter months might represent a genetic adaptation towards longer adult worm survival, or a lower rate of developmental arrest in the autumn. This study provides insight into highly complex phylogenetic relationships between closely related cyathostomin species; and describes the dynamics of egg shedding and pasture contamination of co-infecting equine gastrointestinal nematode communities. The results could be applied to determine how climatic and management factors affect the equilibrium between hosts and their parasites, and to inform the development of sustainable gastrointestinal nematode control strategies for different host species.     

Host status of wild roe deer in bovine tuberculosis endemic areas

Rarely found infected, roe deer (Capreolus capreolus) are not considered a bovine tuberculosis (bTB) reservoir. However, serial cases discovered between 2010 and 2014 in one of the bTB endemic regions in France threw doubt on the epidemiological role played by this small wild cervid in ecosystems where cattle and other wild animals are both infected. Our objective was to analyse the bTB host status of roe deer as regards infection prevalence within the population and Mycobacterium bovis-induced pathology in this species. From November 2001 to March 2016, 668 roe deer were analysed (culture and/or PCR) through active surveillance implemented in three bTB endemic areas in France (Brotonne forest, Dordogne and Côte d’Or) and 132 through passive surveillance (presence of macroscopic lesions) in the whole country. Only seven roe deer were found infected by M. bovis, exclusively in bTB endemic areas, one through active surveillance (Brotonne forest; n = 203, apparent prevalence 0.49%). On the basis of these results, observed pathological patterns (mainly pulmonary lesions), species social behaviour (less gregarious than other ungulates) and food behaviour (mainly a selective browser), roe deer does not appear to be a true reservoir of bTB. However, once infected, it develops lesions reflecting a clear ability for bacterial excretion and therefore transmission to other species, most likely by indirect contact. It could thus be a spillover host included in a multi-host component reservoir in endemic areas. Consequently, passive surveillance is essential to detect infection and to implement specific management to limit interactions with cattle, where infected roe deer are found.     

Haemonchus contortus and Trichostrongylus colubriformis did not adapt to long-term exposure to sheep that were genetically resistant or susceptible to nematode infections

We tested the hypothesis that Haemonchus contortus and Trichostrongylus colubriformis would adapt to long-term exposure to sheep that were either genetically resistant or susceptible to H. contortus. Sheep genotypes were from lines with 10 years prior selection for low (resistant, R) or high (susceptible, S) faecal worm egg count (WEC) following H. contortus infection. Long-term exposure of H. contortus and T.colubriformis to R or S genotypes was achieved using serial passage for up to 30 nematode generations. Thus, we generated four nematode strains; one strain of each species solely exposed to R sheep and one strain of each species solely exposed to S sheep. Considerable host genotype differences in mean WEC during serial passage confirmed adequate nematode selection pressure for both H. contortus (R 4900 eggs per gram (epg), S 19,900 epg) and T. colubriformis (R 5300 epg, S 13,500 epg). Adaptation of nematode strain to host genotype was tested using seven cross-classified tests for H. contortus, and two cross-classified and one outbred genotype test for T. colubriformis. In the cross-classified design, where each strain infects groups of R, S or randomly bred control sheep, parasite adaptation would be indicated by a significant host genotype by nematode strain interaction for traits indicating parasite reproductive success; specifically WEC and, for H. contortus strains, packed cell volume. We found no significant evidence of parasite adaptation to host genotype (P > 0.05) for either the H. contortus or T. colubriformis strains. Therefore, we argue that nematodes will not adapt quickly to sheep bred for nematode resistance, where selection is based on low WEC, although selecting sheep using a subset of immune functions may increase adaptation risk. Our results support the hypothesis that nematode resistance is determined by many genes each with relatively small effect. In conclusion, selection of sheep for nematode resistance using WEC should be sustainable in the medium to long-term.     

Selective Defecation and Selective Foraging: Antiparasite Behavior in Wild Ungulates?

Selective defecation and selective foraging are two potential antiparasite behaviors used by grazing ungulates to reduce infection by fecal–oral transmitted parasites. While there is some evidence that domestic species use these strategies, less is known about the occurrence and efficacy of these behaviors in wild ungulates. In this study, I examined whether wild antelope use selective defecation and selective foraging strategies to reduce exposure to gastrointestinal nematode parasites. By quantifying parasite levels in the environment in relation to the defecation patterns of three species, dik‐dik (Madoqua kirkii), Grant's gazelle (Gazella granti), and impala (Aepyceros melampus), I found that nematode larval concentrations in pasture were higher in the vicinity of clusters of feces (dung middens) compared to single fecal pellet groups or dung‐free areas. In addition, experimental feeding trials in free‐ranging dik‐dik showed that individuals selectively avoided feeding near concentrations of feces. Given that increased parasite contamination was found in the immediate vicinity of fecal clusters, fecal avoidance could help reduce host consumption of parasites and may therefore be an effective antiparasite behavior for certain species. On the other hand, while the concentration of parasite larvae in the vicinity of middens coupled with host avoidance of these areas during grazing could reduce host contact with parasites, results showing a positive correlation between the number of middens in a habitat and larval abundance at control sites suggest that dung middens might increase and not decrease overall host exposure to parasites. If this is the case, dung midden formation may not be a viable antiparasite strategy.     

Value of identification of gastrointestinal nematode third-stage larvae recovered from faeces and herbage

Strategic parasite control programmes of ruminant gastrointestinal nematodes requires the knowledge of parasite population dynamics. In natural conditions, ruminants, in particular sheep and goats, are infected by different species of gastrointestinal nematodes. The life cycle of these parasites is influenced by a number of factors which include climatic variations. Therefore, it is important to utilise appropriate methods to identify the parasite population both in the host and from the pasture. In this paper faecal larval cultures and pasture larval counts used for herd health monitoring of nematode infections are discussed.     

Vulnerability of Domestic Sheep to Lynx Depredation in Relation to Roe Deer Density

Abstract The Eurasian lynx (Lynx lynx) causes large loss of free-ranging domestic sheep in Norway. We tested whether the observed higher kill rates by male lynx than female lynx were related to an association between the availability of the main natural prey, as measured by roe deer (Capreolus capreolus) habitat suitability, presence of sheep, and habitat selection of male and female lynx. We found that lynx selected areas with high roe deer suitability during summer and winter. Moreover, during summer, compared to male lynx, females had greater selection for roe deer areas and a stronger avoidance for sheep grazing areas, which suggests that previously observed differences in kill rates between male and female lynx can be attributed to sex-specific habitat use during summer. The connection between lynx habitat use and roe deer also was reflected in a positive relationship between the roe deer suitability of a sheep grazing area and the total loss of lambs, which suggests that livestock, rather than being actively selected, are mainly killed by lynx incidentally when encountered during other lynx activities (e.g., searching for natural prey species). Therefore, any management practice that separates lynx and sheep, such as concentrating livestock into small patches or less preferred habitats, may reduce depredation.     

Comparing patterns of human harvest and predation by Eurasian lynx Lynx lynx on European roe deer Capreolus capreolus in a temperate forest

Human harvest is the most important mortality factor for wild ungulates in Europe and can affect several aspects of ungulate biology. There is a growing concern about possible negative side effects of human harvest. To better understand the differences between human and natural mortality, we compared the extent, age and sex structure, nutritional condition, spatial and temporal distribution of human harvest, and natural predation by the Eurasian lynx Lynx lynx on the European roe deer Capreolus capreolus, the most abundant wild ungulate in Europe. Compared to the human harvest, lynx were less likely to kill fawns and yearlings than adults, and among adult deer, lynx were more likely to kill females. The proportion of roe deer with fat-depleted bone marrow was higher among lynx prey than among harvested animals. Average lynx kill rate was estimated to 47.8 roe deer per year, and lynx predation was considerably lower than the human harvest in the same area. While human harvest increased with higher roe deer density, lynx predation was similar across the gradient of roe deer densities. Comparison with other countries indicated that differences between human harvest and natural mortality of ungulates vary considerably in different parts of Europe. Variation in hunting practices and, even more importantly, carnivore predation may have an important role in buffering unwanted side effects of harvest of wild ungulates.     

Dung avoidance as a possible mechanism in competition between wild and domestic ungulates: two experiments with chamois <Emphasis Type="Italic">Rupicapra rupicapra</Emphasis>

Wild ungulates often adjust spatial behaviour where they coexist with livestock. In European mountains, chamois Rupicapra rupicapra or R. pyrenaica commonly avoid alpine pastures used by domestic sheep. Mechanisms leading to competitive losing out of the wild species are not well understood, but mostly, resource competition is inferred and sometimes demonstrated. We hypothesised that chamois need to minimise the risk of intestinal parasite uptake and therefore would avoid pastures contaminated with sheep dung. We tested this in two experiments by contaminating feeding patches of wild and captive chamois with (parasite-free) sheep faeces. Wild chamois did not avoid grazing sites or plots on which sheep dung had been placed at a (low) density representing the commonly encountered situation in the Swiss Alps. Captive chamois strongly reduced browsing time on small trees given for food when the surroundings of the trees were sprayed with a watery faecal solution. We concluded that the odour signalled a potential high risk of parasite infection to the captive chamois, whereas the density of sheep dung on the grazing site of wild chamois was not high enough to be perceived as a risk. The need to minimise endoparasite uptake from faeces may therefore play a role in driving spatial behaviour of wild ungulates and could result in competitive imbalance between wild and domestic ungulates.     

Anthelmintic treatment alters the parasite community in a wild mouse host

Individuals are often co-infected with several parasite species, yet the consequences of drug treatment on the dynamics of parasite communities in wild populations have rarely been measured. Here, we experimentally reduced nematode infection in a wild mouse population and measured the effects on other non-target parasites. A single oral dose of the anthelmintic, ivermectin, significantly reduced nematode infection, but resulted in a reciprocal increase in other gastrointestinal parasites, specifically coccidial protozoans and cestodes. These results highlight the possibility that drug therapy may have unintended consequences for non-target parasites and that host–parasite dynamics cannot always be fully understood in the framework of single host–parasite interactions.     

Deep amplicon sequencing as a powerful new tool to screen for sequence polymorphisms associated with anthelmintic resistance in parasitic nematode populations

Parasitic gastrointestinal nematodes contribute to significant human morbidity and cause billions of dollars per year in lost agricultural production. Control is dependent on the use of anthelmintic drugs which, in the case of livestock parasites, is severely compromised by the widespread development of drug resistance. There are now concerns regarding the emergence of anthelmintic resistance in parasitic nematodes of humans in response to the selection pressure resulting from mass drug administration programs. Consequently, there is an urgent need for sensitive, scalable and accurate diagnostic tools to detect the emergence of anthelmintic resistance. Detecting and measuring the frequency of resistance-associated mutations in parasite populations has the potential to provide sensitive and quantitative assessment of resistance emergence from an early stage. Here, we describe the development and validation of deep amplicon sequencing as a powerful new approach to detect and quantify the frequency of single nucleotide polymorphisms associated with benzimidazole resistance. We have used parasite communities in sheep to undertake a proof-of-concept study of this approach. Sheep provide an excellent host system, as there are multiple co-infecting trichostrongylid nematode species, each likely with a varying prevalence of benzimidazole resistance. We demonstrate that the approach provides an accurate measure of resistance allele frequencies, and can reliably detect resistance alleles down to a frequency of 0.1%, making it particularly valuable for screening mutations in the early stages of resistance. We illustrate the power of the technique by screening UK sheep flocks for benzimidazole resistance-associated single nucleotide polymorphisms at three different codons of the β-tubulin gene in seven different parasite species from 164 populations (95 from ewes and 69 from lambs) in a single MiSeq sequencing run. This approach provides a powerful new tool to screen for the emergence of anthelmintic resistance mutations in parasitic nematode populations of both animals and humans.