Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing.

Basic knowledge on the biology and epidemiology of equine strongylid species still needs to be improved to contribute to the design of better parasite control strategies. Nemabiome metabarcoding is a convenient tool to quantify and identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA gene, with a limited investigation of its predictive performance for cyathostomin communities. Using DNA pools of single cyathostomin worms, this study aimed to provide the first elements to compare performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. Barcode predictive abilities were compared across various mock community compositions of two, five and 11 individuals from distinct species. The amplification bias of each barcode was estimated. Results were also compared between various types of biological samples, i.e., eggs, infective larvae or adults. Bioinformatic parameters were chosen to yield the closest representation of the cyathostomin community for each barcode, underscoring the need for communities of known composition for metabarcoding purposes. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types. However, imperfect correlations were found between relative abundances from infective larvae and other life-stages for Cylicostephanus species using the ITS-2 barcode. While the results remain limited by the considered biological material, they suggest that additional improvements are needed for both the ITS-2 and COI barcodes.

Patterns of variation in equine strongyle community structure across age groups and gut compartments.

BACKGROUND: Equine strongyles encompass more than 64 species of nematode worms that are responsible for growth retardation and the death of animals. The factors underpinning variation in the structure of the equine strongyle community remain unknown. METHODS: Using horse-based strongyle community data collected after horse deworming (48 horses in Poland, 197 horses in Ukraine), we regressed species richness and the Gini-Simpson index upon the horse's age, faecal egg count, sex and operation of origin. Using the Ukrainian observations, we applied a hierarchical diversity partitioning framework to estimate how communities were remodelled across operations, age groups and horses. Lastly, strongyle species counts collected after necropsy (46 horses in France, 150 in Australia) were considered for analysis of their co-occurrences across intestinal compartments using a joint species distribution modelling approach. RESULTS: First, inter-operation variation accounted for > 45% of the variance in species richness or the Gini-Simpson index (which relates to species dominance in communities). Species richness decreased with horse's age (P = 0.01) and showed a mild increase with parasite egg excretion (P < 0.1), but the Gini-Simpson index was neither associated with parasite egg excretion (P = 0.8) nor with horse age (P = 0.37). Second, within-host diversity represented half of the overall diversity across Ukrainian operations. While this is expected to erase species diversity across communities, community dissimilarity between horse age classes was the second most important contributor to overall diversity (25.8%). Third, analysis of species abundance data quantified at necropsy defined a network of positive co-occurrences between the four most prevalent strongyle genera. This pattern was common to necropsies performed in France and Australia. CONCLUSIONS: Taken together, these results show a pattern of ß-diversity maintenance across age classes combined with positive co-occurrences that might be grounded by priority effects between the major species.

Effect of sainfoin (Onobrychis viciifolia) on cyathostomin eggs excretion, larval development, larval community structure and efficacy of ivermectin treatment in horses.

Alternative strategies to chemical anthelmintics are needed for the sustainable control of equine strongylids. Bioactive forages like sainfoin (Onobrychis viciifolia) could contribute to reducing drug use, with the first hints of in vitro activity against cyathostomin free-living stages observed in the past. We analysed the effect of a sainfoin-rich diet on cyathostomin population and the efficacy of oral ivermectin treatment. Two groups of 10 naturally infected horses were enrolled in a 78-day experimental trial. Following a 1-week adaptation period, they were either fed with dehydrated sainfoin pellets (70% of their diet dry matter) or with alfalfa pellets (control group) for 21-days. No difference was found between the average fecal egg counts (FECs) of the two groups, but a significantly lower increase in larval development rate was observed for the sainfoin group, at the end of the trial. Quantification of cyathostomin species abundances with an ITS-2-based metabarcoding approach revealed that the sainfoin diet did not affect the nemabiome structure compared to the control diet. Following oral ivermectin treatment of all horses on day 21, the drug concentration was lower in horses fed with sainfoin, and cyathostomin eggs reappeared earlier in that group. Our results demonstrated that short-term consumption of a sainfoin-rich diet does not decrease cyathostomin FEC but seems to slightly reduce larval development. Consumption of dehydrated sainfoin pellets also negatively affected ivermectin pharmacokinetics, underscoring the need to monitor horse feeding regimes when assessing ivermectin efficacy in the field.

The P-glycoprotein repertoire of the equine parasitic nematode Parascaris univalens.

P-glycoproteins (Pgp) have been proposed as contributors to the widespread macrocyclic lactone (ML) resistance in several nematode species including a major pathogen of foals, Parascaris univalens. Using new and available RNA-seq data, ten different genomic loci encoding Pgps were identified and characterized by transcriptome-guided RT-PCRs and Sanger sequencing. Phylogenetic analysis revealed an ascarid-specific Pgp lineage, Pgp-18, as well as two paralogues of Pgp-11 and Pgp-16. Comparative gene expression analyses in P. univalens and Caenorhabditis elegans show that the intestine is the major site of expression but individual gene expression patterns were not conserved between the two nematodes. In P. univalens, PunPgp-9, PunPgp-11.1 and PunPgp-16.2 consistently exhibited the highest expression level in two independent transcriptome data sets. Using RNA-Seq, no significant upregulation of any Pgp was detected following in vitro incubation of adult P. univalens with ivermectin suggesting that drug-induced upregulation is not the mechanism of Pgp-mediated ML resistance. Expression and functional analyses of PunPgp-2 and PunPgp-9 in Saccharomyces cerevisiae provide evidence for an interaction with ketoconazole and ivermectin, but not thiabendazole. Overall, this study established reliable reference gene models with significantly improved annotation for the P. univalens Pgp repertoire and provides a foundation for a better understanding of Pgp-mediated anthelmintic resistance.

Coccidiosis ­ a problem in backyard rabbitries

This paper focuses on parasites of the genus Eimeria in rabbits kept in two backyard farms ­ from Poland (herd A) and Ukraine (herd B). The concentration McMaster technique and sporulation was applied to determine the level of infection, as well as to identify the species composition. The Eimeria sp. oocysts were present in all collected samples (prevalence = 100%), and four to nine coccidian species were identified in the herd A and B, respectively. Eimeria media was the most common species, and the presence of the most pathogenic E. intestinalis and E. flavescens was observed in both studied rabbitries. The results obtained suggest that coccidiosis may cause a serious risk for rabbits kept in backyard farms, therefore prevention guidelines in relation to the backyard breeding are crucial to be developed.

Tarantobelus arachnicida (Nematoda: Rhabditida) invasion of exotic spiders in Poland

Nematodes of the Brevibuccidae family were stated among spiders of the Theraphosidae family (the South American species), which were bred in Poland. The first sign of infection was anorexia which led to gradually increasing lethargy progressed to a huddled posture. Additionally, a white discharge with nematodes between mouth and chelicerae was noted. All of the derived nematodes were morphologically identified and determined to the species Tarantobelus arachnicida. A molecular analysis covered amplification and sequencing of small subunit ribosomal RNA (18S rRNA). A post mortem examination demonstrated the presence of nematodes not only near the chelicerae, but also inside the intestine, hence the source of infection might be insects used as a food. The research showed that such kind of infection is an important disease, which poses a serious risk to the breeding spiders. To date there is no effective treatment, however, we demonstrated that usage of the Lugol's solution seems to be promising.

Endoparasites of pet reptiles based on coprosopic methods

Due to the growing popularity of reptiles as a household animals and the development of numerous reptile farms, they have become a common sight in veterinary clinics. As parasitic infections represent a serious problem among pet reptiles obtained by captive breeding and from pet shops, the purpose of the present study was to determine the species composition of parasites present in reptiles bred privately or in Cracow Zoological Garden, and those obtained from pet shops. Fecal samples collected from 91 reptiles (30 turtles, 40 lizards, and 21 snakes) were examined using the quantitative McMaster method. Parasite eggs or protozoan oocysts were identified in 59.3% of samples. These included the eggs of the Pharyngodonidae, Ascarididae and Rhabditoidea (Nematoda), and Trematoda, as well as oocysts of Isospora and Eimeria. In addition, pseudoparasites belonging to the Mesostigmata, Demodecidae and Myobiidae were found.

Equine strongyle communities are constrained by horse sex and species dipersal-fecundity trade-off.

BACKGROUND: Equine strongyles are a major health issue. Large strongyles can cause death of horses while cyathostomins (small strongyles) have shown increased resistance to anthelmintics worldwide. Description of strongyle communities have accumulated but little is known about the diversity of these communities and underpinning environmental factors. METHODS: Strongyles were recovered after ivermectin treatment from 48 horses located in six premises in Poland. Correlation between previously published species fecundity and the observed relative abundance and prevalence were estimated. Significance of horse sex was determined at the species level (prevalence, relative abundance) and at the community level (species richness and dissimilarity between communities). RESULTS: Strongyle species fell into two groups, contrasted by their prevalence and relative abundance. Six to nine horses were necessary to sample at least 90% of strongyle community diversity, providing a minimal cut-off to implement sampling trial in the field. Strongyle communities entertained a network of mostly positive interactions and species co-occurrence was found more often than expected by chance. In addition, species fecundity and prevalence were negatively correlated (Pearson's r = -0.71), suggesting functional trade-offs between species dispersal abilities and fecundity. This functional trade-off may underpin species coexistence. Horse sex was also a significant constraint shaping strongyle communities. Indeed, mares generally displayed more similar strongyle communities than stallions (P = 0.003) and Cylicostephanus calicatus was more abundant in stallions suggesting sex-specific interactions (P = 0.006). CONCLUSIONS: While niche partitioning is likely to explain some of the positive interactions between equine strongyle species, coexistence may also result from a functional trade-off between dispersal ability and fecundity. There is significant evidence that horse sex drives strongylid community structure, which may require differential control strategies between mares and stallions.

Cephenemyia stimulator (Diptera) infection in roe deer (Capreolus capreolus) from Kraków area, southern Poland.

UNLABELLED: The aim of the study was to determine the prevalence of botfly (Diptera: Oestridae) larvae infection in roe deer populations (Capreolus capreolus) in the Kraków area on the basis of necropsy and questionnaire surveys. Hunters were surveyed about the age and sex of hunted animals, and the origin of their habitat. All parasite specimens were identified to species in the laboratory. The parasites were found in the nasal cavities, esophagus, and larynx of male roe deer aged 3-8 years, living in forest habitats. The level of infection was relatively low (13%), with the intensity ranging from 1 to 10 larvae per host. Although no fly larvae were found during the dissection of roe deer carcasses, the parasites received from the hunters were identified as Cephenemyia stimulator botflies. These findings are supported by the evidence drawn from the questionnaires completed by the hunters. KEY WORDS: parasites, Cephenemyia stimulator, Capreolus capreolus, necropsy, questionnaire study, Poland.

Endoparasites of exotic ungulates from the Giraffidae and Camelidae families kept ex situ.

Giraffes and camels are popular attractions at zoological gardens. In order to present the diversity of parasites infecting exotic ungulates from zoos, faecal samples from three giraffes and six camels from both the Silesian Zoological Garden in Chorzów, and Kraków Zoological Garden, were examined. The research was carried out over a ten-month period in 2013 and 2014. In total, 100 faecal samples from 18 animals were analysed with the use of the McMaster method. Moreover, coccidian oocysts were incubated to investigate their development and larvoscopic examination was conducted to detect the presence of nematode species. Giraffes were infected with coccidia from the genus Eimeria, and gastrointestinal nematodes from the Strongylida order, and Trichuris and Aonhotheca genera. One male giraffe was uninfected. The level of infection in giraffes was low when compared to camels kept in both of the zoos. Limited contact with other animal species contributed greatly to the lower level of infection in camels from Kraków Zoo than those from Chorzów, which were kept in the same enclosure as alpacas and Shetland ponies.

Lungworm (Nematoda: Protostrongylidae) infection in wild and domestic ruminants from Malopolska region of Poland.

The conducted study has focused on domestic, as well as wild ruminant species. The post mortem examination was carried out on 68 animals, including three wild species: roe deer (Capreolus capreolus) (25 indyviduals), red deer (Cervus elaphus) (6), fallow deer (Dama dama) (5) and two domestic: sheep (Ovis aries) (14) and cattle (Bos taurus) (18). Some of the species have also been investigated in the field by the coproscopical analyses. The faecal samples from roe deer (27), fallow deer (20), red deer (36) and moose (Alces alces) (10) were collected from the environment, while from sheep (10) and goat (Capra hircus) (10)--per rectum. Based on the obtained results the following values were calculated: prevalence, mean intensity and intensity range. The post mortem examination did not reveal pulmonary nematodes neither in domestic nor in wild ungulates, however, the larvae of aforementioned parasites were often stated in the stool samples taken from the environment. All wild species, except fallow deer were infected. Consequently, six species of lungworms have been identified. The first stage larvae of Varestrongylus capreoli occurred in 11 samples of roe deer and Varestrongylus alces in one moose. The larvae of Elaphostrongylus cervi were found in 19 red deer and Varestrongylus sagittatus in 3. Furthermore, Elaphostrongylus alces larvae were noted in 6 moose. Within domestic ruminants only one sheep and two goats were infected by Muellerius capillaris.

Parasite infections in red deer Cervus elaphus from Krakow area, southern Poland.

The study describes the parasitofauna of red deer Cervus elaphus from Kraków area (southern Poland). The study was done in years 2011-2012 and included altogether 6 animals. Five deer originated from the forest areas (hunted) and one came from the urban site (it died in a road accident). In addition to post-mortem examination, coproscopic analyses with sporulation were performed to define Eimeria species diversity. The deer were infected with four species of nematodes: Ashworthius sidemi, Spiculopteragia spiculoptera, Oesophagostomum venulosum and O. sikae, and two species of coccidia: E. elaphi and E. austriaca. The level of parasitie infections was low, but the results indicate the important role of deer as possible transmitter of A. sidemi to other ungulates in examined area.

Zatorska goose - a subject of parasitological research.

The aim of the study was to determine the level of gastrointestinal parasites in a native breed of geese - Zatorska goose - based on coproscopic testing. Faecal samples were collected from 90 young geese in three age groups (5, 7 and 9 weeks old) in 2014. The geese were kept indoors on deep litter and pastured from spring to autumn. The area of the pastures around the buildings where the geese grazed was about 1 hectare, divided into quarters for different age groups. Before grazing, the birds were dewormed with fenbendazole (Fenbenat powder 4%, Naturan). As additional treatment for coccidiosis, coccidiostats were added to the feed. The study was conducted using the McMaster quantitative method with centrifugation (flotation liquid: NaCl and glucose). The birds were shown to be infected with coccidia and nematodes. The prevalence of Eimeria sp. infection (mean 40%) and the number of oocysts per gram of faeces (reaching 5,300 OPG) were highest in the youngest age group of geese. The level of Amidostomum anseris infection was similar in the three age groups, with prevalence from 40% to 50% (nematode egg output ranged from 50 to 350 eggs per gram of faeces, EPG). Capillaria anatis was observed only in 5- and 7-week-old geese.

The Alice - "Follow the White Rabbit" - parasites of farm rabbits based on coproscopy.

The aim of the study, conducted in the years 2011-2013, was to determine the level of gastrointestinal parasites infection in New Zealand White rabbits, kept at the Experimental Station of the University of Agriculture in Krakow. The study showed rabbits protozoan infection with the genus Eimeria, belonging - based on the sporulation method - to the following species: E. magna, E. media, E. perforans, E. stiedae and E. irresidua. The highest prevalence of infection, as well as the intensity of oocysts output (OPG - oocysts per gram of faeces), was noted for E. magna and E. media - respectively 31.4 % (19477.3 OPG), and 40.0 % (14256.07 OPG). The infection of rabbits with Eimeria spp. differed significantly between years. With regard to oocysts output, the level of infection was strongly connected with the age of rabbits, being higher in young animals. However, the range of infection was highest among adults. Among nematodes, Passalurus ambiguus pinworm was regularly found (prevalence reached 21.9%), other species - Trichuris leporis, and Graphidium strigosum were rarely noted. The overall infection with nematodes did not differ between years. Similarly, as in the case of Eimeria older individuals were more often infected by nematodes. We observed some trends in parasite oocysts/eggs output; the protozoan oocysts were recorded more often in faecal samples collected in the evenings, whereas the nematodes eggs occurred frequently in the mornings. This situation may be related to the phenomenon of coprophagy occurring in the mammals of Lagomorpha order. The results of the study indicate that especially coccidiosis constitute permanently throughout the years an important problem in the rabbitry examined.

Genetic variants and increased expression of Parascaris equorum P-glycoprotein-11 in populations with decreased ivermectin susceptibility.

Macrocyclic lactones (MLs) represent the major drug class for control of parasitic infections in humans and animals. However, recently reports of treatment failures became more frequent. In addition to human and ruminant parasitic nematodes this also is the case for the horse-nematode Parascaris equorum. Nevertheless, to date the molecular basis of ML resistance is still not understood. Unspecific resistance mechanisms involving transporters such as P-glycoproteins (Pgps) are expected to contribute to ML resistance in nematodes. Here, complete sequences of two P. equorum Pgps were cloned and identified as orthologs of Caenorhabditis elegans Ppg-11 and an unnamed Caenorhabditis briggsae Pgp designated as Pgp-16 using phylogenetic analysis. Quantitative real-time PCR was used to compare expression between tissues. Significantly higher PeqPgp-11 expression was found in the gut for both genders, whereas for PeqPgp-16 the body wall was identified as predominant expression site. Furthermore, Pgps were analyzed regarding their participation in resistance development. Using SeqDoC analyses, Pgp-sequences of P. equorum populations with different ML susceptibility were compared. This approach revealed three single nucleotide polymorphisms (SNPs) causing missense mutations in the PeqPgp-11 sequence which correlated with decreased ML susceptibility. However, no resistance associated differences in mRNA expression levels were detected between embryonated eggs of these populations. In contrast, comparison of two pre-adult groups with different ivermectin (IVM) susceptibility revealed the presence of the three SNPs and in addition statistically significant PeqPgp-11 overexpression in the group of worms with reduced susceptibility. These results indicate that Pgp-11 might be involved in IVM resistance in P. equorum as it shows increased expression in an IVM exposed life-cycle stage of an IVM resistant population as well as occurrence of putatively resistance associated SNPs in populations with reduced IVM susceptibility. These SNPs are promising diagnostic candidates for detection of ML resistance with potential also for other parasitic nematode species.

Setaria tundra in roe deer (Capreolus capreolus)--new findings in Poland.

Setaria tundra is a filarioid nematode transmitted by mosquitoes, which is sporadically observed in Poland. Some ecological factors, such as the synurbisation of some wild ungulates and the climate changes observed in recent years, could affect the possibility of infection, especially with parasites transmitted by arthropod vectors. The study was conducted to evaluate the presence of Setaria sp. in roe deer populations in different environments. Parasitological dissections of 53 roe deer were performed. The animals were taken from the area of the Cracow agglomeration, and from arable and forest lands near the city. During the autopsy, nematode specimens (one to twelve per host) were found only in the abdominal cavity of roe deer from the urban area. All parasites were classified to Setaria tundra species on the basis of morphology and dimensions. The infection observed was probably associated with the specific environmental conditions of the urban area.