Comparison of morphological and molecular Strongylus spp. identification in equine larval cultures and first report of a patent Strongylus asini infection in a horse.

BACKGROUND: Surveillance of Strongylus vulgaris and other Strongylus spp. in equids is important for targeted intervention in parasite control, requiring reliable routine diagnostic methods. OBJECTIVES: Comparing morphological examination and PCR analyses of larval cultures to identify Strongylus spp. species based on German diagnostic samples from 2018. STUDY DESIGN: Method comparison. METHODS: During the routine diagnostic investigations, in total 712 strongyle-egg positive equine faecal samples were cultured. Third-stage larvae (L3) were morphologically differentiated. For molecular validation, samples were examined using S. vulgaris real-time PCR and Strongylus edentatus/Strongylus equinus/Strongylus asini high-resolution melting PCRs. RESULTS: Based on 28S rRNA PCR, 594 samples positive for nematode DNA were included in the study. The inter-rater reliability to compare morphological and molecular species identification was fair for Strongylus spp. without species identification and for S. edentatus, slight for S. equinus and poor for S. vulgaris. The frequency based on morphological and molecular data in this study were for S. vulgaris 0% and 0.8%, respectively, for S. edentatus 0.3% and 1.5%, respectively, and for S. equinus 2.0% and 0.2%, respectively. Based on molecular analyses, one sample obtained from a domestic horse contained S. asini DNA, which was confirmed by sequencing. MAIN LIMITATIONS: For many samples, no or only incomplete data regarding clinical history, the exact geographical location and whether samples were obtained on individual or farm level, were available. CONCLUSIONS: Results of morphological and molecular examination methods of strongyle L3 from equine samples can differ substantially. Further evaluation of these methods is required to provide reliable and cost-effective methods of screening equine parasites. Further studies using approaches suitable to detect S. asini are needed to evaluate its clinical and epidemiological relevance.

Presence of Equine and Bovine Coronaviruses, Endoparasites, and Bacteria in Fecal Samples of Horses with Colic.

Acute abdominal pain (colic) is one of the major equine health threats worldwide and often necessitates intensive veterinary medical care and surgical intervention. Equine coronavirus (ECoV) infections can cause colic in horses but are rarely considered as a differential diagnosis. To determine the frequency of otherwise undetected ECoV infections in horses with acute colic, fresh fecal samples of 105 horses with acute colic and 36 healthy control horses were screened for viruses belonging to the Betacoronavirus 1 species by RT-PCR as well as for gastrointestinal helminths and bacteria commonly associated with colic. Horses with colic excreted significantly fewer strongyle eggs than horses without colic. The prevalence of anaerobic, spore-forming, gram-positive bacteria (Clostridium perfringens and Clostridioides difficile) was significantly higher in the feces of horses with colic. Six horses with colic (5.7%) and one horse from the control group (2.8%) tested positive for Betacoronaviruses. Coronavirus-positive samples were sequenced to classify the virus by molecular phylogeny (N gene). Interestingly, in three out of six coronavirus-positive horses with colic, sequences closely related to bovine coronaviruses (BCoV) were found. The pathogenic potential of BCoV in horses remains unclear and warrants further investigation.

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.

Genetic variability, cryptic species and phylogenetic relationship of six cyathostomin species based on mitochondrial and nuclear sequences.

Cyathostomins are important intestinal nematode parasites of equines and include 50 accepted species. Their taxonomy has been frequently revised and the presence of cryptic species suggested. Furthermore, usually molecular- and morphology-based phylogenetic analyses give divergent results. In this study, the nucleotide sequences of the nuclear second internal transcribed spacer (ITS-2) and the mitochondrial partial cytochrome c oxidase subunit I (COI) were determined for adults of six cyathostomin species (Coronocyclus coronatus, Coronocyclus labiatus, Cylicocyclus nassatus, Cylicostephanus calicatus, Cylicostephanus longibursatus, Cylicostephanus minutus) collected from different equine species within two geographic regions. Maximum likelihood trees were calculated for ITS-2, COI, and concatenated data. No obvious differentiation was observed between geographic regions or equine host species. As previously reported, Coronocyclus coronatus and Cylicostephanus calicatus revealed a close relationship. Cryptic species were detected in Cylicostephanus minutus and Cylicostephanus calicatus. Cylicocyclus nassatus and Coronocyclus labiatus showed diverse mitochondrial and nuclear haplotypes occurring in different combinations, while Cylicostephanus longibursatus was comparatively homogenous. In conclusion, a combined analysis of nuclear and mitochondrial haplotypes improved resolution of the phylogeny and should be applied to the remaining cyathostomin species and across additional equine host species and geographic regions.

Canine Dracunculus Nematode Infection, Toledo, Spain.

A fragment of a Dracunculus-like worm was extracted from the hind limb of a 2-year-old dog from Toledo, Spain. Cytochrome oxidase I and rRNA sequences confirmed an autochthonous mammalian Dracunculus worm infection in Europe. Sequence analyses suggest close relation to a parasite obtained from a North American opossum.