Comparative sequence analysis of the intergenic spacer region of cyathostome species

Molecular diagnostics for gastrointestinal helminths in equids: Past, present and future

This review is aimed to (i) appraise the literature on the use of molecular techniques for the detection, quantification and differentiation of gastrointestinal helminths (GIH) of equids, (ii) identify the knowledge gaps and, (iii) discuss diagnostic prospects in equine parasitology. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic reviews, we retrieved 54 studies (horses: 50/54; donkeys and zebras: 4/54) from four databases. Polymerase chain reaction (PCR) was employed in all of the studies whereas PCR amplicons were sequenced in only 18 of them. Other techniques used (including modifications of PCR) were reverse line blot, quantitative (q)PCR, restriction fragment length polymorphism, nested-PCR, PCR-directed next-generation sequencing, Southern blotting, single strand conformation polymorphism, PCR-enzyme linked immunosorbent assay, matrix-assisted laser desorption/ionisation-time of flight and random amplification of polymorphic DNA. Most of the studies (53/54) used nuclear ribosomal RNA (including the internal transcribed spacers, intergenic spacer, 5.8 S, 18 S, 28 S and 12 S) as target loci while cytochrome c oxidase subunit 1 and random genomic regions were targeted in only three and one studies, respectively. Overall, to date, the majority of molecular studies have focused on the diagnosis and identification of GIHs of equids (i.e. species of Anoplocephala, Craterostomum, cyathostomins, Oesophagodontus, Parascaris, Strongylus, Strongyloides and Triodontophorus), with a recent shift towards investigations on anthelmintic resistance and the use of high-throughput nemabiome metabarcoding. With the increasing reports of anthelmintic resistance in equid GIHs, it is crucial to develop and apply techniques such as advanced metabarcoding for surveillance of parasite populations in order to gain detailed insights into their diversity and sustainable control. To the best of our knowledge, this is the first systematic review that evaluates molecular investigations published on the diagnosis and quantification of equid GIHs and provides useful insights into important knowledge gaps and future research directions in equid molecular parasitology.

Nematode Species Identification-Current Status, Challenges and Future Perspectives for Cyathostomins

Human and animal health is globally affected by a variety of parasitic helminths. The impact of co-infections and development of anthelmintic resistance requires improved diagnostic tools, especially for parasitic nematodes e.g., to identify resistant species or attribute pathological effects to individual species or particular species combinations. In horses, co-infection with cyathostomins is rather a rule than an exception with typically 5 to 15 species (out of more than 40 described) per individual host. In cyathostomins, reliable morphological species differentiation is currently limited to adults and requires highly specialized expertize while precise morphological identification of eggs and early stage larvae is impossible. The situation is further complicated by a questionable validity of some cyathostomins while others might actually represent cryptic species complexes. Several molecular methods using different target sequences were established to overcome these limitations. For adult worms, PCR followed by sequencing of mitochondrial genes or external or internal ribosomal RNA spacers is suitable to genetically confirm morphological identifications. The most commonly used method to differentiate eggs or larvae is the reverse-line-blot hybridization assay. However, both methods suffer from the fact that target sequences are not available for many species or even that GenBank® entries are unreliable regarding the cyathostomin species. Recent advances in proteomic tools for identification of metazoans including insects and nematodes of the genus Trichinella will be evaluated for suitability to diagnose cyathostomins. Future research should focus on the comparative analysis of morphological, molecular and proteomic data from the same cyathostomin specimen to optimize tools for species-specific identification.

Transcriptome analysis of a parasitic clade V nematode: comparative analysis of potential molecular anthelmintic targets in Cylicostephanus goldi

Clade V nematodes comprise several parasitic species that include the cyathostomins, primary helminth pathogens of horses. Next generation transcriptome datasets are available for eight parasitic clade V nematodes, although no equine parasites are included in this group. Here, we report next generation transcriptome sequencing analysis for the common cyathostomin species, Cylicostephanus goldi. A cDNA library was generated from RNA extracted from 17 C. goldi male and female adult parasites. Following sequencing using a 454 GS FLX pyrosequencer, a total of 475,215 sequencing reads were generated, which were assembled into 26,910 contigs. Using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, 27% of the transcriptome was annotated. Further in-depth analysis was carried out by comparing the C. goldi dataset with the next generation transcriptomes and genomes of other clade V nematodes, with the Oesophagostomum dentatum transcriptome and the Haemonchus contortus genome showing the highest levels of sequence identity with the cyathostomin dataset (45%). The C. goldi transcriptome was mined for genes associated with anthelmintic mode of action and/or resistance. Sequences encoding proteins previously associated with the three major anthelmintic classes used in horses were identified, with the exception of the P-glycoprotein group. Targeted resequencing of the glutamate gated chloride channel α4 subunit (glc-3), one of the primary targets of the macrocyclic lactone anthelmintics, was performed for several cyathostomin species. We believe this study reports the first transcriptome dataset for an equine helminth parasite, providing the opportunity for in-depth analysis of these important parasites at the molecular level. Sequences encoding enzymes involved in key processes and genes associated with levamisole/pyrantel and macrocyclic lactone resistance, in particular the glutamate gated chloride channels, were identified. This novel data will inform cyathostomin biology and anthelmintic resistance studies in future.

New insights into sequence variation in the IGS region of 21 cyathostomin species and the implication for molecular identification

Cyathostomins comprise a group of 50 species of parasitic nematodes that infect equids. Ribosomal DNA sequences, in particular the intergenic spacer (IGS) region, have been utilized via several methodologies to identify pre-parasitic stages of the commonest species that affect horses. These methods rely on the availability of accurate sequence information for each species, as well as detailed knowledge of the levels of intra- and inter-specific variation. Here, the IGS DNA region was amplified and sequenced from 10 cyathostomin species for which sequence was not previously available. Also, additional IGS DNA sequences were generated from individual worms of 8 species already studied. Comparative analysis of these sequences revealed a greater range of intra-specific variation than previously reported (up to 23%); whilst the level of inter-specific variation (3–62%) was similar to that identified in earlier studies. The reverse line blot (RLB) method has been used to exploit the cyathostomin IGS DNA region for species identification. Here, we report validation of novel and existing DNA probes for identification of cyathostomins using this method and highlight their application in differentiating life-cycle stages such as third-stage larvae that cannot be identified to species by morphological means†.

Facing the threat of equine parasitic disease

Horses worldwide are exposed to a complex mixture of intestinal parasitic helminths. When burdens are high, these parasites can seriously compromise health and welfare. Some helminth species have an extremely high prevalence and are difficult to control, not least because there is a limited understanding of their most basic biology. Furthermore, levels of resistance to some of the commonly used anthelmintics are widespread and increasing. The cyathostomins are the most common nematode species affecting equids worldwide. Within this group of parasites are more than 50 different species. Until recent research activities, little was known about the contribution that individual species make to clinical disease, parasite epidemiology and anthelmintic resistance. This review describes some of the recent research advances in the understanding of cyathostomins in these areas. As part of the research effort, molecular tools were developed to facilitate identification of the non-parasitic stages of cyathostomins. These tools have proved invaluable in the investigation of the relative contributions that individual species make to the pathology and epidemiology of mixed infections. At the more applied level, research has also progressed in the development of a diagnostic test that will allow numbers of cyathostomin encysted larvae to be estimated. This test utilises cyathostomin-specific serum antibody responses as markers of infection. As anthelmintic resistance will be the major constraint on parasite control in future, researchers are actively investigating mechanisms of drug resistance and how to improve the detection of resistance in the field. Recent developments in these areas are also outlined.

Three recently recognized species of cyathostomes (Nematoda: Strongylidae) in equids in Kentucky

Three species of cyathostomes--Cylicocyclus ashworthi, Cylicostephanus bidentatus, and Cylicostephanus hybridus were identified recently in horses in Kentucky. General characteristics and distinguishing description of these species are presented. Distribution of these species and their role in the horse strongylid community are discussed. The importance of examining the entire contents of the large intestine or alternatively a high number of specimens in order to recover and identify species residing in low numbers is stressed.

New method for simultaneous species-specific identification of equine strongyles (nematoda, strongylida) by reverse line blot hybridization

The ability of a reverse line blot (RLB) assay to identify 13 common species of equine small strongyles (cyathostomins) and to discriminate them from three Strongylus spp. (large strongyles) was demonstrated. The assay relied on the specific hybridization of PCR-amplified intergenic spacer DNA fragments of the nuclear ribosomal DNA to membrane-bound species-specific probes. All cyathostomins examined were unequivocally identified and simultaneously discriminated from each other and from three large strongyles (Strongylus edentatus, Strongylus equinus, and Strongylus vulgaris). This assay will enable the accurate and rapid identification of equine cyathostomins irrespective of their life cycle stage, opening important avenues for a better understanding of their biology and epidemiology and of the pathogenesis of cyathostomin-associated disease. In particular, this RLB method promises to be a powerful diagnostic tool to determine the roles of individual species in the pathogenesis of mixed infections and to elucidate some aspects of cyathostominosis. Also, it could represent a basic step toward the development of a rapid and simple molecular test for the early detection of drug-resistant genotypes of horse strongyle species.

Molecular diagnosis and equine parasitology

The future implementation of improved and sustainable control strategies for the major equine parasites will be dependent on a greater insight into their basic biology, pathogenicity and epidemiology together with an enhanced ability for accurate diagnosis. This paper will provide a review of the current molecular methods under development for the detection of equine parasites and their application to current scientific questions. In particular, the strongyles are recognised as important pathogens of horses and recent advances made in the study of this parasitic group at the single species level will be addressed. The ribosomal (r)DNA region of the parasite genome has been employed to distinguish between closely related species. Molecular probes designed to this target region were used in combination with PCR technology to allow the identification of individual species within mixed infections. They have been applied to all parasite stages to look at the role of individual species in natural infection, disease and drug resistance. Similar techniques have been developed to detect other equine parasites and these will also be discussed. Further opportunities for employing existing techniques and the need for new diagnostic tools will be highlighted.

The use of nuclear ribosomal DNA markers for the identification of bursate nematodes (order Strongylida) and for the diagnosis of infections

Many bursate nematodes are of major importance to animal health. Animals are often parasitized by multiple species that differ in their prevalence, relative abundance and/or pathogenicity. Implementation of effective management strategies for these parasites requires reliable methods for their detection in hosts, identification to the species level and measurement of intensity of infection. One major problem is the difficulty of accurately identifying and distinguishing many species of bursate nematode because of the remarkable morphological similarity of their eggs and larvae. The inability to identify, with confidence, individual nematodes (irrespective of their life-cycle stage) to the species level by morphological methods has often led to a search for species-specific genetic markers. Studies over the past 15 years have shown that sequences of the internal transcribed spacers of ribosomal DNA provide useful genetic markers, providing the basis for the development of PCR-based diagnostic tools. Such molecular methods represent powerful tools for studying the systematics, epidemiology and ecology of bursate nematodes and, importantly, for the specific diagnosis of infections in animals and humans, thus contributing to improved control and prevention strategies for these parasites.

Identification of strongyle eggs from anthelmintic-treated horses using a PCR-ELISA based on intergenic DNA sequences

The efficacy of five daily fenbendazole (FBZ) treatments was tested against benzimidazole-resistant cyathostomins in naturally infected horses (n=13). Horses were treated with pyrantel embonate (PYR) to remove adult strongyles followed, 7 days later, by a 5-day course of FBZ. The PYR treatment produced an average faecal egg count reduction of 98%. All samples were negative by faecal egg count 7 days after the start of the FBZ treatment. Positive egg counts were observed from 28 days after the start of FBZ treatment and all horses displayed positive faecal egg counts by 77 days after treatment. Strongyle eggs were harvested from the faeces of the horses prior to treatment and then weekly from 42 to 70 days post-treatment. DNA was obtained from eggs in groups of ten. A PCR-ELISA, based on species-specific differences in intergenic DNA sequences, was used to identify the presence of six cyathostomin species. In pre-treatment samples, Cyathostomum catinatum was detected in nine out of the 13 horses and Cylicostephanus longibursatus, Cylicostephanus goldi and Cylicocyclus nassatus, were found in samples from eight animals. Cylicocyclus ashworthi and Cylicocyclus insigne were not detected pre-treatment. After anthelmintic treatment, C. catinatum and C. longibursatus were most frequently detected, followed by C. nassatus, C. goldi and C. ashworthi. C. insigne was detected at only one time point in a sample from a single horse.

Advances in developing molecular-diagnostic tools for strongyloid nematodes of equids: fundamental and applied implications

Infections of equids with parasitic nematodes of the order Strongylida (subfamilies Strongylinae and Cyathostominae) are of major veterinary importance. In last decades, the widespread use of drugs against these parasites has led to problems of resistance within the Cyathostominae, and to an increase in their prevalence and intensity of infection. Novel control strategies, based on improved knowledge of parasite biology and epidemiology, have thus become important. However, there are substantial limitations in the understanding of fundamental biological and systematic aspects of these parasites, which have been due largely to limitations in their specific identification and diagnosis using traditional, morphological approaches. Recently, there has been progress in the development of DNA-based approaches for the specific identification of strongyloids of equids for systematic studies and disease diagnosis. The present article briefly reviews information on the classification, biology, pathogenesis, epidemiology of equine strongyloids and the diagnosis of infections, highlights knowledge gaps in these areas, describes recent advances in the use of molecular techniques for the genetic characterisation, specific identification and differentiation of strongyloids of equids as a basis for fundamental investigations of the systematics, population biology and ecology.

A PCR–ELISA for the identification of cyathostomin fourth-stage larvae from clinical cases of larval cyathostominosis

We report the use of six oligoprobes designed from intergenic spacer region sequences to identify fourth-stage larvae (L4) of the tribe Cyathostominae. Oligoprobes were designed for identification of the following species: Cylicocyclus ashworthi, Cylicocyclus nassatus, Cylicocyclus insigne, Cyathostomum catinatum, Cylicostephanus goldi, and Cylicostephanus longibursatus. A seventh probe was designed as a positive control to identify all these members of the Cyathostominae. The intergenic spacer region was amplified by PCR using conserved primers. Initially, three oligoprobes were used in Southern blot analysis. To facilitate high-throughput identification, these and a further four oligoprobes were developed for use in a PCR-ELISA. All probes were validated for their ability to detect cyathostomin PCR products in the PCR-ELISA, using DNA from morphologically identified adult parasites. Initially, 712 L4 were isolated from the diarrhoeic faeces from horses (n=17) with clinical larval cyathostominosis. PCR products from 522 of these L4 were subjected to analysis, with 413 L4 being identified as one of the aforementioned species. With reference to individual species analysis, 28.5% of the 522 L4 were identified as C. longibursatus, 25.7% as C. nassatus, 15.9% as C. ashworthi, 7.3% as C. goldi and 1.7% as C. catinatum. No L4 were identified as being C. insigne species. When L4 within faeces from individual horses were compared, no sample was found to comprise parasites of one species. The least number of species identified in a single sample was two. This study suggests that clinical larval cyathostominosis is predominantly caused by mixed-species infections.

Equine cyathostome populations: accuracy of species composition estimations

Historically, surveys of equine parasites either are not quantitative in regard to prevalence and intensities of cyathostome species, or if quantitative, are estimates based on the identification of a very small sample of the population. Commonly 100-200 worms are identified. In the current study cyathostomes from 10 ponies were counted and identified to species in subsets of approximately 200 worms each from 5% aliquots of the large intestine contents until all worms in the aliquot were examined. A mean of 10.9+/-4.3 species were identified by examining 200 cyathostomes from each animal. This number increased to 25.2+/-2.6 species when the 5% aliquots were totally examined, indicating that prevalence rates from species with low intensities are probably much greater than previous survey data indicate. A statistical model was used to determine how many worms need to be identified to give a 95% confidence level that all species present are identified.

Recommended terminology and advances in the systematics of the Cyathostominea (Nematoda: Strongyloidea) of horses

Terminology for common names for the Tribe Cyathostominea (cyathostomins), and disease caused by the nematodes (cyathostominosis), were recommended to replace the previously used names cyathostomes and cyathostomosis, which are ambiguous, inaccurate or synonymous, by the Third Internal Workshop on the Systematics of Cyathostominea of Horses, held in Stresa, Italy, 28 August 2001. The progress by this international working group at three workshops is reviewed briefly and a list of publications is provided. Included are an annotated checklist by genus and species of 93 species level names and the recognition of 52 species, redescriptions of seven species, and the description of one new species. Upon petition by workshop participants, the International Commission on Zoological Nomenclature placed Cyathostomum tetracanthum Mehlis, 1831 on the "Official List of Specific Names in Zoology", ending more than a century of controversy over the names of cyathostomins. Some progress is described in molecular and morphological systematics and in the development of diagnostic molecular probes. A revised identification key is being prepared to the 52 species of the Tribe Cyathostominea.

Evaluation of the specificity of five oligoprobes for identification of cyathostomin species from horses

Here, we report evaluation of five oligoprobes designed from intergenic spacer (IGS) region sequences for identification of cyathostomin species. Oligoprobes were designed for identification of Cylicocyclus ashworthi, Cylicocyclus nassatus, Cylicostephanus longibursatus, Cylicostephanus goldi and a fifth probe designed to identify all members of this tribe. PCR amplification of IGS DNA from 16 cyathostomin species allowed sequence comparison and identification of four putative species-specific probes. Southern blotting of amplified products from 16 species showed that all probes were species-specific. The fifth probe recognised all 16 cyathostomin species but did not bind to members of the genus Strongylus. Furthermore, these probes were used to identify individual infective L3, eggs and L4 indicating that they will be invaluable to furthering the study of the epidemiology and pathogenesis of these important equine nematodes.

A comparison of the internal transcribed spacer of the ribosomal DNA for Eubothrium crassum and Eubothrium salvelini (Cestoda: Pseudophyllidea), parasites of salmonid fish

The internal transcribed spacers (ITS-1 and ITS-2) and 5.8S subunit of the ribosomal RNA gene of Eubothrium crassum and Eubothrium salvelini, cestode parasites of salmonid fish, were sequenced and compared. The lengths and GC contents of the regions sequenced were 1119 bp and 50.1% for E. crassum, and 1117 bp and 50.5% for E. salvelini, respectively. Sequence alignment and comparison of both taxa showed 97.9% similarity. Within the ITS-1 and ITS-2 of both species, the restriction enzymes MspI and Bsh1236I possessed different cleavage sites and could be employed for rapid differentiation of both species of Eubothrium by PCR-RFLP.

Larval cyathostomiasis

Over the past few years, cyathostomiasis has become increasingly recognized as a clinical problem of horses in the United States. Clinical cyathostomiasis has been reported frequently in Europe for a considerable time. This clinical syndrome is usually related to the sudden release of large numbers of the larval stages of small strongyles from the mucosa of the large intestine. Typical clinical signs include diarrhea, ventral abdominal edema, pyrexia, colic, weight loss, and poor body condition. Hypoalbuminemia and the presence of large numbers of small strongyles being passed in the feces are also characteristic features of the disease. The disease may occur seasonally in late winter and early spring or after drug treatment to remove the luminal stages of small strongyles. Two commercially available drugs, moxidectin and fenbendazole, have been shown to be effective against the encysted larval stages of the parasites. Drug resistance of small strongyles to all classes of currently available antiparasitic compounds except the macrocyclic lactones (ivermectin and moxidectin) is a limiting factor in controlling these parasites and may result in an increased prevalence of clinical cyathostomiasis over time.

Antimicrobic and anthelmintic resistance

Antimicrobial and anthelmintic resistance are growing issues for the equine practitioner. The development of antimicrobial or anthelmintic resistance is a source of significant concern because of increased frequency of treatment failures and increased treatment costs. In addition, antimicrobial resistance may have important consequences for public health. Only through judicious use can the efficacy of antimicrobials and anthelmintics be prolonged. This article discusses the development of resistance and suggestions for control.

Genomic and genetic research on bursate nematodes: significance, implications and prospects

Molecular genetic research on parasitic nematodes (order Strongylida) is of major significance for many fundamental and applied areas of medical and veterinary parasitology. The advent of gene technology has led to some progress for this group of nematodes, particularly in studying parasite systematics, drug resistance and population genetics, and in the development of diagnostic assays and the characterisation of potential vaccine and drug targets. This paper gives an account of the molecular biology and genetics of strongylid nematodes, mainly of veterinary socio-economic importance, indicates the implications of such research and gives a perspective on genome research for this important parasite group, in light of recent technological advances and knowledge of the genomes of other metazoan organisms.

Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference

In order to maximise the positional homology in the primary sequence alignment of the second internal transcribed spacer for 30 species of equine strongyloid nematodes, the secondary structures of the precursor ribosomal RNA were predicted using an approach combining an energy minimisation method and comparative sequence analysis. The results indicated that a common secondary structure model of the second internal transcribed spacer of these nematodes was maintained despite significant interspecific differences (2-56%) in primary sequences. The secondary structure model was then used to refine the primary second internal transcribed spacer sequence alignment. The 'manual' and 'structure' alignments were both subjected to phylogenetic analysis to compare the effect of using different sequence alignments on phylogenetic inference. The topologies of the phylogenetic trees inferred from the manual second internal transcribed spacer alignment were usually different to those derived from the structure second internal transcribed spacer alignment. The results suggested that the positional homology in the second internal transcribed spacer primary sequence alignment was maximised when the secondary structure model was taken into consideration.

Pathogenicity of cyathostome infection

Cyathostomes are now the principle parasitic pathogen of the horse: a remarkable transformation during the last 25 years from virtual obscurity to focus of attention in equine parasitology. This rise to prominence coincides with the marked decrease in prevalence of large strongyle infections as a result of widespread use of modern anthelmintic compounds. On the basis that strongyle-associated diseases continue to commonly occur in the absence of these large strongyle species, clinical attention has turned to the pathogenicity of cyathostomes. Although many horses harbour burdens of tens of thousands of cyathostomes without developing detectable illness, these parasites can result in an inflammatory enteropathy affecting the caecum and colon. Although the principle clinical effect of cyathostomosis is weight loss, affected individuals may exhibit other signs including diarrhoea and/or subcutaneous oedema and/or pyrexia. Clinical cyathostomosis occurs more commonly in young horses in late winter/early spring but there is lifelong susceptibility to cyathostomes and they can cause clinical disease in any age of horse during any season. Animals with cyathostomosis often develop hypoalbuminaemia and/or neutrophilia but there are no clinicopathological features specific for the disease. Experimental infections with cyathostomes have resulted in both clinical and pathological features similar to those of naturally-occuring cyathostomosis cases. From the experimental infection studies, it is evident that cyathostomes are pathogenic at times of both penetration into and emergence from the large intestinal mucosa. An unusual feature of cyathostome biology is the propensity for arrested larval development within the large intestinal mucosa for more than 2 years. From limited studies it appears that this arrested larval development is favoured by: feedback from luminal to mucosal worms; larger size of challenge dose of larvae and trickle (versus single bolus) infection. During arrested larval development cyathostomes have minimal susceptibility to all anthelmintic compounds, thus, limiting the effectiveness of therapeutic and/or control strategies. Although, the relative importance of individual cyathostomes is not known, the development of species-specific DNA methods for identification of cyathostomes provides a means by which the pathogenicity of different species might be established.