Genetic evidence for hybridisation between Haemonchus contortus and Haemonchus placei in natural field populations and its implications for interspecies transmission of anthelmintic resistance

Hybridization and introgression of the mitochondrial genome between the two species Anisakis pegreffii and A. simplex (s.s.) using a wide genotyping approach: evolutionary and ecological implications

Anisakis pegreffii and A. simplex (s.s.) are the two zoonotic anisakids infecting cetaceans as well as pelagic/demersal fish and squids. In European waters, A. pegreffii prevails in the Mediterranean Sea, while A. simplex (s.s.) in the NE Atlantic Ocean. Abiotic conditions likely play a significant role in shaping their geographical distribution. The Iberian Atlantic and Alboran Sea waters are sympatric areas of the two species. A total of 429 adults and L3 stage from both sympatric and allopatric areas were studied by a wide nuclear genotyping approach (including newly and previously found diagnostic single nucleotide polymorphisms (SNPs) at nuclear DNA (nDNA) and microsatellite DNA loci) and sequenced at mitochondrial DNA (mtDNA) cox2. Admixture between the two species was detected in the sympatric areas studied by STRUCTURE Bayesian analysis; NEWHYBRIDS revealed different categories of hybridization between the two species, representing approximately 5%. A tendency for F1 female hybrids to interbreed with the parental species at the geographical distribution limits of both species was observed. This finding suggests that hybridization occurs when the two parental species significantly differ in abundance. Mitochondrial introgression of A. simplex (s.s.) in A. pegreffii from Mediterranean waters was also detected, likely as a result of past and/or paleo-introgression events. The high level of genetic differentiation between the two species and their backcrosses indicates that, despite current hybridization, reproductive isolation which maintains evolutionary boundaries between the two species, exists. Possible causes of hybridization phenomena are attempted, as well as their evolutionary and ecological implications, also considering a sea warming scenario in European waters.

Abattoir Countrywide Survey of Dairy Small Ruminants' Haemonchosis in Greece and Associated Risk Factors

OBJECTIVES

The objectives of this study were to (i) determine the prevalence of Haemonchus contortus infections in dairy sheep and goats in continental and insular Greece, based on an abattoir survey, and (ii) to evaluate potential host-related risk factors including the age and sex, as well as the altitude, the management system, the co-existence of goats and sheep, the season, and the anthelmintic treatment, on the occurrence of haemonchosis.

METHODS

In total, 1004 abomasa of small ruminants were examined to evaluate the prevalence of Haemonchus spp. Moreover, a structured questionnaire was used to obtain relevant information regarding animal and farm characteristics. Haemonchus-like helminths were collected from the abomasa and used for the molecular species identification; a fragment of 321 base pairs of the internal transcribed spacer 2 sequence of nuclear DNA was amplified.

RESULTS

The prevalence of mono-species H. contortus infection of small ruminants was 37.2%. For sheep, a multivariable analysis revealed the anthelmintic treatment (treatment with pro/benzimidazoles), the age (lambs under 2 months old), and the management system (intensive management system) as significant factors for preventing H. contortus infection. Likewise, the management system (intensive management system), the anthelmintic treatment (treatment with macrocyclic lactones and their combination with pro/benzimidazoles), the altitude of the farms (farms located over 300 m above sea level), and the season (spring and summer) were significant risk factors in preventing H. contortus infection in goats.

CONCLUSION

These findings emphasize the urgent need for targeted management practices and region-specific veterinary protocols to effectively reduce parasitic burdens.

Insights into the genetic diversity of Angiostrongylus spp. causing human angiostrongyliasis and implications for molecular identification and diagnosis

Angiostrongylus cantonensis and Angiostrongylus costaricensis are known human pathogens responsible for eosinophilic angiostrongyliasis and abdominal angiostrongyliasis, respectively. Humans are accidental hosts, where infection occurs through the consumption of the infective larva stage 3 in intermediate or paratenic hosts. The proven method for abdominal angiostrongyliasis diagnosis is the histological examination through tissue biopsy, while the diagnosis of eosinophilic angiostrongyliasis is the detection of larva in the cerebrospinal fluid. As there is molecular evidence of cryptic species within A. cantonensis and A. costaricensis lineages, along with morphological similarities within both lineages, accurate species identification and disease diagnosis may be challenging. Moreover, species within the lineages share similar intermediate and definitive hosts and geographic distribution. For example, both A. cantonensis and Angiostrongylus malaysiensis (a closely related species in A. cantonensis lineage) overlap in their geographic distribution in Southeast Asia. Additionally, variations in the molecular makeup of A. costaricensis and A. cantonensis lineages may impact the pathogenicity, infectivity, and disease severity of angiostrongyliasis. Understanding of the genetic diversity of both lineages is a cornerstone for improved diagnosis and disease intervention, especially in a changing global environment. To shed light and provide insights into the genetic diversity of the Angiostrongylus lineages causing human angiostrongyliasis, we aim to present an up-to-date review of the studies conducted and genetic markers used for A. costaricensis and A. cantonensis lineages. The implications for accurate molecular identification and diagnosis of human angiostrongyliasis are also discussed.

Molecular insights versus morphological traits: rethinking identification of the closely related Angiostrongylus cantonensis and Angiostrongylus malaysiensis

BACKGROUND

The closely related Angiostrongylus cantonensis and Angiostrongylus malaysiensis have been reported to coexist in Thailand and share similar hosts and life cycles. Recently, in an angiostrongyliasis outbreak in Thailand, both A. cantonensis and A. malaysiensis were found in the cerebrospinal fluid of affected patients. Morphological similarities, overlapping distribution, shared hosts and habitats, and the close genetics of the two Angiostrongylus species can complicate accurate species identification. Addressing these challenges, this study aims to evaluate whether a correlation between the morphological and genetic identities of A. cantonensis and A. malaysiensis can improve species identification accuracy.

METHODS

Angiostrongylus spp. specimens from five zoogeographical regions in Thailand were subjected to morphological and molecular identification using the mitochondrial cytochrome b gene and the nuclear internal transcribed spacer 2 region (ITS2). The morphological characters for males and females were then validated using the species identity obtained from the nuclear ITS2 region.

RESULTS

The results revealed that morphological misidentifications between these two closely related species are common due to overlapping morphological characters. Although certain male traits such as body length and width aided species differentiation, female traits were found to be less reliable. Furthermore, hybrid forms (8.2%) were revealed through the ITS2 results, which can further complicate morphological identification. Mito-nuclear discordance was also present in 1.9% of the Angiostrongylus specimens from Thailand, suggesting a complex historical interbreeding between the species.

CONCLUSIONS

Based on our findings, we suggest that nuclear ITS2 is a reliable marker for species identification of A. cantonensis and A. malaysiensis, especially in regions where both species coexist. Additionally, the scope and consequences of hybridization between the two closely related Angiostrongylus species should be further investigated in Thailand.

Characterization and population genetics of Haemonchus contortus in Merino sheep in Lesotho

Haemonchus contortus is the most pathogenic and economically restrictive gastrointestinal nematode in the small ruminant industry globally. Morbidity, poor cross-bodily state, and mortality of sheep in Lesotho suggest the presence of H. contortus. The present study investigated the morphological, molecular, and population genetics of H. contortus third-stage larvae infecting sheep in four ecological zones (EZ) of Lesotho. Coprocultures were prepared for larval morphological identification and PCR determination. Larvae were identified morphologically as 100% H. contortus. The Second Internal Transcribed Spacer (ITS-2) gene of the ribosomal DNA of H. contortus isolates in the present study revealed nucleotide homology ranging from 97 to 100% when compared with selected GenBank reference sequences. Pairwise evolutionary divergence among H. contortus isolates was low, with 0.01318 recorded as the highest in the present study. Five haplotypes resulted from 14 Lesotho sequences. Haplotype diversity and nucleotide diversity were 0.76923 and 0.00590, respectively. Genetic differentiation among isolates was low but not statistically significant. An analysis of molecular variance revealed that most molecular variation was distributed within topographic populations at 94.79% (FST = 0.05206, p > 0.05) and 5.21% among populations. There was high gene flow and no definite population genetic structure among Lesotho isolates.

Advances in diagnosis of gastrointestinal nematodes in livestock and companion animals

Diagnosis of gastrointestinal nematodes in livestock and companion animals has been neglected for years and there has been an historical underinvestment in the development and improvement of diagnostic tools, undermining the undoubted utility of surveillance and control programmes. However, a new impetus by the scientific community and the quickening pace of technological innovations, are promoting a renaissance of interest in developing diagnostic capacity for nematode infections in veterinary parasitology. A cross-cutting priority for diagnostic tools is the development of pen-side tests and associated decision support tools that rapidly inform on the levels of infection and morbidity. This includes development of scalable, parasite detection using artificial intelligence for automated counting of parasitic elements and research towards establishing biomarkers using innovative molecular and proteomic methods. The aim of this review is to assess the state-of-the-art in the diagnosis of helminth infections in livestock and companion animals and presents the current advances of diagnostic methods for intestinal parasites harnessing (i) automated methods for copromicroscopy based on artificial intelligence, (ii) immunodiagnosis, and (iii) molecular- and proteome-based approaches. Regardless of the method used, multiple factors need to be considered before diagnostics test results can be interpreted in terms of control decisions. Guidelines on how to apply diagnostics and how to interpret test results in different animal species are increasingly requested and some were recently made available in veterinary parasitology for the different domestic species.

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

Effective gastrointestinal nematode (GIN) 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 GINs. 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 GIN 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 GINs 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 GIN 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 GIN 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 GIN egg embryonation in the lysis buffer storage solution lead to higher yields of DNA compared with ethanol-stored GIN eggs or faeces with GIN 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 GINs in their samples and contribute to large-scale GIN distribution and/or anthelmintic resistance surveys, is an important future direction for the FECPAK^G2 egg nemabiome metabarcoding approach.

Resistance of bovine gastrointestinal nematodes to four classes of anthelmintics in the semiarid region of Paraíba state, Brazil

The effectiveness of four anthelmintic classes on cattle gastrointestinal nematodes in the semi-arid region of Paraiba State, Brazil, was evaluated. Twenty farms were used, testing 40 animals in each one, totaling 800 animals. Cattle were divided into four groups composed with ten animals: I, treated with albendazole sulfoxide 15%; II, treated with ivermectin 1%; III, treated with closantel 25%; IV, treated with levamisole hydrochloride 7.5%. All treatments were administered subcutaneously. For the Fecal Egg Count Reduction Test (FECRT), individual fecal samples were collected on days 0 and 14, and sent for analysis of egg count per gram of feces (EPG) and larval cultures. It was observed that multiresistance was present in 95% (19/20) of the farms. Resistance to ivermectin and albendazole was observed in 95% (19/20), to closantel in 75% (15/20) and to levamisole in 20% (4/20). The most used management system was semi-intensive (75%; 15/20) and the ivermectin was the most reported drug for controlling helminths (65%; 13/20). Haemonchus spp. was the most prevalent helminth genus. It was concluded that the anthelmintic resistance of bovine gastrointestinal nematodes is high in the semi-arid of Paraíba State, Brazil, with multiresistance observed mainly to ivermectin, albendazole and closantel.

Genetic diversity and population structure of Haemonchus contortus in goats from Thailand

Haemonchus contortus is one of the most economically important parasitic nematodes affecting small ruminant livestock worldwide. This study was conducted to elucidate the genetic diversity and population structure of this nematode in Thailand based on mitochondrial DNA markers, the nicotinamide dehydrogenase subunit 4 (nad4) and the cytochrome c oxidase subunit 1 (cox1) genes. One hundred and thirty-six adult worms were obtained from 86 abomasa of slaughtered goats from 13 different localities in 5 regions of Thailand. Identification to the genus Haemonchus was done using morphology. DNA sequences of the nuclear ribosomal second internal transcribed spacer (ITS2) identified each specimen to species: three fixed nucleotide (SNP) differences distinguished H. contortus from H. placei. Genetic analysis defined 118 and 122 unique haplotypes in partial sequences of nad4 (alignment length 723 bp) and cox1 (645 bp) genes, respectively. Nucleotide diversities were 0.031 and 0.043 for nad4 and cox1 genes, respectively. Low genetic differentiation was observed among H. contortus samples from various provinces in Thailand. This is the first study on the genetic diversity and population structure of H. contortus of goats in Thailand. This study has provided insights into the transmission dynamics of this parasitic nematode, information which is essential for farm management and parasite control.

The first molecular identification of benzimidazole resistance in Haemonchus contortus from goats in Thailand

Background and Aim

Haemonchus contortus is one of the major trichostrongyloid nematodes affecting small ruminant production worldwide, especially in tropical and subtropical regions. Adult H. contortus suck the blood from the host abomasum leading to anemia and often death in heavily infected animals. The mainstay of parasitic control is an anthelmintic drug, but long-term drug use may cause drug resistance. The aim of this study was to examine benzimidazole resistance in H. contortus of goats from different regions in Thailand by detecting the frequency of the F200Y polymorphism in the β-tubulin isotype 1 gene.

Materials and Methods

A total of 121 H. contortus adults were obtained from 31 naturally infected out of 37 slaughtered goats from city abattoirs in five regions of Thailand. The frequency of the F200Y polymorphism in the β-tubulin isotype 1 gene was detected following the allele-specific polymerase chain reaction protocol.

Results

The overall genotype frequencies in Thailand were homozygous resistant (RR: 24%), heterozygous (SR: 44.6%), and homozygous susceptible (SS: 31.4%). The allele frequencies were resistant allele (R: 46%) and susceptible allele (S: 54%). The R allele frequency and the RR genotype varied from 30% to 65% and 0% to 43.9%, respectively. The frequency of R alleles was significantly higher in the southern region (0.65) as compared to northern (0.30, p=0.001), western (0.38, p=0.04), and central regions (0.30, p=0.03). The RR genotype was also significantly higher in the southern region (43.9%) versus the northern (0 %, p=0.001), western (11.8%, p=0.012), and central regions (17.4%, p=0.001).

Conclusion

This is the first study of the detection of single-nucleotide polymorphisms in codon 200 of the β-tubulin isotype 1 gene of H. contortus from goats in Thailand. These findings are essential and imply that an integrated approach is needed for issues such as drug treatment, farm management, prevention, and control strategies. This is of interest to farmers, veterinarians, and the department of livestock.

Susceptible trichostrongyloid species mask presence of benzimidazole-resistant Haemonchus contortus in cattle

Background

Benzimidazole (BZ) anthelmintics are widely used to control infections with parasitic nematodes, but BZ resistance is an emerging threat among several nematode species infecting humans and animals. In Sudan, BZ-resistant Haemonchus contortus populations were recently reported in goats in South Darfur State. The objective of this study was to collect data regarding the situation of BZ resistance in cattle parasitic nematodes in South Darfur using phenotypic and molecular approaches, besides providing some epidemiological data on nematodes in cattle.

Methods

The faecal egg count reduction test and the egg hatch test (EHT) were used to evaluate benzimidazole efficacy in cattle nematodes in five South Darfur study areas: Beleil, Kass, Nyala, Rehed Al-Birdi and Tulus. Genomic DNA was extracted from pools of third-stage larvae (L3) (n = 40) during trials, before and after treatment, and pools of adult male Haemonchus spp. (n = 18) from abattoirs. The polymorphisms F167Y, E198A and F200Y in isotype 1 β-tubulin genes of H. contortus and H. placei were analysed using Sanger and pyrosequencing.

Results

Prevalence of gastro-intestinal helminths in cattle was 71% (313/443). Reduced albendazole faecal egg count reduction efficacy was detected in three study areas: Nyala (93.7%), Rehed Al-Birdi (89.7%) and Tulus (88.2%). In the EHT, EC₅₀ values of these study areas ranged between 0.032 and 0.037 µg/ml thiabendazole. Genus-specific PCRs detected the genera Haemonchus, Trichostrongylus and Cooperia in L3 samples collected after albendazole treatment. Sanger sequencing followed by pyrosequencing assays did not detect elevated frequencies of known BZ resistance-associated alleles in codon F167Y, E198A and F200Y in isotype 1 β-tubulin gene of H. placei (≤ 11.38%). However, polymorphisms were detected in H. contortus and in samples with mixed infections with H. contortus and H. placei at codon 198, including E198L (16/58), E198V (2/58) and potentially E198Stop (1/58). All pooled L3 samples post-albendazole treatment (n = 13) were identified as H. contortus with an E198L substitution at codon 198.

Conclusions

To the knowledge of the authors, this is the first report of reduced albendazole efficacy in cattle in Sudan and is the first study describing an E198L substitution in phenotypically BZ-resistant nematodes collected from cattle.

Haemonchosis: A Challenging Parasitic Infection of Sheep and Goats

The paper reviews the challenges about haemonchosis-a significant and common parasitic infection of small ruminants. Haemonchus contortus is a highly pathogenic parasite that localises in the abomasum of affected animals and exerts its pathogenicity by blood-sucking activity, adversely affecting the health and productivity of animals. The first challenge is the uneven distribution of the infection globally, this being more prevalent in tropical and subtropical and warm temperate and summer rainfall regions than in cool and cold temperate and arid regions; hence, this leads in differences in the approaches required for its control. Another challenge is the widespread presence of Haemonchus strains resistant to the various anthelmintics available: Benzimidazoles, imidazothiazoles, macrocyclic lactones, closantel and monepantel, which makes the control of the infection difficult. The third challenge refers to the difficulty of diagnosing the disease, given that field evidence can provide suspicion about the infection, which needs to be subsequently confirmed by laboratory tests through parasitological or molecular techniques. The final challenge relates to the difficulties in the control of the infection and the necessity to use pharmaceutical products cautiously and with a planned approach, to avoid further development of anthelmintic resistance, also given that use of a recently licenced vaccine is not widespread. In conclusion, at the moment, we should be concerned, but not worried, about this infection, and apply correctly the appropriate health management plans.

Using cerebrospinal fluid to confirm Angiostrongylus cantonensis as the cause of canine neuroangiostrongyliasis in Australia where A. cantonensis and Angiostrongylus mackerrasae co-exist

Both Angiostrongylus cantonensis and Angiostrongylus mackerrasae have been identified along the east coast of Australia. A lack of A. mackerrasae genomic data until 2019, however, has precluded the unequivocal identification of the Angiostrongylus species responsible for neuroangiostrongyliasis in accidental hosts such as dog and man. The availability of a whole-genome data for A. mackerrasae, including mtDNA and ITS2 rDNA, enables discrimination of A. cantonensis from A. mackerrasae. The aim of this study was to develop diagnostic PCR assays to determine the species of Angiostrongylus based on the detection of Angiostrongylus DNA sequences in the cerebrospinal fluid (CSF) of canine patients with eosinophilic meningitis. An in silico workflow utilising available cytochrome c oxidase 1 (cox1) primers streamlined the laboratory work into empirical steps, allowing optimisation and selection of a PCR assay that met the required criteria for discrimination of A. cantonensis and A. mackerrasae DNA in low-template CSF samples. The adopted cox1 qPCR assay specifically amplified and enabled the differentiation of A. cantonensis from A. mackerrasae DNA and confirmed the presence of A. cantonensis DNA in 11/50 archived CSF samples. The DNA sequences demonstrated the presence of two distinct A. cantonensis cox1 haplotypes in dogs from eastern Australia. Species identification was further confirmed via the adoption of an ITS2 rDNA assay, providing confirmation of only A. cantonensis ITS2 rDNA in the CSF samples. To our knowledge, this is the first study to unequivocally demonstrate the antemortem presence of A. cantonensis DNA in CSF from clinically affected dogs. The study confirmed the long-held assumption that A. cantonensis is the causal agent of neuroangiostrongyliasis but refutes the dogma that there was a single introduction of A. cantonensis into Australia by the demonstration of two distinct A. cantonensis cox1 haplotypes.

Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm

Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants and has become a key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Here, we report using PacBio long-read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome for the MHco3(ISE).N1 isolate. We show a remarkable pattern of conservation of chromosome content with Caenorhabditis elegans, but almost no conservation of gene order. Short and long-read transcriptome sequencing allowed us to define coordinated transcriptional regulation throughout the parasite's life cycle and refine our understanding of cis- and trans-splicing. Finally, we provide a comprehensive picture of chromosome-wide genetic diversity both within a single isolate and globally. These data provide a high-quality comparison for understanding the evolution and genomics of Caenorhabditis and other nematodes and extend the experimental tractability of this model parasitic nematode in understanding helminth biology, drug discovery and vaccine development, as well as important adaptive traits such as drug resistance.

Haemonchus sp. in beef cattle in Brazil: species composition and frequency of benzimidazole resistance alleles

The aim of the present study was to investigate the occurrence of Haemonchus contortus and Haemonchus placei in beef cattle and the frequency of single nucleotide polymorphisms associated with benzimidazole (BZ)-resistance in Haemonchus spp. in Brazil. For such, fecal samples were collected from 61 beef cattle ranches in 11 Brazilian states. Third-stage larvae (L3) were produced for morphological species identification and DNA extraction. PCR was performed for the analysis of the isotype 1 β-tubulin gene and the products were sequenced to confirm the presence of H. placei and H. contortus. For each field population, pyrosequencing assays were performed to quantify the frequency of the F167Y, E198A and F200Y polymorphisms in the isotype-1 β-tubulin gene. The results of the morphometric analysis of 2345 larvae showed that H. placei was present on all ranches. The analysis of the isotype 1 β-tubulin gene confirmed 100% prevalence for H. placei and 23.7% for H. contortus. Pyrosequencing assays demonstrated single-nucleotide polymorphisms (SNPs) associated with BZ-resistance in all three codons (F167Y, E198A and F200Y) of the isotype 1 β-tubulin gene in H. placei field populations. Frequencies of resistance-associated alleles above background (≥ 15%) were found for at least one codon in 11.4% of the field isolates and maximum frequencies of 30, 21 and 29% were found for codons 167, 198 and 200, respectively, on individual ranches. This study confirms the presence of H. contortus in beef cattle in the major livestock farming states in Brazil and demonstrates that genotypes associated with BZ resistance are present in field populations of Haemonchus spp..

Contrasting patterns of isotype-1 β-tubulin allelic diversity in Haemonchus contortus and Haemonchus placei in the southern USA are consistent with a model of localised emergence of benzimidazole resistance

The benzimidazoles are one of the most important broad-spectrum anthelmintic drug classes for parasitic nematode control in domestic animals and humans. They have been widely used in livestock, particularly in small ruminants for over 40 years. This has resulted in widespread resistance in small ruminant gastrointestinal nematode parasite species, especially Haemonchus contortus. Benzimidazole resistance mutations have also been reported in Haemonchus placei, but only at low frequencies, suggesting resistance is at a much earlier stage of emergence than is the case for H. contortus. Here, we investigate the haplotype diversity of isotype-1 β-tubulin benzimidazole resistance mutations and the population genetic structure of H. contortus and H. placei populations from sheep and cattle from the southern USA. Microsatellite genotyping revealed a low level of genetic differentiation in six H.placei and seven H. contortus populations examined. This is consistent with several previous studies from other regions, mainly in H. contortus, supporting a model of high gene flow between parasite populations. There was a single F200Y(TAC) haplotype present in all six H. placei populations across Georgia, Florida and Arkansas. In contrast, there were at least two different F200Y(TAC) haplotypes (up to four) and two different F167Y(TAC) haplotypes across the seven H. contortus populations studied. These results provide further evidence to support a model for benzimidazole resistance in Haemonchus spp, in which resistance mutations arise from a single, or the small number of locations, in a region during the early phases of emergence, and subsequently spread due to animal movement.

A multi-restriction fragment length polymorphism genotyping approach including the beta-tubulin gene as a new differential nuclear marker for the recognition of the cryptic species Anisakis simplex s.s. and Anisakis pegreffii and their hybridization events

The detection of Anisakis simplex s.s./A. pegreffii putative hybrids has been a controversial issue in spite of the fact that natural hybridization is an extended process across free living and parasitic organisms. Differential traits of biomedical and ecological importance, such as invasive and allergenic potential have been demonstrated in both cryptic species. Therefore, in this work, we discuss about the potential for hybridization between these anisakid species in sympatric zones, implementing a multi-marker Restriction fragment length polymorphism (RFLP) genotyping approach based on the ribosomal DNA internal transcribed spacer 1 (ITS1), the mitochondrial cytochrome C oxidase 2 (Cox-2) and a new nuclear marker, the highly conserved β-tubulin gene (β-TUB). The two cryptic species differed at least in 7 bp in the β-TUB gene and some larvae with heterozygous genotypes at the 7 diagnostic nucleotide positions were found. Taxonomic, population and genealogical analyses served to support the occurrence of hybridization between both species. Predicted restriction endonucleases enzymes were assayed for Cox-2 and β-TUB markers. The implemented multi-marker PCR-RFLP allowed us to detect the two pure parental species, F1 hybrids, hybrid backcrossed progeny and individuals with nuclear-mitochondrial discordance, being a useful, simple and reproducible procedure in any laboratory for epidemiological studies.

Frequency of Resistance to Benzimidazoles of Haemonchus contortus Helminths from Dairy Sheep, Goats, Cattle and Buffaloes in Greece

The study investigated the presence of resistance to benzimidazoles in Haemonchus contortus helminths from ruminant species in Greece through the detection of the Phe/Tyr polymorphism in the amino acid at position 200 of the β-tubulin protein. In total, 288 adult female H. contortus helminths collected from the abomasum of various ruminant animals in Greece were tested. Of these, 96 were collected from sheep, 96 from goats, 48 from cattle, and 48 from buffaloes. The frequencies of the homozygous and heterozygous resistant genotypes at the position 200 of the β-tubulin gene of helminths recovered from sheep were 96.9% and 3.1%, respectively. The frequencies of the homozygous and heterozygous resistant genotypes, respectively, were 100.0% and 0.0% in helminths from goats, 25.0% and 75.0% in helminths from cattle and 8.3% and 91.7% in helminths from buffaloes. In all parasitic populations, no homozygous susceptible genotypes were detected. The present study highlighted, for the first time, the emergence of benzimidazole-resistant H. contortus in goats, cattle, and buffaloes in Greece, using an allele-specific PCR. It is postulated that benzimidazole-resistant alleles were transferred from sheep or goats to cattle and buffaloes at the commonly grazing pastures in Greece.

Large scale screening for benzimidazole resistance mutations in Nematodirus battus, using both pyrosequence genotyping and deep amplicon sequencing, indicates the early emergence of resistance on UK sheep farms

Benzimidazoles (BZ) have been the anthelmintic of choice for controlling Nematodirus battus infections since their release in the 1950s. Despite heavy reliance on this single anthelmintic drug class, resistance was not identified in this nematode until 2010 (Mitchell et al., 2011). The study aimed to explore the prevalence of BZ-resistance mutations in N. battus from UK sheep flocks using deep amplicon sequencing and pyrosequencing platforms. Based on evidence from other gastrointestinal nematodes, resistance in N. battus is likely to be conferred by single nucleotide polymorphisms (SNP) within the β-tubulin isotype 1 locus at codons 167, 198 and 200. Pyrosequencing and deep amplicon sequencing assays were designed to identify the F167Y (TTC to TAC), E198A (GAA to GCA) and F200Y (TTC to TAC) SNPs. Nematodirus battus populations from 253 independent farms were analysed by pyrosequencing; 174 farm populations were included in deep amplicon sequencing and 170 were analysed using both technologies. F200Y was the most prevalent SNP identified throughout the UK, in 12-27% of the populations tested depending on assay, at a low overall individual frequency of 2.2 ± 0.6% (mean ± SEM, based on pyrosequencing results). Four out of the five populations with high frequencies (>20%) of the F200Y mutation were located in NW England. The F167Y SNP was identified, for the first time in this species, in four of the populations tested at a low frequency (1.2% ± 0.01), indicating the early emergence of the mutation. E198A or E198L were not identified in any of the isolates. Results obtained were comparable between both techniques for F200Y (Lins' CCC, r_c = 0.96) with discrepancies being limited to populations with low frequencies. The recent emergence of resistance in this species will provide a unique opportunity to study the early stages of anthelmintic resistance within a natural setting and track its progress in the future.

Field and Molecular Evaluation of Anthelmintic Resistance of Nematode Populations from Cattle and Sheep Naturally Infected Pastured on Mixed Grazing areas at Rio Grande do Sul, Brazil

BACKGROUND

Reports of a lack of efficacy of most of the anthelmintic compounds for ruminants associated with the long-time necessity for creating new molecules have stressed the urgency to adopt alternative methods to control gastrointestinal parasites infection, such as strategies of sharing grazing areas. Therefore, this study aimed to evaluate nematode populations affecting cattle and sheep that share grazing areas before and after treatment with different anthelmintic compounds, and investigate the efficacy of anthelmintic treatment in these naturally infected ruminants at farms in the state of Rio Grande do Sul, Brazil.

METHODS

The presence of co-infections by Haemonchus species was investigated by polymerase chain reaction (PCR) for groups treated with a benzimidazole. Farms were selected by: farmers' consent, presence of 42-60 (or more) calves and sheep per farm with counts of ≥ 200 eggs per gram of feces (EPG), availability of calves and lambs aging from 6 to 9 months, absence of anthelmintic treatment for both species for 60 days before the experimental period, and shared grazing areas between this species on each farm. Animals were distributed into six treatment groups for each ruminant species per farm and treated with: ivermectin, doramectin, moxidectin, levamisole, albendazole, and closantel.

RESULTS

Levamisol was the most effective anthelmintic compound for both ruminant species. In general, Cooperia spp., Haemonchus spp., and Trichostrongylus spp. were the genus present after tested treatments that were ineffective. PCR showed the presence of Haemonchus species co-infections between cattle and sheep.

CONCLUSION

Therefore, this study demonstrated the similarity between nematode population, the presence of multi-resistant nematodes, and the presence of Haemonchus species co-infections affecting different ruminant species that share pastures.

Is there competition between Haemonchus contortus and Haemonchus placei in a pasture grazed by only sheep?

This study aimed to evaluate the dynamics of Haemonchus contortus and Haemonchus placei infections and hybridization between these species in grazing sheep without contact with cattle. On January 14, 2014, sixteen young sheep were infected with 4000 infective H. placei third-stage larvae L3; 11 days later, another group n = 16 was infected with 4000 H. contortus L3. The establishment rates of H. contortus and H. placei L3 were, on average, 61.6 % and 56.8 %, respectively, in the permanent sheep. After the establishment of patent infections, all permanent sheep were allocated together in the same clean pasture where they grazed for the next 12 months. Euthanasia of a sample of the permanent sheep was performed every three months: in May, August, November and February. Two weeks before the sheep were removed for euthanasia, 2 worm-free tracer sheep were introduced to the pasture to evaluate the larval population in the field. The tracer sheep grazed alongside the permanent sheep for 2 weeks. Then, they were housed indoors for 20 days; at the end of this period, they were euthanized. Parasites were recovered from the permanent and tracer sheep and identified using morphological and molecular techniques. A total of 432 worms (from permanent and tracer animals) were analyzed by PCR using species-specific primer pairs. Of these specimens, only two (0.46 %) male worms were identified as hybrids: one was recovered from a permanent animal euthanized in August and the other from a tracer sheep that grazed in May. The last detection of adult H. placei worms occurred in sheep euthanized in May (approximately 3.5 months after the beginning of the grazing period). The morphological evaluation of the L3 produced in fecal cultures showed that H. placei were progressively replaced by H. contortus populations starting in March. The last trace of H. placei L3 was found in August, when a small percentage (0.5 %) of infective larvae with H. placei morphology was identified in a fecal culture. In conclusion, hybridization between H. contortus and H. placei can occur in the field during coinfection. It was demonstrated that H. placei established successfully in artificially infected worm-free sheep; however, with concomitant natural reinfection with H. contortus, the H. placei population showed a rapid decrease and was eliminated within a few months in an environment without cattle.

Development and field evaluation of a species-specific mt-COI targeted SYBR-Green Real Time PCR for detection and quantification of Haemonchus contortus in cattle in Turkey

Haemonchus contortus is one of the most important gastrointestinal nematodes (GINs) infecting sheep, goats, and cattle worldwide. We developed a SYBR Green real-time PCR (qPCR) assay for detection and quantification of H. contortus by using specific primers based on a conserved region of the mitochondrial cytochrome oxidase subunit I (mt-COI) gene, and evaluated this technique in the detection of H. contortus infections in cattle in Central Anatolia Region of Turkey. The newly developed qPCR assay successfully discriminated H. contortus from other GIN species infecting cattle in the specificity evaluations, with a specific melt peak of 77.5 °C. Our results revealed the efficient amplification of the proposed target COI region within the range of plasmid copies, from 2 × 10⁶ to 2 × 10¹ per μl, with 96.9 % efficiency, R² value of 0.999, and a slope of -3.398. Among the 920 cattle fecal samples from the field, 58 samples (6.3 %) were positive with qPCR assay, whereas 45 samples (4.9 %) were positive, as determined by larval culture, suggesting the utility of SYBR Green qPCR. Phylogenetic characterization of the partial COI gene of H. contortus isolates was also evaluated for 100 eggs and third stage larvae recovered from positive cattle faecal samples, which were verified with the qPCR assay prior to analyses. COI sequences were classified into three haplotypes (THC1 to THC3) with intraspecific nucleotide differences of 0.50 to 0.76 %. Phylogenetic analyses revealed that the haplotypes grouped with H. contortus isolates from several countries in a monophyletic cluster, with evidence of at least two main haplogroups. Overall, the SYBR Green qPCR assay was highly specific and sensitive, suggesting that it can be used for screening of H. contortus infections in livestock populations in epidemiological studies and the control of this important parasite.

Development of a deep amplicon sequencing method to determine the species composition of piroplasm haemoprotozoa

Piroplasmosis is caused by tick-borne haemoprotozoa of the genera Theileria and Babesia. These parasitic infections can seriously impact on the health of livestock and production. Piroplasms of multiple species can be present in a single host, but reliable molecular diagnostic tools are needed in order to understand the composition of these complex parasite communities. Theileria and Babesia vary in their epidemiology, drug sensitivity, pathogenicity and interaction with co-infecting species, but are similar in that infected animals become persistent carriers after recovery from primary infection, acting as reservoir hosts. Here, we describe for the first time the use of a deep amplicon sequencing platform to identify proportions of piroplasm species in co-infecting communities and develop the concept of a "haemoprotobiome". First, four phenotypically-verified species of Theileria and Babesia were used to prepare mock DNA pools with random numbers of the parasites amplified by four different numbers of PCR cycles to assess sequence representation for each species. Second, we evaluated the detection threshold of the deep amplicon sequencing assay for each of the four species and to assess the accuracy of proportional quantification of all four species. Finally, we applied the assay to the field samples to afford insight of the species composition of piroplasm communities in small and large ruminants in the Punjab province of Pakistan. The "haemoprotobiome" concept has several potential applications in veterinary and human research, including understanding of responses to drug treatment; parasite epidemiology and ecology; species interactions during mixed infections; and parasite control strategies.

Emergence and the spread of the F200Y benzimidazole resistance mutation in Haemonchus contortus and Haemonchus placei from buffalo and cattle

Benzimidazoles have been intensively (for over 40 years) used in the livestock sector, particularly in small ruminants. This has been led to the widespread emergence of resistance in a number of small ruminant parasite species, especially Haemonchus contortus. In many countries benzimidazole resistance has severely compromised the control of H. contortus in small ruminants; but there is a little information on benzimidazole resistance in H. contortus infecting buffalo and cattle. Resistance to benzimidazoles have also been reported in the large ruminant parasite, Haemonchus placei, but again there is relatively little information on its prevalence. Hence it is very important to understand how resistance-conferring mutations emerge and spread in both parasites in buffalo and cattle hosts in order to develop approaches for the recognition of the problem at an early stage of its development. The present study suggests that the F200Y (TAC) mutation is common in H. contortus, being detected in 5/7 populations at frequencies between 7 and 57%. Furthermore, 6/10 H. placei populations contained the F200Y (TAC) mutation, albeit at low frequencies of between 0.4 and 5%. The phylogenetic analysis suggests that the F200Y (TAC) mutation in H. contortus has emerged on multiple occasions in the region, with at least three independent emergences across the populations. In contrast, the F200Y (TAC) resistance-conferring mutation in H. placei is only seen on a single haplotype. A high level frequency of the resistance haplotypes in the region, suggests that the unique resistance conferring-mutation has spread from a single emergence; likely by anthropogenic animal movement. Overall, these results provide the first clear genetic evidence for the spread of benzimidazole resistance-conferring mutations to multiple different locations from a single emergence in H. placei; while being consistent with previous small ruminant-based observations of multiple emergence of resistance mutations in H. contortus.

Establishment of co-infection and hybridization of Haemonchus contortus and Haemonchus placei in sheep

This study aimed to evaluate the simultaneous infections of Haemonchus contortus and Haemonchus placei in sheep, as well as the production of hybrids. A parental group of lambs (n = 6) were mix-infected with 2000 infective larvae (L3) of H. placei and 2000 L3 of H. contortus. Faecal samples were taken from each of these six lambs to produce the first generation of L3 (F1-L3) in individual cultures. These F1-L3 were used to infect 12 lambs; six of them were euthanized at 42 days (Group F1-42) and six at 84 days (Group F1-84) post infection. Polymerase chain reaction (PCR) analysis, using species-specific primer pairs, was the gold standard method for identification of Haemonchus adult species and hybrids. The establishment rate of both species was similar in the parental group: 51.7% H. contortus and 48.3% H. placei. Of the 219 adult specimens from groups F1-42 and F1-84 analysed by PCR, eight (3.65%) were hybrids, 111 were H. contortus and 100 were H. placei. The morphological evaluation of the F1-L3 from the parental group showed a predominance of larvae with H. contortus size (51.5%) in comparison with H. placei (42.8%). In the second generation of L3 (F2-L3) produced by the F1-lambs, larvae with H. contortus morphology predominated, with 81.5% in the F1-42 group and 84.0% in the F1-84 group. In conclusion, an artificial mixed infection by H. contortus and H. placei was established in lambs and resulted in the production of a small number of hybrids among their offspring.

Population genetics of benzimidazole-resistant Haemonchus contortus and Haemonchus placei from buffalo and cattle: implications for the emergence and spread of resistance mutations

The population genetics of nematode parasites are poorly understood with practical reference to the selection and spread of anthelmintic resistance mutations. Haemonchus species are important to study the nematode population genetics due to their clinical importance in ruminant livestock, and the availability of genomic resources. In the present study, it has been examined that Haemonchus contortus and Haemonchus placei populations from three buffalo and nine cattle hosts. Seventy-three individual adult worms of H. contortus and 148 of H. placei were analysed using a panel of seven microsatellite markers. The number of alleles per locus in H. contortus and H. placei indicated that all populations were polymorphic for the microsatellites used in the present study. Genetic diversity parameters included high levels of allelic richness and heterozygosity, indicating effective population sizes, high mutation rates and high transmission frequencies in the area. Genetic structure parameters revealed low genetic differentiation between and high levels of genetic variation within H. contortus and H. placei populations. Population dynamic analyses showed an absence of heterozygosity excess in both species, suggesting that there was no deviation from genetic drift equilibrium. Our results provide a proof of concept for better understanding of the consequences of specific control strategies, climatic change or management strategies on the population genetics of anthelmintic resistance alleles in Haemonchus spp. infecting co-managed buffalo and cattle.

Helminth infections and hybridization between Haemonchus contortus and Haemonchus placei in sheep from Santana do Livramento, Brazil

The occurrence and intensity of helminth infections were evaluated in sheep from pastures shared with cattle. In 2015 and 2016, young male sheep acquired in Santana do Livramento, Rio Grande do Sul, Brazil, were finished in integrated crop-livestock system. We selected the 12 sheep that showed the highest number of nematode eggs per gram of faeces to search for worms in the gastrointestinal tract. Haemonchus contortus and Trichostrongylus colubriformis were the major parasites. H. contortus presented mean intensities of 1,159 and 257 worms in 2015 and 2016, respectively. T. colubriformis displayed mean intensities of 4,149 and 2,427 worms in 2015 and 2016, respectively. Of the 127 male specimens of Haemonchus spp. analysed by Polymerase Chain Reaction (PCR), 125 were H. contortus, one Haemonchus placei and one hybrid. Other species detected were Cooperia punctata , Cooperia pectinata, Cooperia spatulata, Cooperia curticei, Ostertagia ostertagi, Teladorsagia circumcincta , Trichostrongylus axei, Nematodirus spathiger , and Trichuris ovis. Twenty lambs presented cysts of Taenia hydatigena in the liver and mesentery. One lamb presented Coenurus cerebralis, the larval stage of Taenia multiceps, in the brain. In conclusion, sheep from pasture shared with cattle presented a high diversity of nematode species. H. contortus and H. placei co-infection occur with consequent hybridization.

Molecular marker sequences of cattle Cooperia species identify Cooperia spatulata as a morphotype of Cooperia punctata

The genus Cooperia includes important parasites of ruminants and currently contains 34 accepted species. However, even for those species infecting livestock, there is a considerable lack of molecular information and many species are only identifiable using subtle morphological traits. The present study aimed to provide molecular data to allow diagnosis of Cooperia species infecting cattle. Partial sequences of two mitochondrial (cytochrome oxidase 2, 12S rRNA gene) and two nuclear genes (isotype 1 β tubulin gene including two introns, internal transcribed spacers (ITS) were obtained from morphologically identified specimens of Cooperia pectinata, Cooperia punctata and Cooperia spatulata as well as from larvae of pure Cooperia oncophora and C. punctata laboratory isolates. Pairwise identity of ITS-2 sequences was very high and it was the only region able to identify a specimen as Cooperia sp. However, the ITS-2 was unreliable for diagnosis at the species level. All other marker sequences could not unequivocally be allocated to the genus Cooperia but allowed clear species identification with the exception of the pair C. punctata/C. spatulata for which no significant differences were found for any marker sequence. Maximum-likelihood phylogenetic analyses of individual genes as well as a multi-locus analysis covering all four sequences confirmed that specimen identified as C. spatulata were randomly distributed throughout the C. punctata cluster and formed no group of their own. In contrast, the other Cooperia species formed clearly separated and statistically supported clusters. These data indicate that C. spatulata is most likely only a morphotype of C. punctata and the name should be considered a synonym. Combinations of nuclear and mitochondrial markers should be used to identify morphotypes or cryptic species to benefit from excellent barcoding properties of the latter but allowing proper phylogenetic analyses and controlling for lineage sorting that might occur for mitochondrial genotypes within a species.

High species diversity of trichostrongyle parasite communities within and between Western Canadian commercial and conservation bison herds revealed by nemabiome metabarcoding

Background

Many trichostrongylid nematode species are reported to infect bison, some of which are major causes of disase and production loss in North American bison herds. However, there is little information on the species distribution and relative abundance of these parasites in either commercial or conservation herds. This is largely because trichostrongylid nematode species cannot be distinguished by visual microscopic examination of eggs present in feces. Consequently, we have applied ITS2 rDNA nemabiome metabarcoding to describe the trichostrongyle parasite species diversity in 58 bison production groups derived from 38 commercial North American plains bison (Bison bison bison) herds from across western Canada, and two bison conservation herds located in Elk Island National Park (EINP) [plains bison and wood bison (Bison bison athabascae)] and one in Grasslands National Park (GNP) (plains bison).

Results

We report much higher infection intensities and parasite species diversity in commercial bison herds than previously reported in beef cattle herds grazing similar latitudes. Predominant trichostrongyle parasite species in western Canadian commercial bison herds are those commonly associated with Canadian cattle, with Ostertagia ostertagi being the most abundant followed by Cooperia oncophora. Combined with high fecal egg counts in many herds, this is consistent with significant clinical and production-limiting gastrointestinal parasitism in western Canadian bison herds. However, Haemonchus placei was the most abundant species in five of the production groups. This is both surprising and important, as this highly pathogenic blood-feeding parasite has not been reported at such abundance, in any livestock species, at such northerly latitudes. The presence of Trichostrongylus axei as the most abundant parasite in four herds is also unusual, relative to cattle. There were striking differences in parasite communities between the EINP and commercial bison herds. Most notably, Orloffia bisonis was the predominant species in the wood bison herd despite being found at only low levels in all other herds surveyed.

Conclusions

This study represents the most comprehensive description of parasite communities in North American bison to date and illustrates the power of deep amplicon sequencing as a tool to study species diversity in gastrointestinal nematode communities.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-2880-y) contains supplementary material, which is available to authorized users.

Opportunities and challenges for modelling epidemiological and evolutionary dynamics in a multihost, multiparasite system: Zoonotic hybrid schistosomiasis in West Africa

Multihost multiparasite systems are evolutionarily and ecologically dynamic, which presents substantial trans-disciplinary challenges for elucidating their epidemiology and designing appropriate control. Evidence for hybridizations and introgressions between parasite species is gathering, in part in line with improvements in molecular diagnostics and genome sequencing. One major system where this is becoming apparent is within the Genus Schistosoma, where schistosomiasis represents a disease of considerable medical and veterinary importance, the greatest burden of which occurs in sub-Saharan Africa. Interspecific hybridizations and introgressions bring an increased level of complexity over and above that already inherent within multihost, multiparasite systems, also representing an additional source of genetic variation that can drive evolution. This has the potential for profound implications for the control of parasitic diseases, including, but not exclusive to, widening host range, increased transmission potential and altered responses to drug therapy. Here, we present the challenging case example of haematobium group Schistosoma spp. hybrids in West Africa, a system involving multiple interacting parasites and multiple definitive hosts, in a region where zoonotic reservoirs of schistosomiasis were not previously considered to be of importance. We consider how existing mathematical model frameworks for schistosome transmission could be expanded and adapted to zoonotic hybrid systems, exploring how such model frameworks can utilize molecular and epidemiological data, as well as the complexities and challenges this presents. We also highlight the opportunities and value such mathematical models could bring to this and a range of similar multihost, multi and cross-hybridizing parasites systems in our changing world.

A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry

The parasitic nematode Haemonchus contortus is an economically and clinically important pathogen of small ruminants, and a model system for understanding the mechanisms and evolution of traits such as anthelmintic resistance. Anthelmintic resistance is widespread and is a major threat to the sustainability of livestock agriculture globally; however, little is known about the genome architecture and parameters such as recombination that will ultimately influence the rate at which resistance may evolve and spread. Here, we performed a genetic cross between two divergent strains of H. contortus, and subsequently used whole-genome resequencing of a female worm and her brood to identify the distribution of genome-wide variation that characterizes these strains. Using a novel bioinformatic approach to identify variants that segregate as expected in a pseudotestcross, we characterized linkage groups and estimated genetic distances between markers to generate a chromosome-scale F1 genetic map. We exploited this map to reveal the recombination landscape, the first for any helminth species, demonstrating extensive variation in recombination rate within and between chromosomes. Analyses of these data also revealed the extent of polyandry, whereby at least eight males were found to have contributed to the genetic variation of the progeny analyzed. Triploid offspring were also identified, which we hypothesize are the result of nondisjunction during female meiosis or polyspermy. These results expand our knowledge of the genetics of parasitic helminths and the unusual life-history of H. contortus, and enhance ongoing efforts to understand the genetic basis of resistance to the drugs used to control these worms and for related species that infect livestock and humans throughout the world. This study also demonstrates the feasibility of using whole-genome resequencing data to directly construct a genetic map in a single generation cross from a noninbred nonmodel organism with a complex lifecycle.

A panel of microsatellite markers to discriminate and study interactions between Haemonchus contortus and Haemonchus placei

Haemonchus contortus and Haemonchus placei are two closely related economically important parasites of ruminants. Their close morphological similarity, common occurrence as co-infections and ability to hybridize makes definitive diagnosis and epidemiological studies in field populations challenging. In this paper, we describe the development of a panel of microsatellite markers that can be used to discriminate and study the genetics of these two parasite species in co-infections and mixed field populations. We have identified two additional microsatellites (Hp52 and Hp53), in addition to three previously reported microsatellites (Hcms3561, Hcms53265 and Hcms36) that have a discrete set of alleles between the two species. Multilocus genotyping of worms with this 5 marker panel from 3 geographically diverse H. placei isolates and 4 geographically diverse H. contortus populations allows unambiguous species assignment of individual worms. This panel of markers should provide a valuable resource in studying the biology and epidemiology of these important ruminant parasite species in the field.

A novel snapback primer probe assay for the detection and discrimination of sympatric Haemonchus species using DNA melting analysis

Different sympatric species of Haemonchus parasites infecting ruminants and camels can be distinguished morphologically, but involves tedious microscopic examinations, measurements and several other limitations. Information on internal transcribed spacer-2 (ITS-2) sequence provides confirmatory differentiation of sympatric Haemonchus species. The present study introduces a novel, snapback primer probe based, real time PCR assay for the differentiation of three sympatric Haemonchus species, H. contortus (Hco), H. placei (Hpl) and H. longistipes (Hlo). The assay was designed to amplify a region of 130bp within the ITS-2 gene that included three diagnostic mutational sites capable of discriminating Hco, Hpl and Hlo. Following melt curve analysis, species-specific diagnostic melt peaks were obtained for Hco, Hpl and Hlo with a mean melting temperature of 56.6±0.3°C, 64.4±0.1°C and 54.4±0.1°C respectively. The test for analytical sensitivity revealed the ability of the assay to detect up to 5 copies per reaction. To evaluate the discriminating power of the assay, 174 samples from adult worms and 3rd stage larvae belonging to different Haemonchus species and various other nematode species including Cooperia curticei, Trichostrongylus axei, Trichostrongylus colubriformis, and Teladorsagia circumcincta were tested. Additionally, DNA extracted from 25 fecal egg samples was also tested and the specificity of the assay was verified by sequencing the ITS-2 gene of all the Haemonchus positive and non-Haemonchus samples. The assay worked accurately with 100% specificity in at least three real time PCR platforms. The assay is an effective alternative to the sequencing approach and is expected to be helpful for the screening of individual adult and larval Haemonchus parasites. However, caution needs to be applied while interpreting the results from fecal egg samples due to varying levels of sympatric co-infections from different Haemonchus species. The present study is the first report on the application of snapback primer probe methodology for the differentiation of nematode parasites.

Evolution and Biogeography of Haemonchus contortus: Linking Faunal Dynamics in Space and Time

History is the foundation that informs about the nuances of faunal assembly that are essential in understanding the dynamic nature of the host-parasite interface. All of our knowledge begins and ends with evolution, ecology and biogeography, as these interacting facets determine the history of biodiverse systems. These components, relating to Haemonchus, can inform about the complex history of geographical distribution, host association and the intricacies of host-parasite associations that are played out in physiological and behavioural processes that influence the potential for disease and our capacity for effective control in a rapidly changing world. Origins and evolutionary diversification among species of the genus Haemonchus and Haemonchus contortus occurred in a complex crucible defined by shifts in environmental structure emerging from cycles of climate change and ecological perturbation during the late Tertiary and through the Quaternary. A history of sequential host colonization associated with waves of dispersal bringing assemblages of ungulates from Eurasia into Africa and processes emerging from ecosystems in collision and faunal turnover defined the arena for radiation among 12 recognized species of Haemonchus. Among congeners, the host range for H. contortus is exceptionally broad, including species among artiodactyls of 40 genera representing 5 families (and within 12 tribes of Bovidae). Broad host range is dramatically reflected in the degree to which translocation, introduction and invasion with host switching, has characterized an expanding distribution over time in North America, South America, southern Eurasia, Australia and New Zealand, coincidental with agriculture, husbandry and global colonization by human populations driven particularly by European exploration after the 1500s. African origins in xeric to mesic habitats of the African savannah suggest that historical constraints linked to ecological adaptations (tolerances and developmental thresholds defined by temperature and humidity for larval stages) will be substantial determinants in the potential outcomes for widespread geographical and host colonization which are predicted to unfold over the coming century. Insights about deeper evolutionary events, ecology and biogeography are critical as understanding history informs us about the possible range of responses in complex systems under new regimes of environmental forcing, especially, in this case, ecological perturbation linked to climate change. A deeper history of perturbation is relevant in understanding contemporary systems that are now strongly structured by events of invasion and colonization. The relaxation of abiotic and biotic controls on the occurrence of H. contortus, coincidental with inception and dissemination of anthelmintic resistance may be synergistic, serving to exacerbate challenges to control parasites or to limit the socioeconomic impacts of infection that can influence food security and availability. Studies of haemonchine nematodes contribute directly to an expanding model about the nature of diversity and the evolutionary trajectories for faunal assembly among complex host-parasite systems across considerable spatial and temporal scales.

PCR primers for straightforward differentiation of Haemonchus contortus, Haemonchus placei and their hybrids

Haemonchus contortus and Haemonchus placei are among the major parasites of small ruminants and cattle. Although infection with these nematodes is host-specific, with H. placei predominating in cattle and H. contortus in sheep, cross-infections are observed in areas where both parasites are sympatric, and hybrid offspring can occur. Therefore, a fast and precise method is required for differentiating the parasites. Identification based on spicule morphometry is the most common technique for differentiating Haemonchus species. However, because these measurements overlap between species, morphological analysis is insufficient for differentiating between helminth species. In this work, we present a reliable, conventional polymerase chain reaction (PCR)-based method that uses two species-specific primer pairs to differentiate between H. contortus and H. placei specimens and their hybrids. Each primer pair produces one single and distinct amplification band for each species, which enables the detection of hybrid specimens. These primer pairs were validated by testing eight different populations of H. contortus, H. placei and hybrids.

Microsatellite marker analysis of Haemonchus contortus populations from Pakistan suggests that frequent benzimidazole drug treatment does not result in a reduction of overall genetic diversity

Background

The impact of drug selection pressure on the overall genetic diversity of parasitic nematode populations in the field is poorly understood. In this study, we address this issue for the small ruminant parasite Haemonchus contortus in the Punjab, Pakistan. This region provides an opportunity to compare H. contortus populations that have been subjected to a prolonged period of frequent benzimidazole drug treatments on government farms with parasite populations that have been exposed to little or no drug treatment in neighbouring pastoral herds.

Methods

Adult H. contortus worms were collected from the abomasa of small ruminants from three government farms frequently using benzimidazole drugs, and closed to animal movement, for over 30 years and also from from eighteen pastoral herds subject to minimal drug selection. The frequency of three known benzimidazole resistance associated mutations was determined in each parasite population. For the seven parasite populations in which resistance mutations were found, the diversity, geographical distribution and phylogenetic relationships of isotype-1 β-tubulin benzimidazole resistance haplotypes were determined. In addition, the genetic diversity of the parasite populations on the three government farms were compared with those from four pastoral herds.

Results

The F200Y (TAC) resistance mutation was present at a very high frequency in H. contortus populations from government herds, but not from pastoral herds, consistent with their respective drug selection histories. Population genetic analysis, using a panel of microsatellite markers, revealed that there was little genetic differentiation among the parasite populations with no significant difference in the overall genetic diversity between government and pastoral herds. In addition, sequence analysis of the isotype-1 β-tubulin locus revealed multiple F200Y (TAC) haplotypes demonstrating soft selective sweeps even in government herds with little or no contemporary parasite migration.

Conclusions

The results suggest that, although the frequent drug treatment used on government farms has selected for a high frequency of benzimidazole resistance mutations, there has been little or no reduction in the overall genetic diversity of the selected parasite populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1624-0) contains supplementary material, which is available to authorized users.

Genetic Diversity and Population Structure of Haemonchus contortus

Haemonchus contortus is one of the most successful and problematic livestock parasites worldwide. From its apparent evolutionary origins in sub-Saharan Africa, it is now found in small ruminants in almost all regions of the globe, and can infect a range of different domestic and wildlife artiodactyl hosts. It has a remarkably high propensity to develop resistance to anthelmintic drugs, making control increasingly difficult. The success of this parasite is, at least in part, due to its extremely high levels of genetic diversity that, in turn, provide a high adaptive capacity. Understanding this genetic diversity is important for many areas of research including anthelmintic resistance, epidemiology, control, drug/vaccine development and molecular diagnostics. In this article, we review the current knowledge of H. contortus genetic diversity and population structure for both field isolates and laboratory strains. We highlight the practical relevance of this knowledge with a particular emphasis on anthelmintic resistance research.

The Identification of Haemonchus Species and Diagnosis of Haemonchosis

Diagnosis is often equated with identification or detection when discussing parasitic diseases. Unfortunately, these are not necessarily mutually exclusive activities; diseases and infections are generally diagnosed and organisms are identified. Diagnosis is commonly predicated upon some clinical signs; in an effort to determine the causative agent, identification of genera and species is subsequently performed. Both identification and diagnosis play critical roles in managing an infection, and involve the interplay of direct and indirect methods of detection, particularly in light of the complex and expanding problem of drug-resistance in parasites. Accurate and authoritative identification that is cost- and time-effective, based on structural and molecular attributes of specimens, provides a foundation for defining parasite diversity and changing patterns of geographical distribution, host association and emergence of disease. Most techniques developed thus far have been grounded in assumptions based on strict host associations between Haemonchus contortus and small ruminants, that is, sheep and goats, and between Haemonchus placei and bovids. Current research and increasing empirical evidence of natural infections in the field demonstrates that this assumption misrepresents the host associations for these species of Haemonchus. Furthermore, the capacity of H. contortus to utilize a considerably broad spectrum of ungulate hosts is reflected in our understanding of the role of anthropogenic forcing, the 'breakdown' of ecological isolation, global introduction and host switching as determinants of distribution. Nuanced insights about distribution, host association and epidemiology have emerged over the past 30years, coincidently with the development of increasingly robust means for parasite identification. In this review and for the sake of argument, we would like to delineate the diagnosis of haemonchosis from the identification of the specific pathogen. As a foundation for exploring host and parasite biology, we will examine the evolution of methods for distinguishing H. contortus from other common gastrointestinal nematodes of agriculturally significant and free-ranging wild ruminants using morphological, molecular and/or immunological methods for studies at the species and genus levels.

Insight into species diversity of the Trichostrongylidae Leiper, 1912 (Nematoda: Strongylida) in ruminants

This paper focuses on the species diversity among the Trichostrongylidae Leiper, 1912 (Nematoda: Strongylida), and complexity of the family systematics. Polymorphism (subfamilies: Ostertagiinae, Cooperiinae and Haemonchinae), the presence of cryptic species (genus: Teladorsagia) and hybridization (genera: Cooperia, Haemonchus and Ostertagia) are presented and discussed, considering both morphological and molecular evidence. Some of these phenomena are common, nevertheless not sufficiently understood, which indicates the need for expanding the current state of knowledge thereof. Within the Trichostrongylidae, species distinction supported merely by morphological features is difficult, and requires confirmation by means of molecular methods. The parasitic nematode taxonomy is complicated mainly by the genus Teladorsagia, but complexity may also be expected among other Ostertagiinae (e.g. in the genera Ostertagia and Marshallagia). The data presented here show that the members of the Trichostrongylidae can significantly complicate unambiguous species identification. Hence, it is essential to consider the phenomena mentioned, to gather valid and comparable data on the biodiversity of this family.

Absence of detectable benzimidazole-resistance associated alleles in Haemonchus placei in cattle in Nigeria revealed by pyrosequencing of β-tubulin isotype 1

Trichostrongyles are gastrointestinal parasites that occur globally and can cause subclinical to severe, sometimes life-threatening, infections in ruminants, particularly young animals. Benzimidazoles (BZ) are commonly used for the treatment of gastrointestinal parasites in ruminants. Increasing spread of worm populations with anthelmintics resistance has been reported and is considered a consequence of highly frequent and longstanding use of anthelmintics. To obtain initial information regarding the occurrence of putatively BZ-resistant Nigerian Haemonchus populations, screening based on the molecular analysis of BZ-resistance-associated β-tubulin isotype 1 gene sequence polymorphisms was undertaken. Genomic DNA was isolated from pooled adult Haemonchus sp. from 35 animals from each of the six states of southwestern Nigeria. Sequencing of internal transcribed spacer 2 (ITS-2) and external transcribed spacer (ETS) regions was used to determine the Haemonchus species. Pyrosequencing assays were used for detection of single-nucleotide polymorphisms (SNPs) in the β-tubulin isotype 1 genes of the worms at codons 200 and 167 (TTC/TAC) or 198 (GAA/GCA). Exclusively, Haemonchus placei was detected and allele frequencies obtained at all three positions showed no evidence for the presence of resistance-related alleles. For Lagos State, pools of 10 worms from 30 different animals were analyzed separately for the codon 200 SNP, successfully excluding the presence of resistance-associated SNPs in very low frequencies. These positive findings, showing absence of elevated frequencies of BZ-resistance-associated β-tubulin alleles, have considerable significance since it suggests that farmers can still rely on the efficacy of this important drug class when used for controlling trichostrongyle infections in cattle in Nigeria.