Selective control of parasitic nematodes using bioactivated nematicides.

Parasitic nematodes are a major threat to global food security, particularly as the world amasses 10 billion people amid limited arable land1-4. Most traditional nematicides have been banned owing to poor nematode selectivity, leaving farmers with inadequate means of pest control4-12. Here we use the model nematode Caenorhabditis elegans to identify a family of selective imidazothiazole nematicides, called selectivins, that undergo cytochrome-p450-mediated bioactivation in nematodes. At low parts-per-million concentrations, selectivins perform comparably well with commercial nematicides to control root infection by Meloidogyne incognita, a highly destructive plant-parasitic nematode. Tests against numerous phylogenetically diverse non-target systems demonstrate that selectivins are more nematode-selective than most marketed nematicides. Selectivins are first-in-class bioactivated nematode controls that provide efficacy and nematode selectivity.

Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel ß-tubulin benzimidazole resistance mutation.

Ancylostoma caninum is an important zoonotic gastrointestinal nematode of dogs worldwide and a close relative of human hookworms. We recently reported that racing greyhound dogs in the USA are infected with A. caninum that are commonly resistant to multiple anthelmintics. Benzimidazole resistance in A. caninum in greyhounds was associated with a high frequency of the canonical F167Y(TTC>TAC) isotype-1 ß-tubulin mutation. In this work, we show that benzimidazole resistance is remarkably widespread in A. caninum from domestic dogs across the USA. First, we identified and showed the functional significance of a novel benzimidazole isotype-1 ß-tubulin resistance mutation, Q134H(CAA>CAT). Several benzimidazole resistant A. caninum isolates from greyhounds with a low frequency of the F167Y(TTC>TAC) mutation had a high frequency of a Q134H(CAA>CAT) mutation not previously reported from any eukaryotic pathogen in the field. Structural modeling predicted that the Q134 residue is directly involved in benzimidazole drug binding and that the 134H substitution would significantly reduce binding affinity. Introduction of the Q134H substitution into the C. elegans ß-tubulin gene ben-1, by CRISPR-Cas9 editing, conferred similar levels of resistance as a ben-1 null allele. Deep amplicon sequencing on A. caninum eggs from 685 hookworm positive pet dog fecal samples revealed that both mutations were widespread across the USA, with prevalences of 49.7% (overall mean frequency 54.0%) and 31.1% (overall mean frequency 16.4%) for F167Y(TTC>TAC) and Q134H(CAA>CAT), respectively. Canonical codon 198 and 200 benzimidazole resistance mutations were absent. The F167Y(TTC>TAC) mutation had a significantly higher prevalence and frequency in Western USA than in other regions, which we hypothesize is due to differences in refugia. This work has important implications for companion animal parasite control and the potential emergence of drug resistance in human hookworms.

It's a small world for parasites: evidence supporting the North American invasion of European Echinococcus multilocularis.

Echinococcus multilocularis (Em), the causative agent of human alveolar echinococcosis (AE), is present in the Holarctic region, and several genetic variants deem to have differential infectivity and pathogenicity. An unprecedented outbreak of human AE cases in Western Canada infected with a European-like strain circulating in wild hosts warranted assessment of whether this strain was derived from a recent invasion or was endemic but undetected. Using nuclear and mitochondrial markers, we investigated the genetic diversity of Em in wild coyotes and red foxes from Western Canada, compared the genetic variants identified to global isolates and assessed their spatial distribution to infer possible invasion dynamics. Genetic variants from Western Canada were closely related to the original European clade, with lesser genetic diversity than that expected for a long-established strain and spatial genetic discontinuities within the study area, supporting the hypothesis of a relatively recent invasion with various founder events.

Clonemate cotransmission supports a role for kin selection in a puppeteer parasite.

Host manipulation by parasites is a fascinating evolutionary outcome, but adaptive scenarios that often accompany even iconic examples in this popular field of study are speculative. Kin selection has been invoked as a means of explaining the evolution of an altruistic-based, host-manipulating behavior caused by larvae of the lancet fluke Dicrocoelium dendriticum in ants. Specifically, cotransmission of larval clonemates from a snail first host to an ant second host is presumed to lead to a puppeteer parasite in the ant's brain that has clonemates in the ant abdomen. Clonal relatedness between the actor (brain fluke) and recipients (abdomen flukes) enables kin selection of the parasite's host-manipulating trait, which facilitates transmission of the recipients to the final host. However, the hypothesis that asexual reproduction in the snail leads to a high abundance of clonemates in the same ant is untested. Clonal relationships between the manipulator in the brain and the nonmanipulators in the abdomen are also untested. We provide empirical data on the lancet fluke's clonal diversity within its ant host. In stark contrast to other trematodes, which do not exhibit the same host-manipulating behavioral trait, the lancet fluke has a high abundance of clonemates. Moreover, our data support existing theory that indicates that the altruistic behavior can evolve even in the presence of multiple clones within the same ant host. Importantly, our analyses conclusively show clonemate cotransmission into ants, and, as such, we find support for kin selection to drive the evolution and maintenance of this iconic host manipulation.

Effects of naturally acquired gastrointestinal nematode infection on bovine viral diarrhea virus vaccine-directed antibody response in western Canadian feedlot cattle.

Objective: To determine how gastrointestinal nematode (GIN) infection, reflected by fecal egg counts and Ostertagia ostertagi serum antibody titers, is associated with the antibody response to bovine viral diarrhea virus type 1 (BVDV-1) vaccine antigen in fall-weaned feedlot cattle from western Canada. Animals: Cross-sectional study with 240 steer calves derived from an auction market. Procedure: At feedlot arrival, calves were given a commercial vaccine containing modified live BVDV-1. Serum neutralization antibody titers against BVDV-1 antigens were determined in individual blood samples collected pre-vaccination and 21 d after vaccination. A modified Wisconsin sugar floatation method was used to obtain individual calf GIN egg counts in fecal samples on arrival. Antibody titers against O. ostertagi were determined using an enzyme-linked immunosorbent assay in on-arrival blood samples. Results: Fecal egg counts and O. ostertagi titers were not associated with vaccine antibody-fold changes. Similarly, fecal egg counts and O. ostertagi titers were not associated with vaccine-induced seroconversion. Conclusions: The relatively low GIN burdens, reflected by the overall low fecal egg counts in these fall-weaned feedlot calves, did not have measurable adverse effects on the humoral immune response to BVDV-1 vaccine antigens. Clinical relevance: An adequate response to vaccination is important for cattle welfare and productivity. Conditions that negatively affect this response may vary regionally, such as GIN infection. Understanding this is essential. Although subclinical intestinal parasitism did not noticeably affect the antibody response in these steers, higher GIN burdens and actual immune protection from clinical disease remain to be investigated.

Effets d'une infection par des nématodes gastro-intestinaux d'origine naturelle sur la réponse en anticorps dirigés par le vaccin contre le virus de la diarrhée virale bovine chez les bovins des parcs d'engraissement de l'Ouest canadien. Objectif: Déterminer comment l'infection par les nématodes gastro-intestinaux (GIN), reflétée par le nombre d'oeufs fécaux et les titres d'anticorps sériques d'Ostertagia ostertagi, est associée à la réponse en anticorps à l'antigène du vaccin contre le virus de la diarrhée virale bovine de type 1 (BVDV-1) chez les bovins en parc d'engraissement sevrés à l'automne de l'Ouest canadien. Animaux: Étude transversale auprès de 240 veaux bouvillons issus d'un marché aux enchères. Procédure: À leur arrivée au parc d'engraissement, les veaux ont reçu un vaccin commercial contenant du BVDV-1 vivant modifié. Les titres d'anticorps sériques neutralisants contre les antigènes BVDV-1 ont été déterminés dans des échantillons de sang individuels prélevés avant la vaccination et 21 jours après la vaccination. Une méthode de Wisconsin modifiée de flottation au sucre a été utilisée pour obtenir le nombre d'oeufs GIN de chaque veau dans les échantillons fécaux à l'arrivée. Les titres d'anticorps dirigés contre O. ostertagi ont été déterminés à l'aide d'un dosage immuno-enzymatique dans des échantillons de sang à l'arrivée. Résultats: Le nombre d'oeufs fécaux et les titres d'O. ostertagi n'étaient pas associés aux modifications du titre d'anticorps vaccinaux. De même, le nombre d'oeufs fécaux et les titres d'O. ostertagi n'étaient pas associés à la séroconversion induite par le vaccin. Conclusion: Les charges relativement faibles de GIN, reflétées par le faible nombre global d'oeufs fécaux chez ces veaux d'engraissement sevrés à l'automne, n'ont pas eu d'effets indésirables mesurables sur la réponse immunitaire humorale aux antigènes du vaccin BVDV-1. Pertinence clinique: Une réponse adéquate à la vaccination est importante pour le bien-être et la productivité des bovins. Les conditions qui affectent négativement cette réponse peuvent varier selon les régions, telles que l'infection par les GIN. Comprendre cela est essentiel. Bien que le parasitisme intestinal subclinique n'ait pas sensiblement affecté la réponse en anticorps chez ces bouvillons, des charges de GIN plus élevées et une protection immunitaire réelle contre la maladie clinique restent à étudier.(Traduit par Dr Serge Messier).

A database for ITS2 sequences from nematodes.

BACKGROUND: Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data. RESULTS: Here we present an ITS2 rDNA database for marker gene surveys of both free-living and parasitic nematode populations and the software used to build the database. This is currently the most complete and up-to-date ITS2 database for nematodes and is able to reproduce previous analysis that used a smaller database. CONCLUSIONS: This database is an important resource for researchers working on nematodes and also provides a tool to create ITS2 databases for any given taxonomy.

Assessing anthelmintic resistance risk in the post-genomic era: a proof-of-concept study assessing the potential for widespread benzimidazole-resistant gastrointestinal nematodes in North American cattle and bison.

As genomic research continues to improve our understanding of the genetics of anthelmintic drug resistance, the revolution in DNA sequencing technologies will provide increasing opportunities for large-scale surveillance for the emergence of drug resistance. In most countries, parasite control in cattle and bison has mainly depended on pour-on macrocyclic lactone formulations resulting in widespread ivermectin resistance. Consequently, there is an increased interest in using benzimidazole drugs which have been used comparatively little in cattle and bison in recent years. This situation, together with our understanding of benzimidazole resistance genetics, provides a practical opportunity to use deep-amplicon sequencing to assess the risk of drug resistance emergence. In this paper, we use deep-amplicon sequencing to scan for those mutations in the isotype-1 ß-tubulin gene previously associated with benzimidazole resistance in many trichostrongylid nematode species. We found that several of these mutations occur at low frequency in many cattle and bison parasite populations in North America, suggesting increased use of benzimidazole drugs in cattle has the potential to result in widespread emergence of resistance in multiple parasite species. This work illustrates a post-genomic approach to large-scale surveillance of early emergence of anthelmintic resistance in the field.

Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus.

BACKGROUND: Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infect livestock and companion animals, and there are growing concerns regarding the reduced efficacy in some human-infective helminths. Understanding the mechanisms by which resistance evolves is the focus of increasing interest; robust genetic analysis of helminths is challenging, and although many candidate genes have been proposed, the genetic basis of resistance remains poorly resolved. RESULTS: Here, we present a genome-wide analysis of two genetic crosses between ivermectin resistant and sensitive isolates of the parasitic nematode Haemonchus contortus, an economically important gastrointestinal parasite of small ruminants and a model for anthelmintic research. Whole genome sequencing of parental populations, and key stages throughout the crosses, identified extensive genomic diversity that differentiates populations, but after backcrossing and selection, a single genomic quantitative trait locus (QTL) localised on chromosome V was revealed to be associated with ivermectin resistance. This QTL was common between the two geographically and genetically divergent resistant populations and did not include any leading candidate genes, suggestive of a previously uncharacterised mechanism and/or driver of resistance. Despite limited resolution due to low recombination in this region, population genetic analyses and novel evolutionary models supported strong selection at this QTL, driven by at least partial dominance of the resistant allele, and that large resistance-associated haplotype blocks were enriched in response to selection. CONCLUSIONS: We have described the genetic architecture and mode of ivermectin selection, revealing a major genomic locus associated with ivermectin resistance, the most conclusive evidence to date in any parasitic nematode. This study highlights a novel genome-wide approach to the analysis of a genetic cross in non-model organisms with extreme genetic diversity, and the importance of a high-quality reference genome in interpreting the signals of selection so identified.

Survey of gastrointestinal nematodes in breeding-age heifers on 6 Saskatchewan dairy farms.

To determine the prevalence, mean fecal egg count intensities, and predominant gastrointestinal nematode species, fresh environmental fecal samples were collected from 30 grazing heifers at monthly intervals (June, July, and August) on 6 Saskatchewan dairy farms in 2016. The population average strongylid prevalence ranged from 67.2% [95% confidence interval (CI): 49.5% to 84.9%] in June to 88.3% (95% CI: 76.7% to 100.0%) in August (P = 0.05) while the mean fecal egg count ranged from 1.7 in June to 9.3 eggs/g of feces in August (P < 0.003). The predominant nematode species were identified using a deep-sequencing nemabiome assay targeting the internal transcribed spacer rDNA genomic locus of both L1 and L3-stage larvae. Cooperia oncophora and Ostertagia ostertagi were predominant on all farms, accounting for > 85% of the species. The results provide important previously unavailable data on the epidemiology of gastrointestinal nematodes (GIN) in fecal samples from these grazing heifers in Saskatchewan.

Examen des nématodes gastro-intestinaux chez les génisses en âge de se reproduire sur six fermes laitières de la Saskatchewan. Afin de déterminer la prévalence, l'intensité du dénombrement moyen d'oeufs dans les fèces et les espèces de nématodes gastro-intestinaux prédominants, des échantillons environnementaux de fèces fraîches furent prélevés de 30 génisses au pâturage à un intervalle mensuel (juin, juillet, et août) sur six fermes laitières de la Saskatchewan en 2016. La prévalence de la population moyenne de strongyles variait de 67,2 % [intervalle de confiance de 95 % (CI) : 49,5 % à 84,9 %] en juin à 88,3 % (CI 95 % : 76,7 % à 100,0 %) en août (P = 0,05) alors que le dénombrement moyen des oeufs dans les fèces variait de 1,7 en juin à 9,3 oeufs/g de fèces en août (P < 0,003). Les espèces de nématodes prédominantes furent identifiées à l'aide d'un test de séquençage profond du némabiome visant l'ADNr du locus génomique de l'espaceur interne transcrit des stades larvaires L1 et L3. Cooperia oncophora et Ostertagia ostertagi étaient prédominants sur toutes les fermes, représentant > 85 % des espèces. Ces résultats fournissent des données importantes non-disponibles auparavant sur l'épidémiologie de GIN dans des échantillons de fèces provenant de ces génisses au pâturage en Saskatchewan.(Traduit par Dr Serge Messier).

Epidemiology of gastrointestinal nematode infections in grazing yearling beef cattle in Saskatchewan.

The objective of this study was to provide contemporary data on the epidemiology of gastrointestinal nematode parasite infections of grazing yearling beef cattle in the province of Saskatchewan. Fecal samples (n = 1290) were collected over 4 time periods during the summer grazing season from 21 separately managed groups of cattle. Fecal egg counts (FEC) were estimated using generalized estimating equations with a negative binomial distribution with log link function, adjusting for clustering of samples within each herd for each time period. Nematodirus spp. and Trichuris spp. eggs were enumerated separately and were detected in 5.7% (73/1290) and 1.7% (22/1290) of samples, respectively. One or more strongyle-type eggs were detected in 79.5% (1025/1290) of the samples and FEC increased by 2.8 times over the summer grazing season. Interestingly, FEC were ~3.4 times higher on pastures located in dark brown versus brown soil zones, a finding that warrants further investigation.

Épidémiologie des infections aux nématodes gastro-intestinaux chez les bovins d'un an en pâturage en Saskatchewan. L'objectif de cette étude consistait à fournir des données contemporaines sur l'épidémiologie des infections aux parasites nématodes gastro-intestinaux des bovins de boucherie âgés d'un an en pâturage dans la province de la Saskatchewan. Des échantillons fécaux (n = 1290) ont été prélevés pendant quatre périodes durant la saison de pâturage estival auprès de 21 groupes de bovins gérés séparément. Les comptes d'œufs dans les fèces (CŒF) ont été estimés en utilisant des équations d'estimation généralisées ayant une distribution binomiale négative en lien avec la fonction log, en ajustant pour le regroupement des échantillons au sein de chaque troupeau pour chaque période. Les œufs de Nematodirus spp. et de Trichuris spp. ont été énumérés séparément et ont été détectés dans 5,7 % (73/1290) et 1,7 % (22/1290) des échantillons, respectivement. Un ou plusieurs œufs de type strongyle ont été détectés dans 79,5 % (1025/1290) des échantillons et les CŒF ont augmenté de 2,8 fois pendant la saison de pâturage estival. Fait intéressant, les CŒF étaient de ~3,4 fois supérieurs dans les pâturages situés dans des zones de sol brun foncé comparativement à du sol brun, une constatation qui justifie de nouvelles investigations.(Traduit par Isabelle Vallières).

Treatment with Cestode Parasite Antigens Results in Recruitment of CCR2+ Myeloid Cells, the Adoptive Transfer of Which Ameliorates Colitis.

Awareness of the immunological underpinnings of host-parasite interactions may reveal immune signaling pathways that could be used to treat inflammatory disease in humans. Previously we showed that infection with the rat tapeworm, Hymenolepis diminuta, used as a model helminth, or systemic delivery of worm antigen (HdAg) significantly reduced the severity of dinitrobenzene sulfonic acid (DNBS)-induced colitis in mice. Extending these analyses, intraperitoneal injection of HdAg dose-dependently suppressed dextran sodium sulfate (DSS)-induced colitis, and this was paralleled by reduced gamma interferon (IFN-γ), interleukin-17 (IL-17), and tumor necrosis factor alpha (TNF-α) production and increased IL-10 production from mitogen-activated splenocytes. Treatment with HdAg resulted in a CCR2-dependent recruitment of CDllb+ F4/80+ Ly6Chi Gr-1lo monocyte-like cells into the peritoneum 24 h later that were predominantly programmed death ligand 1 (PD-L1) positive and CXCR2 negative. In vitro assays indicated that these cells were unable to suppress T cell proliferation but enhanced IL-10 and IL-4 production from activated T cells. Adoptive transfer of the HdAg-recruited monocytic cells into naive mice blocked DSS-induced colitis. These findings add to the variety of means by which treatment with parasitic helminth-derived antigens can ameliorate concomitant disease. A precise understanding of the mechanism(s) of action of HdAg and other helminth-derived antigens (and a parallel consideration of putative side effects) may lead to the development of novel therapies for human idiopathic disorders such as inflammatory bowel disease.

Onchocerca lupi Nematodes in Dogs Exported from the United States into Canada.

The Onchocerca lupi nematode is an emerging helminth capable of infecting pets and humans. We detected this parasite in 2 dogs that were imported into Canada from the southwestern United States, a region to which this nematode is endemic. We discuss risk for establishment of O. lupi in Canada.

Negative covariance between parasite load and body condition in a population of feral horses.

In wild and domestic animals, gastrointestinal parasites can have significant impacts on host development, condition, health, reproduction and longevity. Improving our understanding of the causes and consequences of individual-level variation in parasite load is therefore of prime interest. Here we investigated the relationship between strongyle fecal egg count (FEC) and body condition in a unique, naturalized population of horses that has never been exposed to anthelmintic drugs (Sable Island, Nova Scotia, Canada). We first quantified variation in FEC and condition for 447 individuals according to intrinsic (sex, age, reproductive status, social status) and extrinsic (group size, location, local density) variables. We then quantified the repeatability of measurements obtained over a field season and tested for covariance between FEC and condition. FECs were high relative to other horse populations (mean eggs per gram ± SD = 1543·28 ± 209·94). FECs generally decreased with age, were higher in lactating vs non-lactating females, and unexpectedly lower in males in some part of the island. FECs and condition were both spatially structured, with patterns depending on age, sex and reproductive status. FECs and condition were both repeatable. Most notably, FECs and condition were negatively correlated, especially in adult females.

Survey of gastrointestinal nematode parasites in Saskatchewan beef herds.

A survey of gastrointestinal parasites in Saskatchewan beef herds was conducted over the summer of 2014. Fecal samples were collected on 3 occasions during the summer grazing season from beef cows and calves from 14 herds. The mean number of strongylid eggs per gram of feces recovered from calves increased 9-fold (95% CI: 4.5 to 18) over the summer period, while egg counts in the cows remained constant over the same period. The prevalence and infection intensities of gastrointestinal nematode parasites in cow-calf herds in Saskatchewan were comparable to what is seen in cattle grazing in the northern regions of the United States and for which anthelmintic treatments have resulted in positive production benefits.

Enquête sur les parasites nématodes gastro-intestinaux chez les troupeaux de bovins de boucherie de la Saskatchewan. Une enquête sur les parasites gastro-intestinaux dans des troupeaux bovins de la Saskatchewan a été réalisée à l'été 2014. Des échantillons fécaux ont été prélevés à trois occasions durant la saison de pâturage de l'été auprès des bovins de boucherie et des veaux provenant de 14 troupeaux. Le nombre moyen d'œufs de strongylidés par gramme de fèces prélevées chez les veaux a augmenté de neuf fois (IC de 95 % : de 4,5 à 18) pendant la période de l'été, tandis que les numérations d'œufs chez les vaches sont demeurées constantes pendant la même période. La prévalence et l'intensité des infections par les parasites nématodes gastro-intestinaux chez les troupeaux veaux-vaches de la Saskatchewan étaient comparables à ceux des régions de pâturage du nord des États-Unis où des traitements anthelminthiques ont eu des résultats positifs sur la production.(Traduit par Isabelle Vallières).

Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes.

MOTIVATION: Gene models from draft genome assemblies of metazoan species are often incorrect, missing exons or entire genes, particularly for large gene families. Consequently, labour-intensive manual curation is often necessary. We present Figmop (Finding Genes using Motif Patterns) to help with the manual curation of gene families in draft genome assemblies. The program uses a pattern of short sequence motifs to identify putative genes directly from the genome sequence. Using a large gene family as a test case, Figmop was found to be more sensitive and specific than a BLAST-based approach. The visualization used allows the validation of potential genes to be carried out quickly and easily, saving hours if not days from an analysis. AVAILABILITY AND IMPLEMENTATION: Source code of Figmop is freely available for download at https://github.com/dave-the-scientist, implemented in C and Python and is supported on Linux, Unix and MacOSX. CONTACT: curran.dave.m@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Introgression of ivermectin resistance genes into a susceptible Haemonchus contortus strain by multiple backcrossing.

Anthelmintic drug resistance in livestock parasites is already widespread and in recent years there has been an increasing level of anthelmintic drug selection pressure applied to parasitic nematode populations in humans leading to concerns regarding the emergence of resistance. However, most parasitic nematodes, particularly those of humans, are difficult experimental subjects making mechanistic studies of drug resistance extremely difficult. The small ruminant parasitic nematode Haemonchus contortus is a more amenable model system to study many aspects of parasite biology and investigate the basic mechanisms and genetics of anthelmintic drug resistance. Here we report the successful introgression of ivermectin resistance genes from two independent ivermectin resistant strains, MHco4(WRS) and MHco10(CAVR), into the susceptible genome reference strain MHco3(ISE) using a backcrossing approach. A panel of microsatellite markers were used to monitor the procedure. We demonstrated that after four rounds of backcrossing, worms that were phenotypically resistant to ivermectin had a similar genetic background to the susceptible reference strain based on the bulk genotyping with 18 microsatellite loci and individual genotyping with a sub-panel of 9 microsatellite loci. In addition, a single marker, Hcms8a20, showed evidence of genetic linkage to an ivermectin resistance-conferring locus providing a starting point for more detailed studies of this genomic region to identify the causal mutation(s). This work presents a novel genetic approach to study anthelmintic resistance and provides a "proof-of-concept" of the use of forward genetics in an important model strongylid parasite of relevance to human hookworms. The resulting strains provide valuable resources for candidate gene studies, whole genome approaches and for further genetic analysis to identify ivermectin resistance loci.

A set of nematode rRNA cistron databases and a primer assessment tool to enable more flexible and comprehensive metabarcoding.

The ITS-2-rRNA has been particularly useful for nematode metabarcoding but does not resolve all phylogenetic relationships, and reference sequences are not available for many nematode species. This is a particular issue when metabarcoding complex communities such as wildlife parasites or terrestrial and aquatic free-living nematode communities. We have used markerDB to produce four databases of distinct regions of the rRNA cistron: the 18S rRNA gene, the 28S rRNA gene, the ITS-1 intergenic spacer and the region spanning ITS-1_5.8S_ITS-2. These databases comprise 2645, 254, 13,461 and 10,107 unique full-length sequences representing 1391, 204, 1837 and 1322 nematode species, respectively. The comparative analysis illustrates the complementary value but also reveals a better representation of Clade III, IV and V than Clade I and Clade II nematodes in each case. Although the ITS-1 database includes the largest number of unique full-length sequences, the 18S rRNA database provides the widest taxonomic coverage. We also developed PrimerTC, a tool to assess primer sequence conservation across any reference sequence database, and have applied it to evaluate a large number of previously published rRNA cistron primers. We identified sets of primers that currently provide the broadest taxonomic coverage for each rRNA marker across the nematode phylum. These new resources will facilitate more comprehensive metabarcoding of nematode communities using either short-read or long-read sequencing platforms. Further, PrimerTC is available as a simple WebApp to guide or assess PCR primer design for any genetic marker and/or taxonomic group beyond the nematode phylum.

Next-generation sequencing technologies for helminth diagnostics and surveillance in ruminants: shifting diagnostic barriers.

Helminth infections in grazing ruminants are a major issue for livestock farming globally, but are unavoidable in outdoor grazing systems and must be effectively managed to avoid deleterious effects to animal health, and productivity. Next-generation sequencing (NGS) technologies are transforming our understanding of the genetic basis of anthelmintic resistance (AR) and epidemiological studies of ruminant gastrointestinal parasites. They also have the potential to not only help develop and validate molecular diagnostic tests but to be directly used in routine diagnostics integrating species-specific identification and AR into a single test. Here, we review how these developments have opened the pathway for the development of multi-AR and multispecies identification in a single test, with widespread implications for sustainable livestock farming for the future.

Multiple UDP glycosyltransferases modulate benzimidazole drug sensitivity in the nematode Caenorhabditis elegans in an additive manner.

Xenobiotic biotransformation is an important modulator of anthelmintic drug potency and a potential mechanism of anthelmintic resistance. Both the free-living nematode Caenorhabditis elegans and the ruminant parasite Haemonchus contortus biotransform benzimidazole drugs by glucose conjugation, likely catalysed by UDP-glycosyltransferase (UGT) enzymes. To identify C. elegans genes involved in benzimidazole drug detoxification, we first used a comparative phylogenetic analysis of UGTs from humans, C. elegans and H. contortus, combined with available RNAseq datasets to identify which of the 63 C. elegans ugt genes are most likely to be involved in benzimidazole drug biotransformation. RNA interference knockdown of 15 prioritized C. elegans genes identified those that sensitized animals to the benzimidazole derivative albendazole (ABZ). Genetic mutations subsequently revealed that loss of ugt-9 and ugt-11 had the strongest effects. The "ugt-9 cluster" includes these genes, together with six other closely related ugts. A CRISPR-Cas-9 deletion that removed seven of the eight ugt-9 cluster genes had greater ABZ sensitivity than the single largest-effect mutation. Furthermore, a double mutant of ugt-22 (which is not a member of the ugt-9 cluster) with the ugt-9 cluster deletion further increased ABZ sensitivity. This additivity of mutant phenotypes suggest that ugt genes act in parallel, which could have several, not mutually exclusive, explanations. ugt mutations have different effects with different benzimidazole derivatives, suggesting that enzymes with different specificities could together more efficiently detoxify drugs. Expression patterns of ugt-9, ugt-11 and ugt-22 gfp reporters differ and so likely act in different tissues which may, at least in part, explain their additive effects on drug potency. Overexpression of ugt-9 alone was sufficient to confer partial ABZ resistance, indicating increasing total UGT activity protects animals. In summary, our results suggest that the multiple UGT enzymes have overlapping but not completely redundant functions in benzimidazole drug detoxification and may represent "druggable" targets to improve benzimidazole drug potency.