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Monepantel resistance was diagnosed during routine monitoring of the effectiveness of a farm’s roundworm control strategy. Weaned lambs had become ill thrifty and developed diarrhoea, despite the routine use of monepantel. This clinical presentation was caused by trichostrongylosis. The faecal egg count reduction was 76.7% (95% CI: 55.1–82.2%) following treatment with 2.5 mg/kg monepantel. Predominantly Trichostrongylus vitrinus along with small proportions of Oesophagostomum venulosum and Trichostrongylus vitrinus were identified by deep amplicon sequencing of pools of larvae recovered from pre and post monepantel treatment coprocultures and on postmortem examinations. The undifferentiated FECRT showed resistance to monepantel, but not to levamisole, ivermectin, or moxidectin. Examination of farm anthelmintic treatment and animal movement records suggested that treatments before movement onto silage aftermaths, putatively with low numbers of susceptible nematodes in refugia , may have placed a high selection pressure on monepantel resistance. Effective control of parasitic gastroenteritis using anthelmintic drugs is a prerequisite for sustainable sheep production. This case reiterates the need for care when combining anthelmintic treatments with movements to safe grazing, and the value of monitoring of anthelmintic efficacy as part of iterative planned animal health management. [ABSTRACT FROM AUTHOR]

ABSTRACT: The selection, development and dissemination of anthelmintic resistance in cattle nematodes, particularly in Cooperia oncophora, is an area of concern with increasing reports from within the UK. Chronic Cooperia infections have the potential to lead to production losses in young animals. With these facts in mind it is important to consider nematodes and treatment inefficacy when assessing ill thrift, diarrhoea and/or lower productivity than expected in young animals. With no new anthelmintic class likely to emerge onto the cattle market in the near future it is essential to maintain the efficacy of current compounds. [ABSTRACT FROM AUTHOR]

• First confirmed case of benzimidazole resistant Ostertagia ostertagi in UK cattle. • Applied and molecular tools used to confirm fenbendazole resistant Ostertagia. • Clinical disease associated with fenbendazole resistance. • Zero percentage fenbendazole efficacy based on worm burden assessment. • F200Y and F167Y mutations associated with resistance. The prevalence of anthelmintic resistance in the bovine nematode Cooperia oncophora has been well documented globally but lack of efficacy against the more pathogenic nematode species Ostertagia ostertagi is less common. The sensitivity of an O. ostertagi isolate to the benzimidazole class of anthelmintic was investigated using classical parasitological techniques following apparent clinical failure of controlled release fenbendazole capsule administration in first season grazers at pasture. A controlled efficacy test (CET) was conducted in conjunction with sequencing of the β-tubulin isotype 1 gene of larvae pre- and post-fenbendazole administration. Twelve helminth-naïve calves were infected experimentally with 20,000 third stage larvae; six received oral fenbendazole (7.5 mg/kg bodyweight) 28 days post infection. Total abomasal nematode burdens were compared between treatment and control groups to determine efficacy. Fenbendazole resistance in O. ostertagi was confirmed with a total treatment failure in reducing worm burden: efficacy of 0%. Sequence analysis of the β-tubulin isotype-1 gene from forty-five infective larvae from both control and treated groups was performed. The three commonest single nucleotide polymorphisms (SNPs) associated with benzimidazole resistance, namely F167Y, E198A and F200Y, were examined. The predominant resistance-associated SNPs were F200Y (78 % control and 79 % treated groups) and F167Y (remaining genotypes) and emphasises the importance of these SNPs in clinical disease in this isolate. The development of diagnostic molecular tools based on a characterised field-derived isolate of benzimidazole-resistant Ostertagia will enable future prevalence surveys to be undertaken to assess the possible risk posed by resistance in this economically important species. [ABSTRACT FROM AUTHOR]

ABSTRACT: With the apparent increase in anthelmintic resistance there is a need to ensure that producers follow best advice recommendations on treating animals. It is generally accepted that the blanket use of anthelmintics in all classes of stock is unsustainable and there is a need to incorporate sustainable integrated parasite management practices with appropriate and practicable use of efficient treatments. Refugia i.e. the parasite population that is unexposed to anthelmintic treatment and available for ingestion by a susceptible host, is considered an area of importance when considering the timing and formulation of treatment strategies and is discussed more fully within the article. [ABSTRACT FROM AUTHOR]

• Sequence polymorphism can counfound RNAseq analysis in genetically diverse organisms due to read mapping biases. • Optimising read mapping and excluding highly polymorphic genes reduces differential gene expression analysis biases. • Genetically divergent strains of Haemonchus contortus have very high levels of inter-strain transcriptional diversity. • Analyses of inter-strain differential expression must consider sequence polymorphism and overall transcriptional diversity. Differential expression analysis between parasitic nematode strains is commonly used to implicate candidate genes in anthelmintic resistance or other biological functions. We have tested the hypothesis that the high genetic diversity of an organism such as Haemonchus contortus could complicate such analyses. First, we investigated the extent to which sequence polymorphism affects the reliability of differential expression analysis between the genetically divergent H. contortus strains MHco3(ISE), MHco4(WRS) and MHco10(CAVR). Using triplicates of 20 adult female worms from each population isolated under parallel experimental conditions, we found that high rates of sequence polymorphism in RNAseq reads were associated with lower efficiency read mapping to gene models under default TopHat2 parameters, leading to biased estimates of inter-strain differential expression. We then showed it is possible to largely compensate for this bias by optimising the read mapping single nucleotide polymorphism (SNP) allowance and filtering out genes with particularly high single nucleotide polymorphism rates. Once the sequence polymorphism biases were removed, we then assessed the genuine transcriptional diversity between the strains, finding ≥824 differentially expressed genes across all three pairwise strain comparisons. This high level of inter-strain transcriptional diversity not only suggests substantive inter-strain phenotypic variation but also highlights the difficulty in reliably associating differential expression of specific genes with phenotypic differences. To provide a practical example, we analysed two gene families of potential relevance to ivermectin drug resistance; the ABC transporters and the ligand-gated ion channels (LGICs). Over half of genes identified as differentially expressed using default TopHat2 parameters were shown to be an artifact of sequence polymorphism differences. This work illustrates the need to account for sequence polymorphism in differential expression analysis. It also demonstrates that a large number of genuine transcriptional differences can occur between H. contortus strains and these must be considered before associating the differential expression of specific genes with phenotypic differences between strains. [ABSTRACT FROM AUTHOR]

• Ivermectin efficacy based on FECRT conducted in-field and under controlled conditions ranged between 52% and 86%. • In the controlled efficacy trial, ivermectin efficacy against adult and L3/L4 worms differed, being 5% v 94% respectively. • This is the first report of anthelmintic resistance in pigs in the United Kingdom. • Wider surveillance is necessary for the detection of nematode resistance in pigs. In 2016 suspected reduced ivermectin (IVM) efficacy in O esophagostomum species in pigs was reported in England. Following this initial report, APHA raised awareness amongst private pig veterinary practitioners of the need to monitor the efficacy of the worm control on pig units. In 2017 another veterinary practitioner highlighted a potential in-field lack of IVM efficacy in treating Oesophagostomum species in sows on another breeder-finisher unit. In this trial, the efficacy of IVM against Oesophagostomum species worms has been investigated to determine whether suspected reduced efficacy (52% reduction in mean faecal egg count 14 days post ivermectin administration) on a mixed indoor and outdoor breeder-finisher pig farm in England reflected true IVM resistance under controlled experimental conditions. On days 0 and 40 of the trial, twenty helminth-naive pigs were artificially infected per os with 5000 Oesophagostomum L3 obtained from the farm under investigation. The pigs were allocated to treatment or control groups (n = 10 per group). Treatment group pigs received IVM (0.3 mg kg body weight) by sub-cutaneous injection as per manufacturer's instructions on day 44. Control group animals were left untreated. Faecal worm egg counts were monitored throughout the trial from day 15 post infection to determine time to patency. On day 50 all pigs were euthanased to assess the worm burdens. Resistance to IVM was confirmed in Oesophagostomum dentatum based on the results of a faecal egg count reduction test (FECRT) and a controlled efficacy test (CET). Efficacy based on mean reduction in faecal egg count of IVM-treated pigs compared to untreated control pigs was 86%. Mean reduction in IVM-treated pig worm burdens was 5% against an adult worm population and 94% against an L3/L4 population. The apparent discrepancy between FECRT and CET efficacy results appears to be due to egg development and/or oviposition suppression in IVM-treated female worms. The detection of IVM resistance in Oesophagostomum species worms for the first time in UK pigs is particularly important considering the global situation where resistance to pyrantel, levamisole and benzimidazole anthelmintics in Oesophagostomum species in pigs have already been reported. The results also provide an opportunity to discuss the wider issue of anthelmintic usage and efficacy on pig farms and highlight the need for wider surveillance for the occurrence of anthelmintic resistance in pigs. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Deep amplicon sequencing is a powerful new tool for drug resistance single nucleotide polymorphism (SNP) screening. • Deep amplicon sequencing is validated by pyrosequence genotyping of individual nematode larvae. • There is an high frequency of benzimidazole resistance SNPs in many nematode species on UK sheep farms. • Observed resistance SNP frequencies differ greatly between species under the same drug selection. Abstract Parasitic gastrointestinal nematodes contribute to significant human morbidity and cause billions of dollars per year in lost agricultural production. Control is dependent on the use of anthelmintic drugs which, in the case of livestock parasites, is severely compromised by the widespread development of drug resistance. There are now concerns regarding the emergence of anthelmintic resistance in parasitic nematodes of humans in response to the selection pressure resulting from mass drug administration programs. Consequently, there is an urgent need for sensitive, scalable and accurate diagnostic tools to detect the emergence of anthelmintic resistance. Detecting and measuring the frequency of resistance-associated mutations in parasite populations has the potential to provide sensitive and quantitative assessment of resistance emergence from an early stage. Here, we describe the development and validation of deep amplicon sequencing as a powerful new approach to detect and quantify the frequency of single nucleotide polymorphisms associated with benzimidazole resistance. We have used parasite communities in sheep to undertake a proof-of-concept study of this approach. Sheep provide an excellent host system, as there are multiple co-infecting trichostrongylid nematode species, each likely with a varying prevalence of benzimidazole resistance. We demonstrate that the approach provides an accurate measure of resistance allele frequencies, and can reliably detect resistance alleles down to a frequency of 0.1%, making it particularly valuable for screening mutations in the early stages of resistance. We illustrate the power of the technique by screening UK sheep flocks for benzimidazole resistance-associated single nucleotide polymorphisms at three different codons of the β-tubulin gene in seven different parasite species from 164 populations (95 from ewes and 69 from lambs) in a single MiSeq sequencing run. This approach provides a powerful new tool to screen for the emergence of anthelmintic resistance mutations in parasitic nematode populations of both animals and humans. [ABSTRACT FROM AUTHOR]

Parasitic roundworm infections are ubiquitous in grazing livestock. Chemical control through the frequent ‘blanket’ administration of anthelmintics (wormers) has been, and remains, the cornerstone in controlling these infections, but this practice is unsustainable. Alternative strategies are available but, even with the plethora of best practice advice available, have yet to be integrated into routine farming practice. This is probably due to a range of factors, including contradictory advice from different sources, changes to advice following increased scientific understanding, and top-down knowledge exchange patterns. In this article, we discuss the worm control options available, the translation of new best practice advice from science bench to field, and ideas for future work and directions. [ABSTRACT FROM AUTHOR]

Climate change has the potential to impair livestock health, with consequences for animal welfare, productivity, greenhouse gas emissions, and human livelihoods and health. Modelling has an important role in assessing the impacts of climate change on livestock systems and the efficacy of potential adaptation strategies, to support decision making for more efficient, resilient and sustainable production. However, a coherent set of challenges and research priorities for modelling livestock health and pathogens under climate change has not previously been available. To identify such challenges and priorities, researchers from across Europe were engaged in a horizon-scanning study, involving workshop and questionnaire based exercises and focussed literature reviews. Eighteen key challenges were identified and grouped into six categories based on subject-specific and capacity building requirements. Across a number of challenges, the need for inventories relating model types to different applications (e.g. the pathogen species, region, scale of focus and purpose to which they can be applied) was identified, in order to identify gaps in capability in relation to the impacts of climate change on animal health. The need for collaboration and learning across disciplines was highlighted in several challenges, e.g. to better understand and model complex ecological interactions between pathogens, vectors, wildlife hosts and livestock in the context of climate change. Collaboration between socio-economic and biophysical disciplines was seen as important for better engagement with stakeholders and for improved modelling of the costs and benefits of poor livestock health. The need for more comprehensive validation of empirical relationships, for harmonising terminology and measurements, and for building capacity for under-researched nations, systems and health problems indicated the importance of joined up approaches across nations. The challenges and priorities identified can help focus the development of modelling capacity and future research structures in this vital field. Well-funded networks capable of managing the long-term development of shared resources are required in order to create a cohesive modelling community equipped to tackle the complex challenges of climate change. [ABSTRACT FROM AUTHOR]