Deep amplicon sequencing as a powerful new tool to screen for sequence polymorphisms associated with anthelmintic resistance in parasitic nematode populations

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.     

Population dynamics of Trichostrongylus colubriformis in sheep: computer model to simulate grazing systems and the evolution of anthelmintic resistance

A computer model was developed to simulate Trichostrongylus colubriformis populations, their level of resistance to the common anthelmintics, host mortalities and acquired immunity. Predictions were based on sheep management practices such as lambing, weaning, sheep/paddock rotation, anthelmintic treatment, the use of controlled release devices (capsules) for anthelmintic delivery and daily meteorological records to determine the development and survival of infective larvae (L3) on pasture. Evolution of drug resistance was determined by a simple genetic system which allowed for up to three genes, each with two alleles, to give a maximum of 27 genotypes associated with one drug or three genotypes for each of three drugs. The model was validated against egg counts, L3 counts on pasture and host mortalities observed in a grazing trial, however, aspects of the model such as the development of drug resistance and use of the model in a variety of climatic zones have yet to be tested against field observations. The model was used to examine the impact of grazing management and capsule use on anthelmintic resistance and sheep production over 20 years using historical weather data. Predictions indicated that grazing management can play a dominant role in parasite control and that capsule use will reduce sheep mortalities and production losses, and in some circumstances will not cause a substantial increase in anthelmintic resistance for up to 5 years.     

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.     

The role of epidemiological knowledge and grazing management for helminth control in small ruminants

There is no single requirement more crucial to the rational and sustainable control of helminth parasites in grazing animals than a comprehensive knowledge of the epidemiology of the parasite as it interacts with the host in a specific climatic, management and production environment. In its absence, anthelmintic treatment is either given suppressively, which provokes resistance, or therapeutically, which risks clinical disease and production losses. Sustainable parasite-control programmes require knowledge of seasonal larval availability, origin of larvae contributing to any peaks and climatic requirements for worm egg hatching, larval development and survival. Control measures based on this knowledge include strategic anthelmintic treatments and various forms of grazing management. While these measures can reduce the frequency of anthelmintic treatment required, their effect on selection for drench resistance is more problematical, unless they can be combined with other forms of control to reduce our current dependence on anthelmintics.     

Survey of parasite control programs used in captive wild ruminants

The purpose of this study was to document, through a mailed questionnaire survey, the methods of parasite control currently used in captive wild ruminants. There was a 69% overall response to the survey. The majority of respondents indicated that they used parasite surveillance and identification techniques similar to those used for domestic ruminants. Of the four major anthelmintic drug classes, the benzimidazoles and ivermectin were used most commonly. Many of the parasite control programs had high treatment frequencies which were similar to dosing frequencies reported to result in anthelmintic resistance in domestic animals. Lack of effectiveness by benzimidazoles was perceived to be a problem by many respondents.     

No Evidence for Resistance to Fenbendazole in Trichostrongylus tenuis,a Nematode Parasite of the Red Grouse

ABSTRACT The parasitic nematode Trichostrongylus tenuis has a detrimental effect on red grouse (Lagopus lagopus scoticus) at the individual and population levels. Treatment using grit coated with the anthelmintic fenbendazole hydrochloride reduces parasite infection and increases grouse density. However, a frequent and low dose of anthelmintic increases selection pressure for parasite resistance, a serious practical and economic problem. We used an egg hatch assay to test resistance of T. tenuis from 12 moors in northern England, which differed in grit treatment intensity. The anthelmintic concentration that prevented 50% and 95% of T. tenuis eggs from hatching (ED₅₀ and ED₉₅, respectively) did not differ among moors and were not related to treatment. We suggest annual monitoring and responsible anthelmintic use to prevent resistance so that medicated grit continues to enhance red grouse management.     

A model for nematodiasis in New Zealand lambs.

A strategic model is described for the epidemiology of mixed nematode infections in New Zealand lambs. The model successfully reproduces known patterns of parasite epidemiology and production loss in lambs under currently implemented control strategies. The variation in model output during sensitivity analysis was within acceptable limits defined by field data. Model output was most sensitive to variation in parameters affecting survival and migration of the free-living stages and host resistance to infection, suggesting that these factors are most influential in regulating parasite populations. It is intended to use the model to focus research on key aspects of nematode epidemiology and control and, following the incorporation of appropriate genetic mechanisms, anthelmintic resistance.     

Density dependence and the spread of anthelmintic resistance

Variation in the strength of selection pressures acting upon different subpopulations may cause density-dependent regulatory processes to act differentially on particular genotypes and may influence the rate of selection of adaptive traits. Using host-helminth parasite systems as examples, we investigate the impact of different positive and negative density dependence on the potential spread of anthelmintic resistance. Following chemotherapy, the negative density-dependent processes restricting parasite population growth will be relaxed, increasing the genetic contribution of resistant parasites to the next generation. Simple deterministic models of directly transmitted nematodes that merge population dynamics and genetics show that the frequency of drug-resistant alleles may increase faster in species whose population size is down-regulated by density-dependent parasite fecundity than in species with density-dependent establishment or parasite mortality. A genetically structured population dynamics model of an indirectly transmitted nematode is used to highlight how population regulation will influence the resistance allele frequency in different parasite lifestages. Results indicate that surveys aimed at monitoring the evolution of drug resistance should consider carefully which life stage to sample, and the time following treatment samples should be collected. Anthelmintic resistance offers a good opportunity to apply fundamental evolutionary and ecological principles to the management of a potentially crucial public health problem.     

An analysis of genetic diversity and inbreeding in Wuchereria bancrofti: implications for the spread and detection of drug resistance

Estimates of genetic diversity in helminth infections of humans often have to rely on genotyping (immature) parasite transmission stages instead of adult worms. Here we analyse the results of one such study investigating a single polymorphic locus (a change at position 200 of the beta-tubulin gene) in microfilariae of the lymphatic filarial parasite Wuchereria bancrofti. The presence of this genetic change has been implicated in benzimidazole resistance in parasitic nematodes of farmed ruminants. Microfilariae were obtained from patients of three West African villages, two of which were sampled prior to the introduction of mass drug administration. An individual-based stochastic model was developed showing that a wide range of allele frequencies in the adult worm populations could have generated the observed microfilarial genetic diversity. This suggests that appropriate theoretical null models are required in order to interpret studies that genotype transmission stages. Wright's hierarchical F-statistic was used to investigate the population structure in W. bancrofti microfilariae and showed significant deficiency of heterozygotes compared to the Hardy-Weinberg equilibrium; this may be partially caused by a high degree of parasite genetic differentiation between hosts. Studies seeking to quantify accurately the genetic diversity of helminth populations by analysing transmission stages should increase their sample size to account for the variability in allele frequency between different parasite life-stages. Helminth genetic differentiation between hosts and non-random mating will also increase the number of hosts (and the number of samples per host) that need to be genotyped, and could enhance the rate of spread of anthelmintic resistance.     

Using C. elegans Forward and Reverse Genetics to Identify New Compounds with Anthelmintic Activity

BackgroundThe lack of new anthelmintic agents is of growing concern because it affects human health and our food supply, as both livestock and plants are affected. Two principal factors contribute to this problem. First, nematode resistance to anthelmintic drugs is increasing worldwide and second, many effective nematicides pose environmental hazards. In this paper we address this problem by deploying a high throughput screening platform for anthelmintic drug discovery using the nematode Caenorhabditis elegans as a surrogate for infectious nematodes. This method offers the possibility of identifying new anthelmintics in a cost-effective and timely manner.Conclusions/SignificanceThe challenge of anthelmintic drug discovery is exacerbated by several factors; including, 1) the biochemical similarity between host and parasite genomes, 2) the geographic location of parasitic nematodes and 3) the rapid development of resistance. Accordingly, an approach that can screen large compound collections rapidly is required. C. elegans as a surrogate parasite offers the ability to screen compounds rapidly and, equally importantly, with specificity, thus reducing the potential toxicity of these compounds to the host and the environment. We believe this approach will help to replenish the pipeline of potential nematicides.     

Anthelmintic resistance in nematodes: extent, recent understanding and future directions for control and research

Resistance has now been reported to all of the broad spectrum anthelmintic types currently available, namely to the benzimidazoles, levamisole/morantel and to ivermectin. The problem causes most concern for parasite control in sheep, but anthelmintic resistance has also been reported in nematodes of horses, goats, pigs and more recently cattle. Our understanding of the factors which select rapidly for resistance has increased and programmes of worm control which minimize selection for anthelmintic resistance are being developed and tested. One of the greatest problems encountered in attempting to reduce the selection for overt drug resistance is the need for more sensitive tests for developing resistance. In the long term, new approaches to chemotherapy and to overcoming anthelmintic resistance problems will arise from improving our understanding of the modes of action of, and mechanisms of resistance to, anthelmintics at the level of the receptor proteins and their genes.     

Levamisole resistance in Trichostrongylus colubriformis: a sex-linked recessive character

Reciprocal crosses between susceptible and levamisole resistant strains of Trichostrongylus colubriformis produced F1 offspring consistent with resistance being inherited as a sex-linked recessive character. The resistance status of the offspring of the backcrosses of the F1 to both parental strains supported this hypothesis. The results are consistent with resistance being controlled by a single gene, or a tightly linked group of genes, but indicate that other autosomal loci have minor effects. The results contrast with the reported observations that resistance to the benzimidazole anthelmintics is polygenic and autosomal. The results are discussed relative to a general evolutionary model for anthelmintic resistance which predicts that selection from the upper extreme of an anthelmintic tolerance distribution results in polygenicity.     

Novel epidemiological model of gastrointestinal nematode infection to assess grazing cattle resilience by integrating host growth,parasite, grass and environmental dynamics

Gastrointestinal nematode (GIN) infections are ubiquitous and often cause morbidity and reduced performance in livestock. Emerging anthelmintic resistance and increasing change in climate patterns require evaluation of alternatives to traditional treatment and management practices. Mathematical models of parasite transmission between hosts and the environment have contributed towards the design of appropriate control strategies in ruminants, but have yet to account for relationships between climate, infection pressure, immunity, resources, and growth. Here, we develop a new epidemiological model of GIN transmission in a herd of grazing cattle, including host tolerance (body weight and feed intake), parasite burden and acquisition of immunity, together with weather-dependent development of parasite free-living stages, and the influence of grass availability on parasite transmission. Dynamic host, parasite and environmental factors drive a variable rate of transmission. Using literature sources, the model was parametrised for Ostertagia ostertagi, the prevailing pathogenic GIN in grazing cattle populations in temperate climates. Model outputs were validated on published empirical studies from first season grazing cattle in northern Europe. These results show satisfactory qualitative and quantitative performance of the model; they also indicate the model may approximate the dynamics of grazing systems under co-infection by O. ostertagi and Cooperia oncophora, a second GIN species common in cattle. In addition, model behaviour was explored under illustrative anthelmintic treatment strategies, considering impacts on parasitological and performance variables. The model has potential for extension to explore altered infection dynamics as a result of management and climate change, and to optimise treatment strategies accordingly. As the first known mechanistic model to combine parasitic and free-living stages of GIN with host feed-intake and growth, it is well suited to predict complex system responses under non-stationary conditions. We discuss the implications, limitations and extensions of the model, and its potential to assist in the development of sustainable parasite control strategies.     

Anthelmintic treatment alters the parasite community in a wild mouse host

Individuals are often co-infected with several parasite species, yet the consequences of drug treatment on the dynamics of parasite communities in wild populations have rarely been measured. Here, we experimentally reduced nematode infection in a wild mouse population and measured the effects on other non-target parasites. A single oral dose of the anthelmintic, ivermectin, significantly reduced nematode infection, but resulted in a reciprocal increase in other gastrointestinal parasites, specifically coccidial protozoans and cestodes. These results highlight the possibility that drug therapy may have unintended consequences for non-target parasites and that host–parasite dynamics cannot always be fully understood in the framework of single host–parasite interactions.     

Anthelmintic resistance and the control of ovine ostertagiasis: a drug action model for genetic selection

A site-specific genetic prediction model is presented, which examines the influences of different anthelmintic treatment regimens on selecting for drug resistance within a sheep management system. The model exploits the power of modern microcomputers to integrate factors such as parasite strain, geographic location, management practice and genetic fitness to identify effective control regimens which do not lead to resistant Ostertagia circumcincta strains over a 30-year horizon. The potential use of the model as a farm level management-support tool is discussed.     

Anthelmintic resistance revisited: under-dosing, chemoprophylactic strategies, and mating probabilities

Deterministic and stochastic models are used to examine the evolution of anthelmintic resistance among trichostrongylid parasites of domestic ruminants. We find that the relative selection pressures exerted by chemoprophylactic (preventive) control strategies, chemotherapeutic (salvage) control strategies, and regimens involving "under-dosing" are critically dependent on a variety of host and parasite parameters (particularly host immunity and grazing behaviour, parasite fecundity, and the survival of the free-living stages on the pasture). Chemoprophylactic strategies are not necessarily more likely to exert a stronger selection pressure than chemotherapeutic strategies. Similarly, as one reduces dosage levels, there is a range of dose levels where under-dosing promotes resistance and a range of dose levels where under-dosing impedes resistance. The most dangerous dose is either that necessary to kill all the susceptible homozygotes, or that necessary to kill all the susceptible homozygotes and all the heterozygotes. Which one prevails depends upon model parameters. The stochastic formulation indicates that spatial heterogeneity in transmission may be a significant force in promoting the spread of resistant genotypes--at least when infection is at low levels.     

Anthelmintic tolerance in free-living and facultative parasitic isolates of Halicephalobus (Panagrolaimidae)

SUMMARY Studies on anthelmintic resistance in equine parasites do not include facultative parasites. Halicephalobus gingivalis is a free-living bacterivorous nematode and a known facultative parasite of horses with a strong indication of some form of tolerance to common anthelmintic drugs. This research presents the results of an in vitro study on the anthelmintic tolerance of several isolates of Halicephalobus to thiabendazole and ivermectin using an adaptation of the Micro-Agar Larval Development Test hereby focusing on egg hatching and larval development. Panagrellus redivivus and Panagrolaimus superbus were included as a positive control. The results generally show that the anthelmintic tolerance of Halicephalobus to both thiabendazole and ivermectin was considerably higher than that of the closely related Panagrolaimidae and, compared to other studies, than that of obligatory equine parasites. Our results further reveal a remarkable trend of increasing tolerance from fully free-living isolates towards horse-associated isolates. In vitro anthelmintic testing with free-living and facultative parasitic nematodes offers the advantage of observing drug effect on the complete life cycle as opposed to obligatory parasites that can only be followed until the third larval stage. We therefore propose Halicephalobus gingivalis as an experimental tool to deepen our understanding of the biology of anthelmintic tolerance.     

Development and control of resistance to anthelmintics

The effect of the genetic and biological factors on resistance are generally beyond the control of the operator. However, an understanding of these factors can enable the “resistance risk” (Georghiou, 1983), to be assessed when designing strategies to aid in the control of resistance. The important operator controlled factors relate to the frequency of anthelmintic usage, its efficiency and relation to previously used compounds and integration with stock management.The small post-treatment parasitic sub-population which remains after anthelmintic treatment is likely to have a higher resistance gene frequency compared to the larger pre-treatment parasitic and the freeliving sub-population on pasture. Where treatment frequencies approach the pre-patent period for nematodes, only resistant worms will persist. Likewise if stock are moved after treatment to a pasture free of nematode larvae, subsequent generations will result from the resistant worms carried over, which once again will lead to a resistant population. However, in either of these situations there would initially be a substantial reduction in the size of the parasite population. The subsequent aim is to prevent the increase in the size of the resistant population to the level where production losses occur.The complexities of the association between resistance, anthelmintic usage and stock management indicate the need to understand not just the general factors that effect resistance but also the ecological factors pertinent to a particular region and grazing enterprise. Difficulties will be faced by extension workers who will need to acquire the relevant knowledge to integrate anthelmintic treatment with management strategies that are acceptable to farmers. Some encouragement for the success of this comes from the rapid acceptance of the “Wormkill” drenching program introduced in New South Wales (Dash et al., 1985).     

Anthelmintics for ruminants

There is now a wide range of potent broad-spectrum anthelmintics for cattle and small ruminants, including the benzimidazoles, the avermectins, tetrahydropyrimidines and imidothiazoles which are highly efficacious against parasite gastroenteritis and bronchitis. Fascioliasis can be controlled with the salicy-lanilide and related phenolic compounds, the benzimidazoles, albendazole and triclabendazole the latter being the first flukicide with excellent activity against all stages of liver fluke infestation.The major developments for anthelmintic therapy have been and will be in the use of intraruminal boluses with either sustained release or pulse release of anthelmintic and other methods for group medication. The implications of such strategies for helminth resistance and individual immunity require further evaluation.