Non-invasive assessment of parasitic nematode species diversity in wild Soay sheep using molecular markers

World Association for the Advancement of Veterinary Parasitology (W.A.A.V.P.): Third edition of the guideline for evaluating efficacy of anthelmintics in ruminants (bovine, ovine, caprine)

This guideline is aimed at those who are involved in the assessment of anthelmintic efficacy in ruminant livestock species (bovine, ovine and caprine). The intent is to provide a framework that can be adopted worldwide for the testing of anthelmintics in ruminants, such that studies carried out in different countries can be compared and thereby unnecessary duplication can be reduced. Recommendations are made for the selection, housing and feeding of study animals, the type of studies required, the method used to conduct those studies, the assessment of results and the standards for defining anthelmintic efficacy.

A molecular assessment of Ostertagia leptospicularis and Spiculopteragia asymmetrica among wild fallow deer in Northern Ireland and implications for false detection of livestock-associated species

BACKGROUND

Wild deer populations utilizing livestock grazing areas risk cross-species transmission of gastrointestinal nematode parasites (GINs), including GINs with anthelmintic resistance (AR) traits. Wild deer have been shown to carry problematic GIN species such as Haemonchus contortus and Trichostrongylus species in the UK, but the presence of livestock GINs in Northern Ireland deer populations is unknown. Also, is it not known whether AR traits exist among GINs of deer such as Ostertagia leptospicularis and Spiculopteragia asymmetrica in pastureland where anthelmintics are heavily used.

METHODS

Adult-stage GIN samples were retrieved from Northern Irish wild fallow deer abomasa. Individual specimens were subject to a species-specific PCR analysis for common sheep and cattle GIN species with ITS-2 sequence analysis to validate species identities. In addition, the beta-tubulin gene was subject to sequencing to identify benzimidazole (BZ) resistance markers.

RESULTS

ITS-2 sequencing revealed O. leptospicularis and S. asymmetrica, but species-specific PCR yielded false-positive hits for H. contortus, Teladorsagia circimcincta, Trichostrongylus axei, T. colubriformis, T. vitrinus and Ostertagia ostertagi. For beta-tubulin, O. leptospicularis and S. asymmetrica yielded species-specific sequences at the E198 codon, but no resistance markers were identified in either species at positions 167, 198 or 200 of the coding region.

DISCUSSION

From this report, no GIN species of significance in livestock were identified among Northern Ireland fallow deer. However, false-positive PCR hits for sheep and cattle-associated GINs is concerning as the presence of deer species in livestock areas could impact both deer and livestock diagnostics and lead to overestimation of both GIN burden in deer and the role as of deer as drivers of these pathogens. ITS-2 sequences from both O. leptospicularis and S. asymmetrica show minor sequence variations to geographically distinct isolates. AR has been noted among GINs of deer but molecular analyses are lacking for GINs of wildlife. In producing the first beta-tubulin sequences for both O. leptospicularis and S. asymmetrica, we report no BZ resistance in this cohort.

CONCLUSIONS

This work contributes to genetic resources for wildlife species and considers the implications of such species when performing livestock GIN diagnostics.

Molecular identification of Haemonchus contortus in sheep from Upper Egypt

Introduction

Haemonchus spp. are considered the most important strongylid nematodes with a worldwide distribution. The parasite's blood-sucking nature can lead to severe anemia in infected animals. Despite its widespread impact, there is a dearth of comprehensive data on morphological and molecular identification methods for Haemonchus spp. in sheep from Upper Egypt. To address this gap, our current study aimed to assess the prevalence of Haemonchus spp. in 400 sheep fecal samples.

Methods

We employed microscopic examination and molecular techniques, using polymerase chain reaction (PCR) targeting the 18S gene for precise identification. Additionally, the potential risk factors associated with the infection by the parasite in sheep were explored.

Results

The study pointed out that 33.00% (132 of 400) of the examined sheep were infected with Haemonchus spp. Sheep age and seasonal variability were found to be significant factors (p < 0.05) associated with the infection. Notably, sheep under 2 years old exhibited a higher risk, with an infection rate of 43.75% (84 out of 192), than their older counterparts. Furthermore, all reported infections were exclusively observed during the cold season, constituting 58.93% (132 out of 224) of cases. By contrast, no statistically significant association (p > 0.05) was found between the sex of the examined sheep and the occurrence of haemonchosis. Employing molecular methods, we isolated and identified the parasite through PCR analysis of cultured larvae, which were then subsequently confirmed as Haemonchus contortus via phylogenetic analysis.

Discussion

The study concluded that there was a relatively high occurrence of H. contortus among sheep from Upper Egypt. We recommend the implementation of stringent and effective control measures to combat the infection and safeguard livestock health.

Molecular identification and phylogenetic analysis of gastrointestinal nematodes in different populations of Kazakh sheep

Gastrointestinal nematode (GIN) infection in sheep has been recognized globally as a major problem challenging animal health and production. The objective of this study is to use a molecular diagnosis of the prevalence for gastrointestinal nematode (GIN) dominant species of Kazakh sheep and its hybrid (Kazakh × Texel). The internal transcribed spacer 2 (ITS-2) sequences of ribosomal DNA (rDNA) were used as the target sequence. In the study, three dominant species of nematodes, namely Haemonchus contortus, Trichostrongylus spp., and Teladorsagia (Ostertagia) circumcincta from the Kazakh sheep and the F1 and F2 generations of Texel × Kazakh sheep hybrids were subjected to molecular identification and phylogenetic analysis. The fecal and single larva genomic DNA were extracted and amplified by PCR using specific primers to determine the infection rate of the three nematode species. In addition, the PCR products were sequenced and analyzed using bioinformatics methods to construct a phylogenetic tree. The results showed that all the three species had their ITS-2 specific amplified. According to the sequence homology analysis of PCR products, the results showed a high homology (above 98.5% homology) with H. contortus, Trichostrongylus spp., T. circumcincta ITS-2 sequences in GenBank. Phylogenetic analysis showed that the ITS-2 sequences of the three species were on the same branch as the ITS-2 sequences of the same species in NCBI. And on different branches from those of the ITS-2 sequences of different families, genera and species. Sequences carried out on three species from different samples showed a close relationship and little genetic difference in phylogenetic tree. The infection rates based on fecal DNA were 35.59, 25.55, and 11.24% for H. contortus, Trichostrongylus spp., and T. circumcincta, respectively. While the infection rates based on larva DNA, were 24.07, 18.89, and 13.26% for H. contortus, Trichostrongylus spp., and T. circumcincta, respectively. The seasonal prevalence of the three dominant species in spring was significantly higher than that in autumn and winter. And there was no significant difference between Kazakh, F1 and F2 sheep considering the infection rate of the studied three species of nematodes. This study provides valuable molecular approaches for epidemiological surveillance and for assisting in the control of Nematodirus infection in sheep.

Molecular and phylogenetic characterization of zoonotic Trichostrongylus species from goats for the first time in Bangladesh

BACKGROUND

Trichostrongylus is one of the most important nematodes infecting animals and humans. The current study was designed to identify the Trichostrongylus species infecting goats by multiplex PCR and phylogenetic analysis.

METHODS

A total of 124 goats' viscera were collected from different abattoirs of Mymensingh division. Trichostrongylus species were isolated and characterized based on morphometry, multiplex PCR and phylogenetic analysis.

RESULTS

Among 124 viscera of goats, 39 were positive with two species, Trichostrongylus colubriformis and Trichostrongylus vitrinus, revealing an overall 31.45% prevalence. Morphological identification of Trichostrongylus species was confirmed by multiplex PCR amplification of the ITS2 gene and sequencing. Partial sequencing of the ITS2 gene of two species revealed seven single nucleotide polymorphisms (three transitions and four transversions) in this study. The neighbor-joining phylogenetic tree demonstrated that T. colubriformis and T. vitrinus isolates were clustered together with the reference sequences that belong to the clade A and B without any geographical boundaries.

CONCLUSIONS

This is the first report on molecular and phylogenetic analysis of Trichostrongylus species from ruminants in Bangladesh. These results provide the baseline data for understanding the zoonosis and epidemiology of this parasite in Bangladesh and global perspectives.

Low-Molecular-Weight Secondary Metabolites from Fungi: Cerrena unicolor as a New Proposal of an Effective Preparation against Rhabditis Nematodes

Plants and fungi are known as a valuable source of natural medicines used in the treatment of various diseases. Many of them are used to treat human and animal gastrointestinal diseases caused by parasites. The aim of this study was to investigate for the first time the antinematode properties of extracellular low-molecular subfractions (ex-LMS) obtained from the liquid growth medium of idiophasic Cerrena unicolor cultures. The fungal fractions were isolated according to a procedure previously described by Jaszek et al. The in vitro tests were performed using nematodes of the Rhabditis genus. As demonstrated by the results, the total fraction with a molecular weight < 10 kDa (CU-A) and the 0.02−1.5 kDa fraction (CU-B) had nematicidal activity. It was found that the analyzed substances induced movement disturbances caused by the paralysis of the back part of the nematode’s body. The degree of body paralysis was proportional to the increase in the concentration of the tested fractions. Summarizing the obtained results in the context of the available literature data, it seems that C. unicolor may be a good new candidate for research on nematode infections.

Characterizing parasitic nematode faunas in faeces and soil using DNA metabarcoding

Background

Gastrointestinal parasitic nematodes can impact fecundity, development, behaviour, and survival in wild vertebrate populations. Conventional monitoring of gastrointestinal parasitic nematodes in wild populations involves morphological identification of eggs, larvae, and adults from faeces or intestinal samples. Adult worms are typically required for species-level identification, meaning intestinal material from dead animals is needed to characterize the nematode community with high taxonomic resolution. DNA metabarcoding of environmental samples is increasingly used for time- and cost-effective, high-throughput biodiversity monitoring of small-bodied organisms, including parasite communities. Here, we evaluate the potential of DNA metabarcoding of faeces and soil samples for non-invasive monitoring of gastrointestinal parasitic nematode communities in a wild ruminant population.

Methods

Faeces and intestines were collected from a population of wild reindeer, and soil was collected both from areas showing signs of animal congregation, as well as areas with no signs of animal activity. Gastrointestinal parasitic nematode faunas were characterized using traditional morphological methods that involve flotation and sedimentation steps to concentrate nematode biomass, as well as using DNA metabarcoding. DNA metabarcoding was conducted on bulk samples, in addition to samples having undergone sedimentation and flotation treatments.

Results

DNA metabarcoding and morphological approaches were largely congruent, recovering similar nematode faunas from all samples. However, metabarcoding provided higher-resolution taxonomic data than morphological identification in both faeces and soil samples. Although concentration of nematode biomass by sedimentation or flotation prior to DNA metabarcoding reduced non-target amplification and increased the diversity of sequence variants recovered from each sample, the pretreatments did not improve species detection rates in soil and faeces samples.

Conclusions

DNA metabarcoding of bulk faeces samples is a non-invasive, time- and cost-effective method for assessing parasitic nematode populations that provides data with comparable taxonomic resolution to morphological methods that depend on parasitological investigations of dead animals. The successful detection of parasitic gastrointestinal nematodes from soils demonstrates the utility of this approach for mapping distribution and occurrences of the free-living stages of gastrointestinal parasitic nematodes.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04935-8.

Rapid preparation of gastrointestinal nematode eggs from faeces for PCR identification

Detection of gastrointestinal nematodes (GIN) as both a qualitative and quantitative test is highly desirable. Methods such as multiplex and qPCR are capable of providing such results, but can be laborious and expensive. This paper presents a rapid, low-cost method of preparing GIN egg from faecal samples that produces DNA suitable for PCR analysis. We also describe a set of primers that are suitable for single-tube multiplex PCR.

Phylogenetic analysis of Trichostrongylus vitrinus isolates from southwest Iran

Background

Trichostrongylus is one of the most important zoonotic trichostrongylid nematodes, infecting mostly livestock. Data on its genetic characteristics are lacking in Iran.

Methods

We determined the phylogenetic relationships of Trichostrongylus species in three counties of Kohgiloyeh and Boyerahmad (K-B) province, southwest Iran. Small intestine and abomasum of 70 sheep and goats were investigated.

Results

A total of 35 isolates of Trichostrongylus worms were detected and all were genetically identified as Trichostrongylus vitrinus. Analysis of 321 bp of the internal transcribed spacer 2 (ITS2) of ribosomal DNA revealed 16 genotypes. All genotypes were single nucleotide polymorphisms, including some hypervariable points. All sequences were trimmed to 170 bp, compared with sequences on GenBank including short sequences from other endemic foci of Iran and other countries and all isolates were used to generate a maximum likelihood phylogenetic tree, which consisted of two clades A and B. Clade A included isolates from Iran, Russia, New Zealand, Australia and the UK; clade B only contained South African isolates. Most clade A isolates (north, southwest and west Iran, Russia, New Zealand, Australia and UK) were in a similar phylogenetic position. One subclade was detected in clade A (isolates from Southwest Iran, New Zealand and UK).

Conclusions

We hypothesize that drug resistant T. vitrinus may account for its exclusive detection in our samples. The high similarity of genotypes from Iran, New Zealand and UK may be due to their close political relationships during the colonial era. More research is needed to understand better the phylogeny of T. vitrinus and its relationship with drug resistance and human transmission.

DNA Footprints: Using Parasites to Detect Elusive Animals, Proof of Principle in Hedgehogs

Simple Summary

Nocturnal and elusive animals are notoriously difficult to count—hedgehogs being a prime example. Therefore, any reliable way to demonstrate the presence of a particular animal, within a given area, would be a valuable addition to many ecologists’ tool kits. The proposed method is based upon the idea that you can find a parasite, specific to a vertebrate animal of interest that has a life stage within an invertebrate host. Molecular detection of these parasites is then carried out in the more abundant and easily collected invertebrate intermediate host. The key to this proposed method is the specificity of the parasite to the vertebrate animal and its detection in the invertebrate intermediate hosts. Crenosoma striatum is specific to hedgehogs and was chosen as the parasite to develop the molecular survey tool for hedgehogs, an elusive nocturnal species of considerable interest at present. Results revealed the presence of the nematode only at a site known to be inhabited by hedgehogs confirming the potential of this method to improve the accuracy of recording hedgehog populations.

Abstract

The Western European Hedgehog (Erinaceous europaeus) is a nocturnal animal that is in decline in much of Europe, but the monitoring of this species is subjective, prone to error, and an inadequate basis for estimating population trends. Here, we report the use of Crenosoma striatum, a parasitic nematode specific to hedgehogs as definitive hosts, to detect hedgehog presence in the natural environment. This is achieved through collecting and sampling the parasites within their intermediate hosts, gastropoda, a group much simpler to locate and sample in both urban and rural habitats. C. striatum and Crenosoma vulpis were collected post-mortem from the lungs of hedgehogs and foxes, respectively. Slugs were collected in two sessions, during spring and autumn, from Skomer Island (n = 21), which is known to be free of hedgehogs (and foxes); and Pennard, Swansea (n = 42), known to have a healthy hedgehog population. The second internal transcribed spacer of parasite ribosomal DNA was used to develop a highly specific, novel, PCR based multiplex assay. Crenosoma striatum was found only at the site known to be inhabited by hedgehogs, at an average prevalence in gastropods of 10% in spring and autumn. The molecular test was highly specific: One mollusc was positive for both C. striatum and C. vulpis, and differentiation between the two nematode species was clear. This study demonstrates proof of principle for using detection of specific parasite DNA in easily sampled intermediate hosts to confirm the presence of an elusive nocturnal definitive host species. The approach has great potential as an adaptable, objective tool to supplement and support existing ecological survey methods.

Investigation of a gamasid mite infestation in a UK textile mill caused by Dermanyssus gallinae (DeGeer, 1778) (Mesostigmata: Dermanyssidae) special lineage L1

A recurrent mite infestation affecting a room used to inspect fabric in a UK textile mill was investigated to allay concerns of any potential health risks to factory staff, and to inform the unknown risk of downgrading of the product. The approach integrated conventional morphological examination of adult female mites by referring to published identification keys, with molecular speciation based on amplification of a 16S ribosomal DNA fragment. The methods enabled the mites to be unambiguously identified as Dermanyssus gallinae 'special lineage L1'. Subsequent investigations showed the source of infestation to be pigeons nesting in the air ducts, with the gamasid mites moving into the room once the young birds had fledged. This is the first report of D. gallinae 'special lineage L1' in northern Europe. Previous reports of nosocominal gamasoidosis caused by D. gallinae 'special lineage L1' originating from feral pigeon populations have been from southern Europe. Confirmation of the mite identity was important in allowing the mill to take remedial and preventive action. In this clinical communication, we provide images of the key morphological features used to identify D. gallinae and describe a molecular protocol to confirm 'special lineage L1'.

Prevalence of gastrointestinal parasites in free-range yaks (Bos grunniens) in Gansu Province, Northwest China

BACKGROUND

Little information about the prevalence of gastrointestinal parasites in yaks (Bos grunniens) in northwest China is available. Therefore, the objective of the study was to quantify faecal egg counts of gastrointestinal parasites (helminths and coccidia) in free-range yaks from Gannan Tibetan Autonomous Prefecture, Gansu Province, Northwest China.

RESULTS

Parasites were detected in 290 of 733 (39.56%) faecal samples. The results showed that Strongylidae, Trichuris spp. and Eimeria spp. were detected all year round, Strongyloides papillosus was detected in autumn and summer, and Nematodirus spp. was detected in both autumn and spring. In contrast, Fasciola spp. was only detected in spring. The prevalence rates of parasitic infections in different seasons were significantly different.

CONCLUSIONS

To our knowledge, this is the first investigation of gastrointestinal parasites in yaks (Bos grunniens) in Gansu, China. The results demonstrated a high prevalence of gastrointestinal parasitic infections, specifically GN infections, in yaks in GTAP and these infections can cause economic losses to the local cattle industry.

Molecular screening approach to identify protozoan and trichostrongylid parasites infecting one-humped camels (Camelus dromedarius)

Little is known about the diversity of many parasites infecting camels, with most relying on morphological parameters. DNA extracted from different tissues (n = 90) and fecal samples (n = 101) from dromedary camels (Camelus dromedarius) in Egypt were screened for multiple parasites using different molecular markers. Screening of tissue samples (heart) for Toxoplasma gondii and Sarcocystis spp. was performed using B1 and 18S rRNA gene markers, respectively. T. gondii was further genotyped using multiplex multilocus nested PCR-RFLP (Mn-PCR-RFLP). Sarcocystis was analyzed using PCR-RFLP characterization (XbaI and MboI restriction enzymes). A taxonomically challenging but important group of nematodes (Trichostrongylidae family) were screened using the ITS-2 ribosomal DNA (rDNA) species-specific markers. Furthermore, nested PCR was used for the detection of Cryptosporidium spp. (SSU rRNA gene) and positive samples were genotyped after RFLP (SspI and VspI) and sequencing. Cryptosporidium parvum isolates were subtyped by sequence analysis of the 60-kDa glycoprotein gene. This study revealed that many parasites infect the investigated camels, including T. gondii (1.1%), Sarcocystis spp. (64.4%), Cryptosporidium spp. (5.9%) and Trichostrongylidae nematodes (22.7%). The species contribution for nematodes was as follows: Haemonchus spp. (95.6%), Trichostrongylus axei (26%), Trichostrongylus colubriformis (65.2%) and Cooperia oncophora (60.8%). Mn-PCR-RFLP typing for Toxoplasma was only successful for three markers: 5'-SAG2 (type II), 3'-SAG2 (type II) and alt. SAG2 (type II). PCR-RFLP using XbaI showed possible mixed Sarcocystis infection. Moreover, the Cryptosporidium genotypes detected were C. parvum (IIdA19G1 and IIaA15G1R1), Cryptosporidium rat genotype IV and a novel genotype (camel genotype). This approach revealed the unique Cryptosporidium genotypes infecting the investigated camels, and the high genetic diversity of the investigated parasites.

An appraisal of natural products active against parasitic nematodes of animals

Here, the scientific and patent literature on the activities of purified natural compounds has been reviewed, with the aim of assessing their suitability as anthelmintic drug discovery starting points. Only compounds described as active against parasitic nematodes of animals or against the model nematode Caenorhabditis elegans have been analysed. Scientific articles published since 2010 and patents granted from 2000, both inclusive, have been included in this analysis. The results show a scarcity of novel chemical structures, a limited follow-up of compounds disclosed before 2010 and a bias towards the screening of plant products, almost to the exclusion of other sources, when microbial extracts have, historically, provided most starting points for anti-infective drugs. All plant products published in this period were previously known, alerting to the high re-discovery rates of a limited number of chemical classes from this source. The most promising compounds described in the literature reviewed here, namely the linear nemadectin-derivatives, are novel and of bacterial origin. Patented but otherwise unpublished spiroketal structures also appear as interesting scaffolds for future development. The patent literature confirmed that it is possible to patent derivatives of previously known products, making them valid starting points for translational research.

The population genetics of parasitic nematodes of wild animals

Parasitic nematodes are highly diverse and common, infecting virtually all animal species, and the importance of their roles in natural ecosystems is increasingly becoming apparent. How genes flow within and among populations of these parasites - their population genetics - has profound implications for the epidemiology of host infection and disease, and for the response of parasite populations to selection pressures. The population genetics of nematode parasites of wild animals may have consequences for host conservation, or influence the risk of zoonotic disease. Host movement has long been recognised as an important determinant of parasitic nematode population genetic structure, and recent research has also highlighted the importance of nematode life histories, environmental conditions, and other aspects of host ecology. Commonly, factors influencing parasitic nematode population genetics have been studied in isolation, such that an integrated view of the drivers of population genetic structure of parasitic nematodes is still lacking. Here, we seek to provide a comprehensive, broad, and integrative picture of these factors in parasitic nematodes of wild animals that will be a useful resource for investigators studying non-model parasitic nematodes in natural ecosystems. Increasingly, new methods of analysing the population genetics of nematodes are becoming available, and we consider the opportunities that these afford in resolving hitherto inaccessible questions of the population genetics of these important animals.

Molecular confirmation of Hymenolepis hibernia in field mice (Apodemus sylvaticus) from St Kilda has potential to resolve a host-parasite relationship

Insular wildlife populations provide opportunities to examine biological questions in systems that are relatively closed and potentially tractable, striking examples being the long-term studies of ecology and evolution in the red deer and feral sheep populations on the Hebridean islands of Rum and St Kilda. In the case of parasitology, Understanding of parasitic infections insular wildlife populations in conjunction with knowledge of their origins has the potential to add a fresh perspective to disease control in humans and domestic animals. In the case of parasitology, understanding infections of insular wildlife populations, in conjunction with knowledge of their origins, has the potential to add a fresh perspective to disease control in humans and domestic animals. With this in mind, gross and molecular examination for the presence of cyclophyllidean tapeworms was performed on the viscera and rectal contents of 17 preserved specimens of Apodemus sylvaticus field mice and on the naturally voided faeces of a further four mice on the remote archipelago of St Kilda. Molecular speciation of hexacanth embryos extracted from the faeces of two mice, using nucleotide sequence analysis of the ribosomal cytochrome c-oxidase subunit-1, confirmed infection with Hymenolepis hibernia. Phylogenetic analysis showed that these were genetically distinct from Hymenolepis diminuta, previously reported in the insular A. sylvaticus mice, and from other published H. hibernia haplotypes. There was insufficient hymenolepidid tapeworm phylogeographic variation to resolve the origins of the co-evolved St Kilda mice, primarily due to a lack of published H. hibernia Cox-1 sequence data across the parasite's geographical range. Nevertheless, the Maximum Likelihood haplotype tree shows the potential for molecular parasitology to resolve a host-parasite relationship once more data become available. Morphological diagnostic features of zoonotic H. hibernia eggs are also described.

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First identification of Hymenolepis hibernia in Apodemus sylvaticus hirtensis mice.

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Molecular speciation of hexocanth eggs.

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Morphological description of Hymenolepis hibernia eggs.

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Maximum likelihood hymenolepidid tapeworm haplotype tree.

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Consideration of parasite origins and those of co-evolved hosts.

Hidden in plain sight - Multiple resistant species within a strongyle community

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PCR speciation highlighted parasite species diversity on a commercial UK sheep farm.

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Species diversity confounded interpretation of faecal egg count data and bioassays.

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These tests detected only moderate resistance to benzimidazoles and ivermectin.

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Post-treatment populations were composed almost entirely of Teladorsagia circumcincta.

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Ivermectin strongly selected for a highly dual-resistant and pathogenic species.

Ovine parasitic gastroenteritis is a complex disease routinely treated using anthelmintics. Although many different strongyle species may contribute to parasitic gastroenteritis, not all are equally pathogenic: in temperate regions, the primary pathogen is Teladorsagia circumcincta. In this study we investigated benzimidazole and ivermectin resistance on a commercial sheep farm in southeast Scotland. We assessed the impact of species diversity on the diagnosis of resistance using the faecal egg count reduction test and in vitro bioassays, and correlated the results with the frequency of benzimidazole resistance-associated genotypes measured in the T. circumcincta population by pyrosequencing of the β-tubulin isotype-1 gene.

Faecal egg count reduction test results showed efficacies of 65% for albendazole and 77% for ivermectin, indicating moderate resistance levels on the farm. However, PCR speciation of the same populations pre- and post-treatment revealed that removal of susceptible species had masked the presence of a highly resistant population of T. circumcincta. Less than 25% of individuals in the pre-treatment populations were T. circumcincta, the remainder consisting of Cooperia curticei, Chabertia ovina, Oesophagostomum venulosum and Trichostrongylus spp. In contrast, post-treatment with albendazole or ivermectin, the majority (88% and 100% respectively) of the populations consisted of T. circumcincta. The egg hatch test for benzimidazole resistance and the larval development test for ivermectin resistance were carried out using eggs obtained from the same populations and the results were broadly consistent with the faecal egg count reduction test. Thirty individual T. circumcincta from each sampling time point were assessed for benzimidazole resistance by pyrosequencing, revealing a high frequency and diversity of resistance-associated mutations, including within the population sampled post-ivermectin treatment.

These results highlight the potential diversity of parasite species present on UK farms, and their importance in the diagnosis of anthelmintic resistance. On this particular farm, we demonstrate the presence of a highly dual-resistant population of T. circumcincta, which was strongly selected by treatment with either benzimidazoles or ivermectin, while other potentially less pathogenic species were removed.

A method for single pair mating in an obligate parasitic nematode

Parasitic nematode species have extremely high levels of genetic diversity, presenting a number of experimental challenges for genomic and genetic work. Consequently, there is a need to develop inbred laboratory strains with reduced levels of polymorphism. The most efficient approach to inbred line development is single pair mating, but this is challenging for obligate parasites where the adult sexual reproductive stages are inside the host, and thus difficult to experimentally manipulate. This paper describes a successful approach to single pair mating of a parasitic nematode, Haemonchus contortus. The method allows for polyandrous mating behaviour and involves the surgical transplantation of a single adult male worm with multiple immature adult females directly into the sheep abomasum. We used a panel of microsatellite markers to monitor and validate the single pair mating crosses and to ensure that the genotypes of progeny and subsequent filial generations were consistent with those expected from a mating between a single female parent of known genotype and a single male parent of unknown genotype. We have established two inbred lines that both show a significant overall reduction in genetic diversity based on microsatellite genotyping and genome-wide single nucleotide polymorphism. There was an approximately 50% reduction in heterozygous SNP sites across the genome in the MHco3.N1 line compared with the MoHco3(ISE) parental strain. The MHco3.N1 inbred line has subsequently been used to provide DNA template for whole genome sequencing of H. contortus. This work provides proof of concept and methodologies for forward genetic analysis of obligate parasitic nematodes.

Reliable molecular differentiation of Trichuris ovis and Trichuris discolor from sheep (Ovis orientalis aries) and roe deer (Capreolus capreolus) and morphological characterisation of their females: morphology does not work sufficiently

The main aim of the study was to evaluate associations between morphological variability of Trichuris females from sheep and roe deer and their rDNA polymorphism in whipworm populations from the Czech Republic. The results introduced the use of new molecular markers based on the internal transcribed spacer (ITS)1-5.8S RNA-ITS2 region polymorphisms, as useful tools for the unambiguous differentiation of congeners Trichuris ovis and Trichuris discolor. These markers revealed both parasites in roe deer and in sheep; however, T. ovis females predominated in sheep while T. discolor females occurred mostly in roe deer. Additional analysis of ITS1-5.8 rRNA-ITS2 discovered the genetic uniformity of the analysed T. discolor but high haplotype variation of T. ovis. Simultaneously, molecularly designated female individuals of both species were categorised into four morphotypes (MT) on the basis of morphology of genital pore area. MT1 and MT4 (vulvar opening on everted vaginal appendage/on visible cuticular bulge) occurred only in T. ovis, MT2 (uneverted vagina-vulvar opening without any elevation) was identified only in T. discolor and MT3 (transient type of vulvar opening on a small swelling) was observed in both species. Statistical analysis of biometric data confirmed that morphology of vulva is not a reliable marker for the species determination. On the basis of the ITS1-5.8S RNA-ITS2 region variability, we carried out a phylogenetic analysis (maximum likelihood method, Hasegawa-Kishino-Yano model) which showed that T. ovis haplotypes from the Czech Republic and Ireland and T. discolor haplotypes from the Czech Republic, Spain, Iran and Japan are sister OTUs.

Diagnosis, Treatment and Management of Haemonchus contortus in Small Ruminants

Haemonchus contortus is a highly pathogenic, blood-feeding nematode of small ruminants, and a significant cause of mortalities worldwide. Haemonchosis is a particularly significant threat in tropical, subtropical and warm temperate regions, where warm and moist conditions favour the free-living stages, but periodic outbreaks occur more widely during periods of transient environmental favourability. The clinical diagnosis of haemonchosis is based mostly on the detection of anaemia in association with a characteristic epidemiological picture, and confirmed at postmortem by the finding of large numbers of H. contortus in the abomasum. The detection of impending haemonchosis relies chiefly on periodic monitoring for anaemia, including through the 'FAMACHA' conjunctival-colour index, or through faecal worm egg counts and other laboratory procedures. A range of anthelmintics for use against H. contortus is available, but in most endemic situations anthelmintic resistance significantly limits the available treatment options. Effective preventative programmes vary depending on environments and enterprise types, and according to the scale of the haemonchosis risk and the local epidemiology of infections, but should aim to prevent disease outbreaks while maintaining anthelmintic efficacy. Appropriate strategies include animal management programmes to avoid excessive H. contortus challenge, genetic and nutritional approaches to enhance resistance and resilience to infection, and the monitoring of H. contortus infection on an individual animal or flock basis. Specific strategies to manage anthelmintic resistance centre on the appropriate use of effective anthelmintics, and refugia-based treatment schedules. Alternative approaches, such as biological control, may also prove useful, and vaccination against H. contortus appears to have significant potential in control programmes.

Failure of ivermectin treatment in Haemonchus contortus infected-Swedish sheep flocks

Control of gastrointestinal nematodes of veterinary importance in Swedish sheep flocks is primarily based on recurring strategic anthelmintic treatments after detection of strongyle eggs in faeces samples. This study reports reduced efficacy of ivermectin (IVM) against Haemonchus contortus in naturally infected Swedish sheep flocks. Faecal egg count reduction tests (FECRT) and examinations of H. contortus-specific DNA with qPCR on larval cultures were applied to samples from 11 sheep flocks (A-K) in south-eastern Sweden between 2013 and 2014. Four of these flocks (D, E, J and K) had been in direct contact with flock H, where IVM treatment failure was first observed in October 2013, some years after the introduction of imported dairy sheep. In flock H, the resistance status to IVM was also confirmed by a larval developmental test. IVM concentrations 15-20 times higher than for susceptible strains of H. contortus were required to kill the larvae. In addition, faeces samples were obtained from 37 other Swedish sheep farms where the treatment response to IVM was screened initially in six animals using FEC and qPCR 7-10days after administration of IVM. Six farms where the majority was identified with this pre-screening test (B, C, F, G, I and K), were also investigated in more detail with FECRT as described above after the animals had been allocated to groups and treated orally or injected with a minimum of 0.2mg IVM, 0.2mg doramectin (farm F) or 0.2mg moxidectin per kg body weight (farm A and B). Four flocks (farm A, D, G and I) were also treated with 4.8mg albendazole and/or 7.5mg levamisole per kg body weight. Pre-treatment faeces samples were collected from 15 animals on the same day as deworming. Post-treatment samples were collected 7-10days later, whenever possible from 10 animals per group with the highest pre-treatment egg counts. Based on FECRT results, IVM efficacy to H. contortus was reduced on six farms (C, D, E, G, H and I) out of 11 farms studied with FECRT. This is the first report of IVM treatment failure in H. contortus-infected sheep in Sweden.

Co-Infection and Wild Animal Health: Effects of Trypanosomatids and Gastrointestinal Parasites on Coatis of the Brazilian Pantanal

Wild animals are infected by diverse parasites, but how they influence host health is poorly understood. We examined the relationship of trypanosomatids and gastrointestinal parasites with health of wild brown-nosed coatis (Nasua nasua) from the Brazilian Pantanal. We used coati body condition and hematological parameters as response variables in linear models that were compared using an information theoretic approach. Predictors were high/low parasitemias by Trypanosoma cruzi and T. evansi, and indices representing the abundance of distinct groups of gastrointestinal parasites. We also analyzed how host health changed with host sex and reproductive seasonality. Hemoparasites was best related to coati body condition and hematological indices, whereas abundance of gastrointestinal parasites was relatively less associated with coati health. Additionally, some associations were best predicted by models that incorporated reproductive seasonality and host sex. Overall, we observed a lower health condition during the breeding season, when coatis are under reproductive stress and may be less able to handle infection. In addition, females seem to handle infection better than males. Body condition was lower in coatis with high parasitemias of T. evansi, especially during the reproductive season. Total red blood cell counts, packed cell volume, platelets and eosinophils were also lower in animals with high T. evansi parasitemias. Total white blood cell counts and mature neutrophils were lower in animals with high parasitemias for both Trypanosoma species, with neutrophils decreasing mainly during the reproductive season. Overall, decreases in hematological parameters of females with T. evansi high parasitemias were less evident. For T. cruzi, monocytes decreased in individuals with high parasitemias. High abundances of microfilariae in the bloodstream, and cestode eggs and coccidian oocysts in feces were also associated with coati blood parameters. This study shows the potential value of examining hematological parameters as an approach to better understand the ecological relevance of parasite-host interactions.

A combined parasitological molecular approach for noninvasive characterization of parasitic nematode communities in wild hosts

Most hosts are concurrently or sequentially infected with multiple parasites; thus, fully understanding interactions between individual parasite species and their hosts depends on accurate characterization of the parasite community. For parasitic nematodes, noninvasive methods for obtaining quantitative, species-specific infection data in wildlife are often unreliable. Consequently, characterization of gastrointestinal nematode communities of wild hosts has largely relied on lethal sampling to isolate and enumerate adult worms directly from the tissues of dead hosts. The necessity of lethal sampling severely restricts the host species that can be studied, the adequacy of sample sizes to assess diversity, the geographic scope of collections and the research questions that can be addressed. Focusing on gastrointestinal nematodes of wild African buffalo, we evaluated whether accurate characterization of nematode communities could be made using a noninvasive technique that combined conventional parasitological approaches with molecular barcoding. To establish the reliability of this new method, we compared estimates of gastrointestinal nematode abundance, prevalence, richness and community composition derived from lethal sampling with estimates derived from our noninvasive approach. Our noninvasive technique accurately estimated total and species-specific worm abundances, as well as worm prevalence and community composition when compared to the lethal sampling method. Importantly, the rate of parasite species discovery was similar for both methods, and only a modest number of barcoded larvae (n = 10) were needed to capture key aspects of parasite community composition. Overall, this new noninvasive strategy offers numerous advantages over lethal sampling methods for studying nematode-host interactions in wildlife and can readily be applied to a range of study systems.

The emergence of resistance to the benzimidazole anthlemintics in parasitic nematodes of livestock is characterised by multiple independent hard and soft selective sweeps

Anthelmintic resistance is a major problem for the control of parasitic nematodes of livestock and of growing concern for human parasite control. However, there is little understanding of how resistance arises and spreads or of the "genetic signature" of selection for this group of important pathogens. We have investigated these questions in the system for which anthelmintic resistance is most advanced; benzimidazole resistance in the sheep parasites Haemonchus contortus and Teladorsagia circumcincta. Population genetic analysis with neutral microsatellite markers reveals that T. circumcincta has higher genetic diversity but lower genetic differentiation between farms than H. contortus in the UK. We propose that this is due to epidemiological differences between the two parasites resulting in greater seasonal bottlenecking of H. contortus. There is a remarkably high level of resistance haplotype diversity in both parasites compared with drug resistance studies in other eukaryotic systems. Our analysis suggests a minimum of four independent origins of resistance mutations on just seven farms for H. contortus, and even more for T. circumincta. Both hard and soft selective sweeps have occurred with striking differences between individual farms. The sweeps are generally softer for T. circumcincta than H. contortus, consistent with its higher level of genetic diversity and consequent greater availability of new mutations. We propose a model in which multiple independent resistance mutations recurrently arise and spread by migration to explain the widespread occurrence of resistance in these parasites. Finally, in spite of the complex haplotypic diversity, we show that selection can be detected at the target locus using simple measures of genetic diversity and departures from neutrality. This work has important implications for the application of genome-wide approaches to identify new anthelmintic resistance loci and the likelihood of anthelmintic resistance emerging as selection pressure is increased in human soil-transmitted nematodes by community wide treatment programs.

Genetics and infection dynamics of Paratrichosoma sp in farmed saltwater crocodiles (Crocodylus porosus)

Paratrichosoma-associated helminthiasis has been identified in saltwater crocodiles under intensive farming conditions. The development of sustainable integrated management practices is dependent on a detailed understanding of Paratrichosoma population genetics and infection dynamics. This study investigated the genetic relationships of Paratrichosoma sp in a population of commercially farmed saltwater crocodiles, Crocodylus porosus, in northern Australia. 18S ribosomal RNA gene sequence data were obtained from Paratrichosoma sp eggs present in the epidermis of infected animals. A high level of genetic diversity was distributed within the Paratrichosoma sp population (241 variable positions in the 1094 bp alignment), indicating an accelerated rate of nucleotide base-pair substitutions in this genus of nematodes. Several possible environmental correlates of the incidence and intensity of helminthiasis, including season, rainfall, and mean monthly temperature, were investigated by visual inspection of crocodile skins. Stepwise logistic regression revealed a significant negative linear relationship (P = 0.011, R (2) = 32.69 %) between mean monthly rainfall and the incidence of monthly Paratrichosoma-associated helminthiasis. Variation in the severity of Paratrichosoma-associated helminthiasis could not be explained by any of the independent environmental variables included within an ordinal regression analysis. The large genetic diversity in these nematodes indicates a high probability of anthelmintic resistant alleles occurring in the population. We discuss how the spread of these alleles may be mitigated by adopting targeted treatment protocols.

Towards the molecular characterisation of parasitic nematode assemblages: an evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis

Identifying factors which regulate temporal and regional structuring within parasite assemblages requires the development of non-invasive techniques which facilitate both the rapid discrimination of individual parasites and the capacity to monitor entire parasite communities across time and space. To this end, we have developed and evaluated a rapid fluorescence-based method, terminal restriction fragment length polymorphism (T-RFLP) analysis, for the characterisation of parasitic nematode assemblages in macropodid marsupials. The accuracy with which T-RFLP was capable of distinguishing between the constituent taxa of a parasite community was assessed by comparing sequence data from two loci (the ITS+ region of nuclear ribosomal DNA and the mitochondrial CO1) across ∼20 species of nematodes (suborder Strongylida). Our results demonstrate that with fluorescent labelling of the forward and reverse terminal restriction fragments (T-RFs) of the ITS+ region, the restriction enzyme Hinf1 was capable of generating species specific T-RFLP profiles. A notable exception was within the genus Cloacina, in which closely related species often shared identical T-RFs. This may be a consequence of the group's comparatively recent evolutionary radiation. While the CO1 displayed higher sequence diversity than the ITS+, the subsequent T-RFLP profiles were taxonomically inconsistent and could not be used to further differentiate species within Cloacina. Additionally, several of the ITS+ derived T-RFLP profiles exhibited unexpected secondary peaks, possibly as a consequence of the restriction enzymes inability to cleave partially single stranded amplicons. These data suggest that the question of T-RFLPs utility in monitoring parasite communities cannot be addressed without considering the ecology and unique evolutionary history of the constituent taxa.

Advances in the diagnosis of key gastrointestinal nematode infections of livestock, with an emphasis on small ruminants

Parasitic nematodes (roundworms) of livestock have major economic impact globally. In spite of the diseases caused by these nematodes and some advances in the design of new therapeutic agents (anthelmintics) and attempts to develop vaccines against some of them, there has been limited progress in the establishment of practical diagnostic techniques. The specific and sensitive diagnosis of gastrointestinal nematode infections of livestock underpins effective disease control, which is highly relevant now that anthelmintic resistance (AR) is a major problem. Traditional diagnostic techniques have major constraints, in terms of sensitivity and specificity. The purpose of this article is to provide a brief background on gastrointestinal nematodes (Strongylida) of livestock and their control; to summarize conventional methods used for the diagnosis and discuss their constraints; to review key molecular-diagnostic methods and recent progress in the development of advanced amplification-based and sequencing technologies, and their implications for epidemiological investigations and the control of parasitic diseases.

Next-generation molecular-diagnostic tools for gastrointestinal nematodes of livestock, with an emphasis on small ruminants: a turning point?

Parasitic nematodes of livestock have major economic impact worldwide. Despite the diseases caused by these nematodes, some advances towards the development of new therapeutic agents and attempts to develop effective vaccines against some of them, there has been limited progress in the development of practical diagnostic methods. The specific and sensitive diagnosis of parasitic nematode infections of livestock underpins effective disease control, which is now particularly important given the problems associated with anthelmintic resistance in parasite populations. Traditional diagnostic methods have major limitations, in terms of sensitivity and specificity. This chapter provides an account of the significance of parasitic nematodes (order Strongylida), reviews conventional diagnostic techniques that are presently used routinely and describes advances in polymerase chain reaction (PCR)-based methods for the specific diagnosis of nematode infections. A particular emphasis is placed on the recent development of a robotic PCR-based platform for high-throughput diagnosis, and its significance and implications for epidemiological investigations and for use in control programmes.

Direct and indirect costs of co-infection in the wild: Linking gastrointestinal parasite communities, host hematology, and immune function

Most animals are concurrently infected with multiple parasites, and interactions among these parasites may influence both disease dynamics and host fitness. However, the sublethal costs of parasite infections are difficult to measure and the effects of concomitant infections with multiple parasite species on individual physiology and fitness are poorly described for wild hosts. To understand the direct and indirect physiological costs of co-infection, we investigated the relationships among gastrointestinal parasite richness, species identity, and abundance and host hematological parameters, body condition, and investment in lymphocyte defenses. Using aggregate-scale parasite data from African buffalo (Syncerus caffer), we found few direct or indirect associations between infection and hematology in male hosts, and no significant associations were observed in female hosts or with respect to body condition in either sex. These results suggest that only strong physiological effects are detectable with aggregate-scale parasite data, and that hematological variables may be more sensitive to changes in condition than standard body fat condition indices. Analyses accounting for parasite species identity in female buffalo revealed that different parasites show distinct relationships with host hematology, body condition, and immune investment. However, four of six species-specific associations were obscured when parasites were considered in combination. Overall, fitness-related physiological mediators such as hematological indices may provide assessments of direct and indirect effects of parasite infection, particularly when parasite species identity and community composition are considered.

Molecular diagnosis of infections and resistance in veterinary and human parasites

Since 1977, >2000 research papers described attempts to detect, identify and/or quantify parasites, or disease organisms carried by ecto-parasites, using DNA-based tests and 148 reviews of the topic were published. Despite this, only a few DNA-based tests for parasitic diseases are routinely available, and most of these are optional tests used occasionally in disease diagnosis. Malaria, trypanosomiasis, toxoplasmosis, leishmaniasis and cryptosporidiosis diagnosis may be assisted by DNA-based testing in some countries, but there are very few cases where the detection of veterinary parasites is assisted by DNA-based tests. The diagnoses of some bacterial (e.g. lyme disease) and viral diseases (e.g. tick borne encephalitis) which are transmitted by ecto-parasites more commonly use DNA-based tests, and research developing tests for these species makes up almost 20% of the literature. Other important uses of DNA-based tests are for epidemiological and risk assessment, quality control for food and water, forensic diagnosis and in parasite biology research. Some DNA-based tests for water-borne parasites, including Cryptosporidium and Giardia, are used in routine checks of water treatment, but forensic and food-testing applications have not been adopted in routine practice. Biological research, including epidemiological research, makes the widest use of DNA-based diagnostics, delivering enhanced understanding of parasites and guidelines for managing parasitic diseases. Despite the limited uptake of DNA-based tests to date, there is little doubt that they offer great potential to not only detect, identify and quantify parasites, but also to provide further information important for the implementation of parasite control strategies. For example, variant sequences within species of parasites and other organisms can be differentiated by tests in a manner similar to genetic testing in medicine or livestock breeding. If an association between DNA sequence and phenotype has been demonstrated, then qualities such as drug resistance, strain divergence, virulence, and origin of isolates could be inferred by DNA-based tests. No such tests are in clinical or commercial use in parasitology and few tests are available for other organisms. Why have DNA-based tests not had a bigger impact in veterinary and human medicine? To explore this question, technological, biological, economic and sociological factors must be considered. Additionally, a realistic expectation of research progress is needed. DNA-based tests could enhance parasite management in many ways, but patience, persistence and dedication will be needed to achieve this goal.

Anthelmintic resistance in Swedish sheep flocks based on a comparison of the results from the faecal egg count reduction test and resistant allele frequencies of the beta-tubulin gene

A faecal egg count reduction test (FECRT) survey was conducted during the grazing season 2006 and 2007 to provide an updated indication of the prevalence of anthelmintic resistance in sheep flocks in Sweden. A total of 1330 faecal samples from 90 flocks on 45 farms, with a minimum of 20 ewes each, was collected by local sheep veterinarians. Per treatment group, approximately 15 lambs were dewormed either with oral suspensions of ivermectin (Ivomec vet.) or albendazole (Valbazen vet.). The efficacy on each farm was investigated either in 2006 or 2007 by faecal egg counts collected on the day of treatment and in a new sample from the same animals 7-10 days later. Third-stage larvae (L3) were initially identified morphologically from pooled cultures. These were then used as the source of genomic DNA template for two molecular tests. The first was a PCR-based test for specific identification of Haemonchus contortus, and the second was a Pyrosequencing assay for the analysis of benzimidazole (BZ) resistance targeting the P200 mutation in the parasite's beta-tubulin gene. Larval cultures indicated that Teladorsagia and Trichostrongylus were the predominant genera, but Haemonchus was diagnosed in 37% of the flocks. The PCR results revealed an almost 100% agreement with those farms that had previously been shown to have Haemonchus present, even when the % prevalence was low (approximately 3%). Only two (4%) of the surveyed farms showed evidence of BZ-resistant worm populations, with H. contortus being the species implicated according to post-treatment larval culture results. The Pyrosequencing assay detected BZ resistant allele frequencies of >40% in the Haemonchus-positive farms and 100% resistant alleles in the clinically most resistant farms. These preliminary results suggest that the FECRT is less sensitive than the molecular test at detecting BZ resistance. However, both tests need to be interpreted carefully, bearing in mind the relative proportions of species present and the starting egg and/or larval counts. Parasitological diagnosis of "clinical" resistance was also found against ivermectin in two flocks. However, both the pre-treatment FECs and the reductions in these were low, and only three lambs that had between 100 and 450 EPG after treatment were involved.

Genetics of mating and sex determination in the parasitic nematode Haemonchus contortus

Genetic analysis of parasitic nematodes has been a neglected area of research and the basic genetics of this important group of pathogens are poorly understood. Haemonchus contortus is one of the most economically significant livestock parasites worldwide and is a key experimental model for the strongylid nematode group that includes many important human and animal pathogens. We have undertaken a study of the genetics and the mode of mating of this parasite using microsatellite markers. Inheritance studies with autosomal markers demonstrated obligate dioecious sexual reproduction and polyandrous mating that are reported here for the first time in a parasitic helminth and provide the parasite with a mechanism of increasing genetic diversity. The karyotype of the H. contortus, MHco3(ISE) isolate was determined as 2n = 11 or 12. We have developed a panel of microsatellite markers that are tightly linked on the X chromosome and have used them to determine the sex chromosomal karyotype as XO male and XX female. Haplotype analysis using the X-chromosomal markers also demonstrated polyandry, independent of the autosomal marker analysis, and enabled a more direct estimate of the number of male parental genotypes contributing to each brood. This work provides a basis for future forward genetic analysis on H. contortus and related parasitic nematodes.

Metazoan-protozoan parasite co-infections and host body weight in St Kilda Soay sheep

For hundreds of years, the unmanaged Soay sheep population on St Kilda has survived despite enduring presumably deleterious co-infections of helminth, protozoan and arthropod parasites and intermittent periods of starvation. Important parasite taxa in young Soay sheep are strongyles (Trichostrongylus axei, Trichostrongylus vitrinus and Teladorsagia circumcincta), coccidia (11 Eimeria species) and keds (Melophagus ovinus) and in older animals, Teladorsagia circumcincta. In this research, associations between the intensity of different parasite taxa were investigated. Secondly, the intensities of different parasite taxa were tested for associations with variation in host weight, which is itself a determinant of over-winter survival in the host population. In lambs, the intensity of strongyle eggs was positively correlated with that of Nematodirus spp. eggs, while in yearlings and adults strongyle eggs and coccidia oocysts were positively correlated. In lambs and yearlings, of the parasite taxa tested, only strongyle eggs were significantly and negatively associated with host weight. However, in adult hosts, strongyles and coccidia were independently and negatively associated with host weight. These results are consistent with the idea that strongyles and coccidia are exerting independent selection on Soay sheep.

Microsatellite analysis reveals marked genetic differentiation between Haemonchus contortus laboratory isolates and provides a rapid system of genetic fingerprinting

Many of the Haemonchus contortus isolates currently used for experimental work were originally derived from different regions of the world and are commonly exchanged between laboratories. In most cases, these are largely genetically uncharacterised other than the analyses conducted on specific genes of interest. We have used a panel of eight microsatellite markers to genetically characterise five different commonly used H. contortus isolates including MHco3 (ISE), the isolate chosen for full genome sequencing as part of the H. contortus genome project. There is an extremely high level of genetic differentiation between each of the isolates except the two which have a common origin, MHco1 (MOSI) and MHco3 (ISE). We have investigated the amplification of microsatellite markers from pooled DNA as a potential method for fingerprinting different isolates. Good estimates of the true allele frequencies can be made by amplification from either pooled adult DNA or bulk L3 DNA for seven out of the eight markers tested. Both single worm genotyping and bulk DNA fingerprinting revealed no genetic differentiation between adult worms in the host and larvae derived from faecal culture. Furthermore, none of the eight markers showed genetic changes when isolates were passaged through different individual hosts. Hence the microsatellite genotyping of bulk larval DNA samples provides a simple and rapid method to genetically define and monitor laboratory isolates, and to determine their relationship with particular field populations.

Macrogeographic population structure in a parasitic nematode with avian hosts

Much remains to be discovered about the population genetic structure of parasites, despite the importance of such knowledge to understanding the processes involved in the spread of drug resistance through populations. Here we present a study of population genetic diversity in Trichostrongylus tenuis, an avian parasitic nematode infecting both poultry and game birds, where anthelmintic use is common. We examined diversity of nicotinamide dehydrogenase subunit 4 (nad4) mtDNA sequences within and between seven locations: five in the UK (red grouse hosts), one in Iceland (domestic goose) and one in Norway (willow grouse). Within-UK comparisons showed high nucleotide diversity (pi=0.015, n=23) but no structure between locations (Phi(ST)=0.022, P=0.27), with over 97% of variation distributed within-hosts. The highest diversity was found in Iceland (pi=0.043, n=4), and the lowest in Norway (pi=0.003, n=4). Differentiation between countries was considerable (Phi(CT)=0.44, P<0.05), in spite of the potential mixing effects of gene flow via migrating wild hosts and the poultry trade. However, significant pairwise F(ST) values were found only between Norway and the other locations. Phylogenetic analysis provided statistical support for a separate clade for Norwegian samples only, with unresolved diversity leading to a star-shaped relationship between Icelandic and UK haplotypes. These results suggest that Norwegian T. tenuis are isolated, but that there is some connectivity between UK and Icelandic populations. Although anthelmintic resistance has not yet been reported for T. tenuis, the population structure is such that emerging resistance has the potential to spread by gene flow over a large geographic scale.

Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries)

A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to gastrointestinal parasites and ectoparasitic keds segregating in the free-living Soay sheep population on St. Kilda (UK). The mapping panel consisted of a single pedigree of 882 individuals of which 588 were genotyped. The Soay linkage map used for the scans comprised 251 markers covering the whole genome at average spacing of 15cM. The traits here investigated were the strongyle faecal egg count (FEC), the coccidia faecal oocyst count (FOC) and a count of keds (Melophagus ovinus). QTL mapping was performed by means of variance component analysis so that the genetic parameters of the study traits were also estimated and compared with previous studies in Soay and domestic sheep. Strongyle FEC and coccidia FOC showed moderate heritability (h(2)=0.26 and 0.22, respectively) in lambs but low heritability in adults (h(2)<0.10). Ked count appeared to have very low h(2) in both lambs and adults. Genome scans were performed for the traits with moderate heritability and two genomic regions reached the level of suggestive linkage for coccidia FOC in lambs (logarithm of the odds=2.68 and 2.21 on chromosomes 3 and X, respectively). We believe this is the first study to report a QTL search for parasite resistance in a free-living animal population and therefore may represent a useful reference for similar studies aimed at understanding the genetics of host-parasite co-evolution in the wild.

Population genetic analysis of the ovine parasitic nematode Teladorsagia circumcincta and evidence for a cryptic species

An understanding of genetic variation in parasite populations, and how it is partitioned, is required to underpin many areas of basic and applied research. Population genetic studies on parasitic nematode populations are still in their infancy and have been dominated by the use of single locus markers. We have used a panel of five microsatellite markers to undertake a genetic study of a number of field and laboratory populations of Teladorsagia circumcincta. High levels of polymorphism were seen in all the populations examined with the majority of diversity being within rather than between populations. There was no detectable genetic differentiation between the UK populations examined although they included both laboratory passaged and field isolates derived from different geographical regions and host species. This broadly supports previous mtDNA sequence diversity studies of this parasite in the UK and USA. However, some between-population genetic differentiation was apparent when several populations from French goats and a laboratory population from New Zealand were examined. Most notably, a population from a French goat farm, which has previously been suggested to contain a cryptic species, showed very high levels of genetic differentiation from all the other populations. Analysis of multi-locus genotypes suggested the presence of two sympatric parasite populations on this farm with little or no gene flow between them. This supports the hypothesis that parasites currently defined as T. circumcincta by routine morphological criteria comprise more than a single species.

Gastrointestinal nematode species burdens and host mortality in a feral sheep population

Every few years a large proportion of the feral sheep on Hirta, St Kilda die due to food shortage. The effects of malnutrition are exacerbated by gastrointestinal nematodes. As found in sheep flocks in mainland Britain, Teladorsagia circumcincta has long been considered the predominant and most pathogenic nematode species in all age classes of Soay sheep. Previous research indicated that intensity of this species showed a negative association with host age and comprised 75% of the entire gastrointestinal burden. Here we present new data that show Trichostrongylus axei and Trichostrongylus vitrinus to be the predominant worm pathogens in young Soay sheep. In the present study, Trichostrongylus spp. burdens declined with host age whereas T. circumcincta actually increased in burden over the first few age classes. Also, male hosts had significantly higher burdens of Trichostrongylus spp. than females, with this genus making up a higher proportion of the strongyle egg producing community in male hosts than female hosts. These new findings raise questions concerning our previous interpretation of the main nematode species contributing to strongyle egg count in the population, and the contrasting infection patterns of these nematode species in unmanaged St Kilda Soay sheep compared with domestic sheep in mainland Britain.

Molecular ecology of parasites: elucidating ecological and microevolutionary processes

We review studies that have used molecular markers to address ecological and microevolutionary processes in parasites. Our goal is to highlight areas of research that may be of particular interest in relation to the parasitic lifestyle, and to draw attention to areas that require additional study. Topics include species identification, phylogeography, host specificity and speciation, population genetic structure, modes of reproduction and transmission patterns, and searching for loci under selection.