A molecular diagnostic tool to replace larval culture in conventional faecal egg count reduction testing in sheep

Occurrence of gastrointestinal nematodes in lambs in Norway, as assessed by copromicroscopy and droplet digital polymerase chain reaction

BACKGROUND

Gastrointestinal nematodes (GINs) have a major impact on sheep production, health, and welfare worldwide. Norway is no exception, but there are only a few studies on the prevalence of GINs in Norwegian sheep. The aim of this study was to investigate the current occurrence of the most important nematodes in sheep flocks in Norway. Faecal samples were collected from flocks in 2021/2022, mainly from three geographical regions in Norway, i.e., northern, eastern, and western. In each of 134 flocks included, individual samples from 10 lambs (autumn) were pooled. Third stage larvae (L3) were cultivated and harvested (Baermann method) from the pooled samples. The DNA was then extracted and further analysed using droplet digital PCR (ddPCR). This enables assessment of the proportions of the three most important nematode species/genera, i.e., H. contortus, T. circumcincta, and Trichostrongylus. The fractional abundance/relative proportion of each species/genus was assessed by performing duplex assays with universal strongyle and species/genus-specific primers and probe sets. In addition, the occurrence of Nematodirus eggs was assessed by standard faecal egg counts (i.e., McMaster method).

RESULTS

Of the 134 flocks sampled, 24 were from the northern region, 31 from eastern, and 71 from western Norway. In addition, some flocks from central (n = 7), and southern (n = 1) Norway were included. Among the sampled flocks, T. circumcincta occurred most commonly (94%), followed by H. contortus (60%) and Trichostrongylus (55%), and Nematodirus (51%). In general, mixed infections were observed, with 38% and 18% of flocks infected with three or all four genera, respectively.

CONCLUSIONS

The results of this study indicate that GINs are widespread in Norway. Teladorsagia circumcincta seems to be present in most flocks based on this screening. Moreover, the results show that Nematodirus spp. infect lambs throughout the country, predominantly N. battus, and indicate that this nematode has become more abundant, which could lead to an increase in nematodirosis.

Faecal egg count reduction tests and nemabiome analysis reveal high frequency of multi-resistant parasites on sheep farms in north-east Germany involving multiple strongyle parasite species

Anthelmintic resistance in sheep parasitic gastrointestinal nematodes is widespread and a severe health and economic issue but prevalence of resistance and involved parasite species are unknown in Germany. Here, the faecal egg count reduction test (FECRT) was performed on eight farms using fenbendazole, ivermectin and moxidectin and on four farms using only moxidectin. A questionnaire was used to obtain data on management practices to potentially identify risk factors for presence of resistance. All requirements of the recently revised WAAVP guideline for diagnosing anthelmintic resistance using the FECRT were applied. Nematode species composition in pre- and post-treatment samples was analysed with the nemabiome approach. Using the eggCounts statistic package, resistance against fenbendazole, ivermectin and moxidectin was found on 7/8, 8/8 and 8/12 farms, respectively. No formal risk factor analysis was conducted since resistance was present on most farms. Comparison with the bayescount R package results revealed substantial agreement between methods (Cohen's κ = 0.774). In contrast, interpretation of data comparing revised and original WAAVP guidelines resulted in moderate agreement (Cohen's κ = 0.444). The FECR for moxidectin was significantly higher than for ivermectin and fenbendazole. Nemabiome data identified 4 to 12 species in pre-treatment samples and treatments caused a small but significant decrease in species diversity (inverse Simpson index). Non-metric multidimensional scaling and k-means clustering were used to identify common patterns in pre- and post-treatment samples. However, post-treatment samples were scattered among the pre-treatment samples. Resistant parasite species differed between farms. In conclusion, the revised FECRT guideline allows robust detection of anthelmintic resistance. Resistance was widespread and involved multiple parasite species. Resistance against both drug classes on the same farm was common. Further studies including additional drugs (levamisole, monepantel, closantel) should combine sensitive FECRTs with nemabiome data to comprehensively characterise the anthelmintic susceptibility status of sheep nematodes in Germany.

Faecal egg count reduction test in goats: Zooming in on the genus level

The faecal egg count reduction test (FECRT) is the most widely used method to assess treatment efficacy against gastrointestinal nematodes (GIN). Information on genera composition of the GIN community is not available with this test and it is commonly obtained by identifying cultured third-stage larvae (L3) or through molecular assays in the post-treatment survey, but results provided are usually only qualitative or semi-quantitative. The updated WAAVP guidelines now recommend assessing anthelmintic efficacy for each GIN genus/species separately (genus-specific FECRT), but this approach is poorly employed in Europe and in goats especially. For this reason, four FECRT trials were conducted using oxfendazole and eprinomectin in two Italian goat farms. Samples were processed individually using the McMaster technique and then pooled to create two samples from faeces of 5 animals each. Pooled samples were analysed using the McMaster and cultured for seven days at 26°C to obtain L3s. The genus-specific FECRT was based on larval identification, integrating coproculture and FEC results. Larvae were identified as Haemonchus, Trichostrongylus, Teladorsagia, Oesophagostomum / Chabertia and Bunostomum. Molecular assays (a multiplex real-time PCR and two end-point PCRs) were also implemented on pooled samples to support the morphological identification. The Spearmann Rho test confirmed a high correlation between the two approaches (Rho = 0.941 and Rho = 0.914 respectively for Haemonchus and Trichostrongylus, the two most common genera). Both oxfendazole and eprinomectin were effective in one farm, while none in the other farm (FECR = 75.9% and 73.3% respectively). In the second farm, the genus-specific FECRT highlighted a different response to treatment among genera: oxfendazole lacked efficacy against both Haemonchus and Trichostrongylus spp., eprinomectin only against Haemonchus, while all other genera were susceptible to both drugs. This study brings new attention on the importance of adopting a genus-specific approach to identify and quantify differences in susceptibility to anthelmintics among genera in goats, providing support for FECRT interpretation, anthelmintic resistance evaluation and evidence-based GIN control.

Correlation of Faecal Egg Counts with Clinical Parameters and Agreement between Different Raters Assessing FAMACHA©, BCS and Dag Score in Austrian Dairy Sheep

Gastrointestinal nematodes, most notably trichostrongylids, are known to cause significant losses in sheep production. Previous studies have shown that monitoring parameters (e.g., FAMACHA©, BCS, dag score) change with increasing egg excretion. These parameters are well known and frequently used for targeted selective treatment. Based on the willingness to participate in this study (based on a previous questionnaire distribution among sheep farmers in Austria) we investigated the associations between faecal egg counts and the FAMACHA©, BCS, and dag scores of 1195 dairy ewes. Faecal samples were analysed using the Mini-FLOTAC technique I and larval culture. Three raters assessed the FAMACHA©, BCS, and dag scores in sheep to calculate the inter-rater agreement and intraclass correlation coefficient. The responses to the questionnaire of 23 farms were used for the evaluation, of which 16 farms were visited. Trichostrongylid eggs were detected in 95% of the faecal samples. The BCS was negatively correlated with the eggs per gram of faeces (EpG) (r = -0.156; p < 0.001) and the FAMACHA© score was slightly positively correlated with EpG (r = 0.196; p < 0.001). A small proportion of sheep (25%) shed the majority of eggs (47% to 84%). A moderate to good agreement for the parameters was found between the raters. In conclusion, the clinical parameters showed only weak correlations with faecal egg counts, and we confirmed that a minority of the flock is responsible for the majority of the pasture contamination with trichostrongylid eggs. Clinical raters should be trained before a study to increase the agreement between them.

Early detection of Pseudocapillaria tomentosa by qPCR in four lines of zebrafish, Danio rerio (Hamilton 1882)

The intestinal nematode Pseudocapillaria tomentosa in zebrafish (Danio rerio) causes profound intestinal lesions, emaciation and death and is a promoter of a common intestinal cancer in zebrafish. This nematode has been detected in zebrafish from about 15% of the laboratories. Adult worms are readily detected about 3 weeks after exposure by either histology or wet mount preparations of the intestine, and larval worms are inconsistently observed in fish before this time. A quantitative PCR (qPCR) test was recently developed to detect the worm in fish and water, and here we determined that the test on zebrafish intestines was effective for earlier detection. Four lines of zebrafish (AB, TU, 5D and Casper) were experimentally infected and evaluated by wet mounts and qPCR at 8, 15-, 22-, 31- and 44-day post-exposure (dpe). At the first two time points, only 8% of the wet mounts from exposed fish were identified as infected, while the same intestines screened by qPCR showed 78% positivity, with low and consistent cycle threshold (Ct) values at these times. Wet mounts at later time points showed a high prevalence of infection, but this was still surpassed by qPCR.

Population genomics of helminth parasites

Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.

Advances in diagnosis of gastrointestinal nematodes in livestock and companion animals

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

Advances in diagnosis and control of anthelmintic resistant gastrointestinal helminths infecting ruminants

Infection with gastrointestinal helminths is widely spread among ruminant causing severe losses and adversely affects the livestock husbandry. Synthetic chemotherapeutics have been utilized throughout years, as a means of combating helminthiasis. Anthelmintic resistance (AR) has a serious concern on livestock industry which, mainly arises as outcome of misuse, improper dosing and frequent utilization of the synthetic drugs.Various gastrointestinal helminths have the capability to survive the therapeutic dose of anthelmintics and become resistant to the major anthelmintic classes. Early diagnosis might delay or reduce the risk of AR. Conventional phenotyping methods were commonly used for detection of anthelmintic resistant helminths, but appeared to lack of sensitivity, especially when the frequency of resistant allele is very low. Several molecular assays were carried out to detect the AR with greater accuracy. Sustainable effective preventive and control measures for gastrointestinal helminths infection remain the corner stone to overcome AR. Rational use of anthelmintics with keeping unexposed proportion of worm populations, could have the potentiality to maintain and prolong the efficacy of anthelmintics. Several alternative anthelmintic treatments might offer valuable solutions either alone or adjunct to synthetic drugs to dilute the spread of resistance alleles among the helminths population. This article reviews current status of various diagnostic methods and control measures for anthelmintic resistant gastrointestinal helminths infecting ruminants and tries to present a practical protocol to avoid or delay the development of AR.

Assessment of three DNA extraction kits for the absolute quantification of strongyle nematode eggs in faecal samples

Background

Haemonchus contortus is one of the most pathogenic gastrointestinal nematodes of small ruminants. The current diagnostic approach for the detection of this species relies on coproscopic methods, which both have low sensitivity and are time consuming. Methods employing detection through DNA amplification, such as droplet digital polymerase chain reaction (ddPCR), offer an advantageous approach to the diagnosis of H. contortus. However, DNA extraction protocols need to be constantly updated for the optimal retrieval of diagnostically usable template. Here, we describe the evaluation of three genomic DNA extraction kits for the detection and quantification of H. contortus ITS2 amplicon DNA from faecal samples, using droplet digital PCR.

Results

DNA samples, extracted from faecal material with the Nucleospin DNA Stool kit, produced the highest amounts of ITS2 amplicon copies and had the lowest coefficient of variation across different dilutions and sample types (fresh or frozen) out of the tested kits (Nucleospin DNA Stool, E.Z.N.A.^® Stool DNA Kit and QIAamp Fast DNA Stool Mini Kit). Furthermore, the protocol of this kit has the fewest number of steps and the price of DNA extraction per sample is reasonable (2.77 €).

Conclusions

The Nucleospin DNA Stool kit is an attractive option for the detection and quantification of H. contortus DNA in faecal samples of small ruminants in a diagnostic setting.

Molecular detection of Strongyloides sp. in Australian Thoroughbred foals

Background

Strongyloides westeri is found in the small intestine of young horses, mainly in foals up to about 16 weeks of age. The main source of infection for foals is through transmammary transmission, and foals can develop acute diarrhoea, weakness, dermatitis and respiratory signs. The epidemiology of S. westeri in Australia is largely unknown. Further, molecular techniques have never been employed for detection of S. westeri in horses. This pilot study aimed to assess the utility of a molecular phylogenetic method for the detection of S. westeri in the faeces of foals.

Methods

Faecal samples were collected from a foal of less than 2 months of age, and eggs of Strongyloides sp. were detected using the modified McMaster technique. DNA was extracted from purified eggs, and a partial fragment of the small subunit of the nuclear ribosomal DNA (18S) was characterised using polymerase chain reaction, DNA sequencing and phylogenetic methods.

Results

Microscopic examination of faeces revealed small ellipsoidal eggs typical of Strongyloides sp. The 18S sequence generated by PCR in this study revealed 98.4% identity with that of a reference sequence of S. westeri available from GenBank. Phylogenetic analyses revealed a polyphyletic clustering of S. westeri sequences.

Conclusion

This is the first study reporting the detection of DNA of Strongyloides sp. in faeces of a foal using a molecular phylogenetic approach targeting the variable region of 18S rDNA. It is anticipated that this study will allow future molecular epidemiological studies on S. westeri in horses.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04966-1.

The identification and semi-quantitative assessment of gastrointestinal nematodes in faecal samples using multiplex real-time PCR assays

BACKGROUND

The diagnosis of gastrointestinal nematode (GIN) infections in ruminants is routinely based on morphological/morphometric analysis of parasite specimens recovered by coprological methods, followed by larval culture (LC) techniques. Such an approach is laborious, time-consuming, requires a skilled expert, and moreover suffers from certain limitations. Molecular tools are able to overcome the majority of these issues, providing accurate identification of nematode species and, therefore, may be valuable in sustainable parasite control strategies.

METHODS

Two multiplex real-time polymerase chain reaction (PCR) assays for specific detection of five main and one invasive GIN species, including an internal amplification control to avoid false-negative results, were designed targeting SSU rRNA and COI genetic markers, as well as established ITS1/2 sequences. The assays were optimized for analysis of DNA extracted directly from sheep faeces and verified for Haemonchus contortus, Teladorsagia circumcincta, Trichostrongylus colubriformis, Nematodirus battus, Chabertia ovina, and Ashworthius sidemi. Semi-quantitative evaluation of infection intensity was enabled using a plasmid construct and a dilution series of sheep faeces with a known number of nematode eggs. Assays were tested on 44 individually collected faecal samples from three farms, and results were compared to those from faecal egg counts (FEC) using the concentration McMaster technique and LC.

RESULTS

Multiplex real-time PCR assays showed great specificity to target nematodes. During the analysis of faecal samples, the assays proved to have higher sensitivity in strongylid-type egg detection over FEC by revealing three false-negative samples, while showing moderate agreement in evaluation of infection intensity. The multiplex assays further clarified GIN species identification compared to LC, which had confused determination of Teladorsagia spp. for Trichostrongylus spp.

CONCLUSIONS

Our multiplex assays proved to be a rapid and accurate approach enabling simultaneous and reliable GIN species identification from faeces and semi-quantitative estimation of the number of eggs present. This approach increases diagnostic value and may add a high degree of precision to evaluation of anthelmintic efficacy, where it is important to identify species surviving after treatment.

Haemonchosis: A Challenging Parasitic Infection of Sheep and Goats

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

Assessment of the F200Y mutation frequency in the β tubulin gene of Haemonchus contortus following the exposure to a discriminating concentration of thiabendazole in the egg hatch test

The ruminant livestock production sector is under threat due to the infections with gastrointestinal nematode parasites and the subsequent development of anthelmintic resistance. One of most common and pathogenic species in small ruminants is Haemonchus contortus. The ability to control the infections with this and other gastrointestinal nematodes relies heavily on the use of anthelmintic drugs. Although resistance to all major classes of anthelmintics has been shown in H. contortus, the precise mechanism of resistance acquisition is only known for benzimidazoles. F200Y (TAC) is a common point mutation in the isotype 1 β tubulin gene which is associated with an effective increase in the resistance towards benzimidazole drugs. Here, we show the utility of using this mutation as a marker in a droplet digital PCR assay to track how two H. contortus laboratory strains, characterized by different resistance levels, change with respect to this mutation, when subjected to increasing concentrations of thiabendazole. Additionally, we wanted to investigate whether exposure to a discriminating dose of thiabendazole in the egg hatch test resulted in the death of all H. contortus eggs with a susceptible genotype. We found the MHco5 strain to maintain an overall higher frequency of the F200Y mutation (80-100%) over all drug concentrations, whilst a steady, gradual increase from around 30%-60% was observed in the case of the MHco4 strain. This is further supported by the dose-response curves, displaying a much higher tolerance of the MHco5 strain (LD₅₀ = 0.38 μg/ml) in comparison to the MHco4 strain (LD₅₀ = 0.07 μg/ml) to the effects of thiabendazole. All things considered, we show that the F200Y mutation is still a viable and reliable marker for the detection and surveillance of benzimidazole drug resistance in H. contortus in Europe.

A survey of gastrointestinal nematode species in red deer (Cervus elaphus) farms in New Zealand using PCR

Gastrointestinal nematodes are recognised as an animal health issue for farmed red deer. The aim of this study was to explore the range of species infecting farmed deer herds and their farm-level prevalence in New Zealand. Faecal samples were collected from 12-24-month-old deer (n = 6-26; mean 19) on 59 farms located in the North (n = 25) and South (n = 34) Islands. Sub-samples of faeces were pooled by farm and cultured to recover third stage larvae. Twenty four larvae were randomly selected and identified to species using a multiplex PCR (total = 1217 larvae). At farm-level the most prevalent nematodes were Oesophagostomum venulosum 83% (n = 49) and the deer-specific nematodes in the subfamily Ostertagiinae (=Ostertagia-type) including, Spiculoptera asymmetrica 73% (n = 43), Ostertagia leptospicularis 47% (n = 28), Spiculoptera spiculoptera 47% (n = 28). The recently identified Trichostrongylus askivali was present on 32% (n = 19) of the farms and Oesophagostomum sikae on 17% (n = 10). In the analysis of the total number of larvae identified, the proportion was in similar order, 45% (n = 548) were O. venulosum, 14% (n = 173) S. asymmetrica, 10% (n = 124) S. spiculoptera, 9% (n = 114) O. leptospicularis, T. askivali, 3% (n = 40) and only 2% were O. sikae (n = 20). This study is the first to show the farm-level prevalence of nematode species in deer in New Zealand and the first to use PCR as a diagnostic tool. It provides data consistent with cross-infection from sheep/cattle to deer, and provided tentative insights into the proportions of the main GIN species across the deer population including O. sikae and T. askivali which have only recently been identified in New Zealand.

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

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

Detection of Haemonchus contortus on sheep farms increases using an enhanced sampling protocol combined with PCR based diagnostics

An enhanced sampling strategy for detection of gastrointestinal parasites of sheep based on faecal sampling covering approximately 10% of the animals in the flock was evaluated with focus on the major sheep pathogen Haemonchus contortus. We also compared traditional diagnostics based on faecal eggs counts (FEC) by microscopy with DNA detection on frozen faeces samples using a droplet digital (dd)PCR assay. The investigation was carried out in 2018 in 20 conventional and 19 organic sheep flocks in Sweden with between 70 and 250 production ewes. On 76 different sampling occasions a total of 810 individual faecal samples were collected. Samples were pooled in the laboratory into 270 triplets which were examined both by microscopy and a ddPCR assay. On most farms (95%) a minimum of three triplets were investigated, first from the ewes prior to turn-out and later from the lambs after they had been grazing for at least six weeks. Extra information about the Haemonchus status was provided on 48% of the 76 sampling occasions by including more triplets compared with the old sampling strategy applied in Sweden before 2015 based on two triplets per sampling occasion irrespective of flock size. At a farm level H. contortus was identified by microscopy in 22 (56%) of the 39 flocks and by ddPCR it was found in 28 (72%) flocks with the enhanced protocol. There was a substantial agreement between the two diagnostic tests (Cohens kappa = 0.70 ± 0.087). No significant differences in infection levels were observed between the two production systems (conventional and organic) irrespective of the diagnostic method used. However, samples from the ewes were more often Haemonchus positive than those from the lambs indicating that the level of parasite control was in general acceptable. Combined, our results show that Haemonchus infection is widespread throughout Sweden. In conclusion, we have validated a practical tool for sheep producers to assess Haemonchus infection with high precision.

The current status of anthelmintic resistance in a temperate region of Australia; implications for small ruminant farm management

Widespread anthelmintic resistance in small ruminants is a constraint on the profitability of the meat/wool industry. Limited published data is available on the prevalence and efficacy of anthelmintics, particularly in Australia where parasites affecting ruminant systems vary greatly between geographic regions. This paper reports on the anthelmintic resistance status in a temperate region of Victoria, Australia, a major sheep producing state largely affected by Trichostrongylus species and Teladorsagia circumcincta. The prevalence of anthelmintic resistance to any product was high (71%), with farms reporting varying levels of drug efficacies (21-100%). Resistance to older chemical groups (i.e. fenbendazole and levamisole) and single active macrocyclic lactone treatments was higher than newer chemical groups and combination treatments. This report provides clarity on anthelmintic resistance in the temperate region of Victoria and more importantly suggests that more comprehensive, regional specific anthelmintic resistance studies are required to understand the real level of chemical resistance threatening the effective control of worms.

In vitro predatory activity of nematophagous fungi isolated from water buffalo feces and from soil in the Mexican southeastern

Nematophagous fungi from the feces of water buffalo and soil from southeastern Mexico were isolated, and their in vitro predatory activity against Haemonchus contortus infective larvae (L3) (HcL3) was assessed. The fungi were isolated by sprinkling soil or feces on water agar plates. Six series of 10 Petri dishes containing a 7-day-old culture of each fungus and a series without fungi as the control were prepared. Five hundred HcL3 were added to each plate. The plates were incubated at room temperature. The average of recovered HcL3 was considered to estimate the larval reduction rate. Four nematophagous fungi isolates corresponding to Arthrobotrys oligospora, var microspora (strains 4-276, 269 and 50-80) and one identified as A. oligospora,var. oligospora (isolates 48-80) were obtained from water buffalo feces. From the soil, five isolates were isolated; three corresponded to A. musiformis (Bajío, Yumca and Macuspana isolates), and two isolates were identified as A. oligospora (Comalcalco and Jalapa de Méndez isolates). The predatory activity of isolates from water buffalo feces ranged between 85.9 and 100%. Meanwhile, the fungi from the soil ranged between 55.5 and 100% (p≤0.05). The nematophagous fungi obtained could have important implications in the control of parasites of importance in the livestock industry.

Genetic variants in dyf-7 validated by droplet digital PCR are not drivers for ivermectin resistance in Haemonchus contortus

Resistance to ivermectin (IVM) in the nematode Haemonchus contortus in small ruminants is an increasing problem throughout the world. Access to molecular diagnostics will allow early detection of IVM resistance, which in turn can limit the spread of resistant isolates. One candidate gene which has recently been suggested as a marker for IVM resistance is that for dye-filling protein (dyf-7). In this study, we critically investigated the suitability of A141G and G153T single nucleotide polymorphisms (SNP) of dyf-7 as a marker in larval cultures collected from sheep farms in Sweden, involving several isolates for which resistance status had been characterised by the faecal egg count reduction test (FECRT). Initially, we designed dyf-7 primers from a worldwide collection of adult Haemonchus contortus DNA. With the sequence data, we created a haplotype network. We then optimised and used the same sets of primers and probes in a droplet digital PCR (ddPCR) assay for precise quantification of dyf-7 allele frequencies in pre- and post-anthelmintic treatment faecal larval cultures. The fractional abundance (FA) of the mutant SNP was within the range 7.8 and 31%. However, the FA was generally stable in samples collected from the same farms, even though they were obtained on different occasions up to 25 months apart. There was also no indication that the level of IVM resistance as measured by the faecal egg count reduction test was higher on farms with high FA. Furthermore, by comparing FA in samples from the same farms pre- and post-IVM treatment, we found no evidence of a correlation between dyf-7 and level of IVM resistance. Based on these results, dyf-7 is not a suitable marker for field testing of IVM resistance in H. contortus.

Droplet digital polymerase chain reaction (ddPCR) as a novel method for absolute quantification of major gastrointestinal nematodes in sheep

In this paper, we present for the first time a new tool, based on Droplet Digital™ Polymerase Chain Reaction (ddPCR), for absolute quantification of key genera of gastrointestinal (GI) nematode parasites of grazing livestock. Four combinations of primers/probe sets targeting the internal transcribed spacer region 2 (ITS2) of the ribosomal RNA gene array were designed using the Primer3 software, following in silico analysis of nucleotide sequences from nematodes of interest downloaded from common databases. The amplified regions include both a universal region for detection of any strongylid gastrointestinal parasite and three different genus specific regions, making it possible to differentiate between the most important GI nematodes of sheep in Sweden: Haemonchus, Teladorsagia and Trichostrongylus. Analysis of samples containing serial dilutions and different mixtures of genomic DNA extracted from different species of adult worms proved useful in assessment of different threshold settings with the QuantaSoft software. Analysis of template DNA from these worms indicated that ddPCR is a viable choice for detection and absolute quantification of the different genera and also in samples with multiple species. Interpretation of the ddPCR results was straightforward and choice of analytical approach had little influence on the final results. Thus, the results obtained in the different analytical approaches seemed to be robust and the concentrations determined were uniform. Furthermore, the linear range of the Haemonchus ddPCR assay was similar to that of real-time PCR (qPCR). Taken together, our data confirm the suitability of ddPCR for detection and absolute quantification of three major sheep pathogens when tested on larval cultures from pooled ovine faeces. The results also indicate that ddPCR can be a useful complement to applications based on conventional egg counting methods such as the faecal egg reduction test (FECRT).

Multiplexed-tandem PCR (MT-PCR) assay to detect and differentiate gastrointestinal nematodes of alpacas

BACKGROUND

Gastrointestinal nematodes (GINs) frequently infect South American camelids (alpacas and llamas) and cause economic losses due to reduced production of fiber, meat and/or leather. Our knowledge about the epidemiology and diagnosis of GINs in llamas and alpacas is limited, and reliable keys for the identification of the third-stage larvae (L3s) of some common nematodes (such as Camelostrogylus mentulatus) that infect alpacas and llamas remain undescribed. In this study, we modified two existing semi-quantitative multiplexed-tandem (MT)-PCR assays, originally developed for the GINs of sheep and cattle, to reliably detect and differentiate the common genera/species of GINs in the faeces of alpacas.

RESULTS

Following the establishment of the MT-PCR assay using positive and negative control samples, alpaca faecal samples were tested to validate the assay to detect and differentiate nematode genera/species, including C. mentulatus, Cooperia spp., Haemonchus spp., Oesophagostomum spp., Ostertagia ostertagi, Teladorsagia circumcincta and Trichostrongylus spp. Sequencing of the MT-PCR products demonstrated specific (100%) amplification of the target nematode genera/species. Additionally, a comparison of results of the MT-PCR assay and the morphological identification of adult worms collected from the same 35 alpacas revealed that there was a good agreement (37-94%) between the two methods. However, some discrepancies were observed between the results of the MT-PCR assay and the morphological identification of adult worms.

CONCLUSIONS

The MT-PCR platform is an accurate, sensitive and rapid method for the diagnosis of GINs in alpacas, and it can be used as a substitute to larval culture to identify common nematodes in the faeces of alpacas and llamas.

Helminths of veterinary and zoonotic importance in Nigerian ruminants: a 46-year meta-analysis (1970-2016) of their prevalence and distribution

BACKGROUND

The livestock industry plays a vital role in the economy of Nigeria. It serves as a major source of income and livelihood for majority of Nigerians who are rural settlers and contributes about 5.2% to the National Gross Domestic Product (GDP). Helminths however, cause economic losses due to reductions in milk production, weight gain, fertility and carcass quality. Zoonotic helminths of livestock origin cause health problems in humans.

METHODS

Using the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines, the prevalence and distribution of helminths of veterinary and zoonotic importance in Nigerian ruminants were determined in a meta-analysis of data published between 1970 and 2016. Data were stratified based on regions, hosts, study periods, sample sizes and study types while helminths were phylogenetically grouped into cestodes, nematodes and trematodes.

RESULTS

Data from 44 studies reported across 19 Nigerian states revealed an overall pooled prevalence estimate (PPE) of 7.48% (95% CI: 7.38-7.57) for helminths of veterinary and zoonotic importance from a total of 320 208 ruminants. We observed a significant variation (P < 0.001) between the PPEs range of 1.90% (95% CI: 1.78-2.02) and 60.98% (95% CI: 58.37-63.55) reported across different strata. High heterogeneity (99.78, 95% CI: 7.38-7.57) was observed. Strongyloides papillosus was the most prevalent (Prev: 32.02%, 95% CI: 31.01-33.11), while, Fasciola gigantica had the widest geographical distribution.

CONCLUSIONS

Helminths of veterinary and zoonotic importance are prevalent in ruminants and well distributed across Nigeria. Our findings show that helminths of ruminants may also be possible causes of morbidity in humans and economic losses in the livestock industry in Nigeria. High heterogeneity was observed within studies and the different strata. Good agricultural practices on farms, standard veterinary meat inspection and adequate hygiene and sanitation in abattoirs, farms and livestock markets need to be implemented in Nigeria in order to reduce the economic, public health and veterinary threats due to these helminths.

A quick and simple benchtop vortex egg-disruption approach for the molecular diagnosis of Fasciola hepatica from ruminant faecal samples

Commonly employed diagnostic methods for Fasciola spp., such as a traditional sedimentation and faecal egg count, or a commercially available coprological ELISA, have limitations in their sensitivity or ability to differentiate species. A reliable DNA isolation method coupled with real-time PCR addresses these issues by providing highly sensitive and quantitative molecular diagnosis from faecal samples. The current study evaluated a standard benchtop vortex for F. hepatica egg disruption in sheep and cattle faecal samples and determined the minimum faecal egg load required for a positive result from un-concentrated (raw) faecal samples. The minimum faecal egg load for a positive real-time PCR result from 150 mg raw faecal sample was 10 and 20 eggs per gram for sheep and cattle, respectively. No significant difference (P = 0.4467) between disruptions on a benchtop vortex for 5 or 10 min was observed when compared to 40 s of disruption at 6.0 m/s in a benchtop homogeniser.

Multiplexed-tandem PCR for the specific diagnosis of gastrointestinal nematode infections in sheep: an European validation study

BACKGROUND

Traditional methods of detecting and identifying gastrointestinal nematode infections in small ruminants, including sheep and goats, are time-consuming and lack in sensitivity and specificity. Recently, we developed an automated multiplexed-tandem (MT)-PCR platform for the diagnosis and identification patent infections with key genera/species of gastrointestinal nematodes of sheep and validated this approach in detailed experiments carried out in Australia. In the present study, we deployed this diagnostic platform in Scotland and Belgium to test samples from naturally infected sheep in these environments and to validate the MT-PCR platform relative to traditional diagnostic methods routinely used by local laboratories.

RESULTS

MT-PCR detected all microscopy positive samples and there was a significant agreement between the results of the different test methods in terms of the species detected and their relative proportion in a test sample, however, for some samples, there were discrepancies between the results of the different test methods. Selective sequencing of purified MT-PCR products demonstrated the results to be 100% specific.

CONCLUSIONS

The MT-PCR platform is an advanced method for the species/genus-specific diagnosis of gastrointestinal nematode infections in small ruminants and has demonstrated utility when deployed in different countries and climatic zones. The platform is user-friendly due to the largely automated procedure and has high versatility in that it can achieve a specific diagnosis from different types of sample templates, including larval culture and faecal samples. With appropriate modifications of the primers used, the MT-PCR platform also provides potential for the diagnosis of a variety of other pathogens of veterinary or medical importance.

A real-time PCR approach to identify anthelmintic-resistant nematodes in sheep farms

Resistance to fenbendazole, ivermectin, and moxidectin was explored by a fecal egg count reduction test in four meat sheep flocks in southwestern France where anthelmintic resistance was suspected. The FECR test results of the present study confirmed the presence of benzimidazole resistance in three out of the four farms and the presence of ivermectin resistance in one flock. In addition, a suspicion of moxidectin resistance was shown in this latter farm. Both conventional morphological and molecular identifications were performed on larval cultures before and after the treatment in the studied farms. A high positive correlation was found between the number of larvae counted under binocular microscope and the number of larvae estimated by the qPCR analysis (R ² = 0.88) and a high Cohen's Kappa value (0.91) in the detection of strongylid larvae in larval cultures. According to qPCR results, Trichostrongylus species demonstrated high levels of BZ resistance and Teladorsagia circumcincta was involved in the IVM resistance in one farm. The molecular procedures used in this study have the potential to be beneficial for anthelmintic resistance surveillance in sheep industry.

Molecular survey of trichostrongyle nematodes in a Bison bison herd experiencing clinical parasitism, and effects of avermectin treatment

North American bison (Bison bison) producers face many challenges, including the potential clinical and economics problems caused by trichostrongyle nematodes within their herds. Little is known about the prevalence, intensity, geographical distribution and clinical significance of these parasites in commercial bison herds, even from regions where bison production has become popular. This study involved a large herd of bison from eastern South Dakota that was experiencing clinical parasitism due to a temporary over-stocking problem. After documenting fecal egg counts (FECs) and trichostrongyle genera present among the 3 main age-categories (i.e. adults, yearlings, calves) of bison during this heavily infected grazing season, the effects of doramectin treatment on the different age groups was also evaluated. This is the first bison study using PCR to identify genera of trichostrongyles in fecal samples. Virtually all 103 bison fecal samples from all 3 age classes were shedding trichostrongyle eggs by the end of the season, and the mean FECs were 34 eggs/g (EPG) among the cows, 125 EPG in the yearlings, and 186 EGP among calves. Based upon this heavily-infected herd, there is evidence that the susceptibility of bison to trichostrongyles is more similar to beef cattle than to sheep. Other parasites such as Moniezia, Nematodirus, Trichuris, and coccidians were also identified in these samples. All but 3 of the 51 samples analyzed with PCR shown at least 1 trichostrongyle genera. Ostertagia was detected in 68.6% of the samples, Cooperia in 80.39%, Haemonchus in at least 73% and Trichostrongylus in 16% of the herd. Most commonly, bison were infected with combinations of Haemonchus/Ostertagia/Cooperia. After treatment with doramectin, the mean FECs dropped by 99.9% for all of the bison age classes.

The Identification of Haemonchus Species and Diagnosis of Haemonchosis

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

Exploring the Gastrointestinal "Nemabiome": Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities

Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal “nemabiome”. The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the ‘nemabiome’ have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions during co-infection, parasite epidemiology, parasite ecology and the response of parasite populations to both drug treatments and control programs.

Prevalence and severity of anthelmintic resistance in ovine gastrointestinal nematodes in Australia (2009-2012)

OBJECTIVE

This study aimed to provide an indication of the prevalence and severity of anthelmintic resistance (AR) in the Australian sheep industry by compiling the results of faecal worm egg count reduction tests (FECRTs).

METHODS

Government and private parasitology laboratories, pharmaceutical companies and veterinarians known to have conducted FECRTs were asked to provide results that conformed to Australian and New Zealand standard diagnostic procedures.

RESULTS

Data were available from a total of 390 tests, with larval differentiation conducted in 222 cases. Pooled results from all states for the macrocyclic lactone (ML) class showed a lower prevalence of AR against combined species for moxidectin (54%) compared with abamectin (77%) and ivermectin (87%). Analysis by state revealed higher levels of ML-resistant Teladorsagia sp. in Tasmania and Western Australia than in other states and ML-resistant Haemonchus sp. was more frequently detected in New South Wales.

CONCLUSION

This compilation of results of FECRTs conducted by Australian parasitology laboratories in 2009-12 showed widespread AR of the common sheep nematodes (Teladorsagia, Trichostrongylus and Haemonchus) to all broad-spectrum anthelmintics, with the exception of monepantel, whether used singly or in combination.

A real-time PCR assay for the diagnosis of gastrointestinal nematode infections of small ruminants

The diagnosis of gastrointestinal nematode infections in small ruminants is central to studying the biology and epidemiology of these parasites and underpins their control. Traditional methods of diagnosis are inaccurate, time-consuming and laborious. Here, we describe a step-by-step protocol for the molecular-based diagnosis of infections by real-time PCR.

The specific diagnosis of gastrointestinal nematode infections in livestock: larval culture technique, its limitations and alternative DNA-based approaches

The specific diagnosis of gastrointestinal nematode infections in ruminants is routinely based on larval culture technique and on the morphological identification of developed third-stage larvae. However, research on the ecology and developmental requirements of different species suggests that environmental conditions (e.g., temperature and humidity) for optimal development to occur vary between the different species. Thus, employing a common culture protocol for all species will favour the development of certain species over others and can cause a biased result in particular when species proportions in a mixed infection are to be determined. Furthermore, the morphological identification of L3 larvae is complicated by a lack of distinctive, obvious features that would allow the identification of all key species. In the present paper we review in detail the potential limitations of larval culture technique and morphological identification and provide account to some modern molecular alternatives to the specific diagnosis of gastrointestinal nematode infection in ruminants.

Current status for gastrointestinal nematode diagnosis in small ruminants: where are we and where are we going?

Gastrointestinal nematode (GIN) parasites pose a significant economic burden particularly in small ruminant production systems. Anthelmintic resistance is a serious concern to the effective control of GIN parasites and has fuelled the focus to design and promote sustainable control of practices of parasite control. Many facets of sustainable GIN parasite control programs rely on the ability to diagnose infection both qualitatively and quantitatively. Diagnostics are required to determine anthelmintic efficacies, for targeted treatment programs and selection of animals for parasite resistant breeding. This review describes much of the research investigated to date to improve the current diagnostic for the above practices which is based on counting the number of parasite eggs in faeces.

Techniques for the diagnosis of Fasciola infections in animals: room for improvement

The common liver fluke, Fasciola hepatica, causes fascioliasis, a significant disease in mammals, including livestock, wildlife and humans, with a major socioeconomic impact worldwide. In spite of its impact, and some advances towards the development of vaccines and new therapeutic agents, limited attention has been paid to the need for practical and reliable methods for the diagnosis of infection or disease. Accurate diagnosis is central to effective control, particularly given an emerging problem with drug resistance in F. hepatica. Traditional coprological techniques have been widely used, but are often unreliable. Although there have been some advances in establishing immunologic techniques, these tools can suffer from a lack of diagnostic specificity and/or sensitivity. Nonetheless, antigen detection tests seem to have considerable potential, but have not yet been adequately evaluated in the field. Moreover, advanced nucleic acid-based methods appear to offer the most promise for the diagnosis of current infection. This chapter (i) provides a brief account of the biology and significance of F. hepatica/fascioliasis, (ii) describes key techniques currently in use, (iii) compares their advantages/disadvantages and (iv) reviews polymerase chain reaction-based methods for specific diagnosis and/or the genetic characterization of Fasciola species.

Resistência anti-helmíntica em nematoides gastrintestinais de pequenos ruminantes: avanços e limitações para seu diagnóstico

A seleção e a crescente disseminação de nematoides resistentes aos anti-helmínticos mais comumente utilizados, benzimidazóis (BZs), imidazotiazóis e lactonas macrocíclicas (LMs), constituem um sério entrave na produção de pequenos ruminantes em todo o mundo. O uso de métodos eficientes e sensíveis para a detecção e o monitoramento da resistência anti-helmíntica no campo torna-se urgente, especialmente para os grupos de BZs e LMs, devido aos constantes relatos de resistência. A obtenção de um diagnóstico preciso e precoce da resistência é extremamente importante para auxiliar a tomada de decisão em programas de controle parasitário, com o objetivo de preservar a vida útil dos produtos e limitar o desenvolvimento da resistência nas populações de nematoides. Os testes in vivo e, mais recentemente, os testes in vitro têm sido desenvolvidos para a detecção de nematoides resistentes aos principais grupos de anti-helmínticos. No entanto, a disponibilidade de testes in vitro validados e o seu uso prático ainda são muito limitados. Embora o teste de redução na contagem de ovos nas fezes (TRCOF, in vivo - indireto) seja o principal método de escolha para a detecção de resistência no campo, vem recebendo críticas quanto à validade dos resultados, e passa por significativas modificações. Além disso, o desenvolvimento de técnicas moleculares a partir de alterações genômicas gerou avanços consideráveis nessa área de investigação, com o uso de mutações nos códons 167, 198 e 200 do gene da β-tubulina como principais SNPs (polimorfismos de nucleotídeo único; do inglês Single Nucleotide Polymorphisms) associados à resistência aos BZs. A presente revisão tem o objetivo de discutir os métodos de diagnóstico disponíveis para a detecção de resistência anti-helmíntica em nematoides de pequenos ruminantes, destacando progressos e obstáculos para seu uso na rotina laboratorial e no campo.

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.

Impact of gastrointestinal parasitic nematodes of sheep, and the role of advanced molecular tools for exploring epidemiology and drug resistance - an Australian perspective

Parasitic nematodes (roundworms) of small ruminants and other livestock have major economic impacts worldwide. Despite the impact of the diseases caused by these nematodes and the discovery of new therapeutic agents (anthelmintics), there has been relatively limited progress in the development of practical molecular tools to study the epidemiology of these nematodes. Specific diagnosis underpins parasite control, and the detection and monitoring of anthelmintic resistance in livestock parasites, presently a major concern around the world. The purpose of the present article is to provide a concise account of the biology and knowledge of the epidemiology of the gastrointestinal nematodes (order Strongylida), from an Australian perspective, and to emphasize the importance of utilizing advanced molecular tools for the specific diagnosis of nematode infections for refined investigations of parasite epidemiology and drug resistance detection in combination with conventional methods. It also gives a perspective on the possibility of harnessing genetic, genomic and bioinformatic technologies to better understand parasites and control parasitic diseases.

Real-time PCR detection for quantification of infection levels with Ostertagia ostertagi and Cooperia oncophora in cattle faeces

A quantitative real-time polymerase chain reaction (qPCR) based on hydrolysis (TaqMan) probes is described for robust and sensitive detection of the infection levels with eggs and third stage larvae (L3) of Cooperia oncophora and Ostertagia ostertagi isolated from cattle faeces. The current microscopic method for identification of strongyle nematodes in cattle faeces is labour-intensive where reliable species determination also requires trained expertise, which is increasingly lacking. The goal of this study was to develop a sustainable non-labour intensive diagnostic qPCR assay to detect and determine the levels of infection with the two most common gastro-intestinal nematodes (GIN) in cattle faeces targeting the second internal transcribed spacer of nuclear ribosomal DNA (ITS2) region (rDNA). According to our results, this procedure allows to reliably detect the relative proportions of eggs and L3 for each of the two species. This assay produced consistent results when mixtures with known numbers of L3 of both species were tested, although it was also demonstrated that the calculated copy numbers of ITS2 between single L3 sometimes varied very much. In addition, a positive correlation (r(2)=0.23) between the proportion of eggs and L3 in different paired samples collect in the field was observed for both species. Thus, for the first time a qPCR assay is reported, which can discriminate between the two most important cattle nematode parasites in temperate regions. This is of major importance to the livestock sector as it can be used with great precision to demonstrate strategic treatment efficacy that is important for the detection of anthelmintic resistance (AR).

Development and validation of real-time PCR for rapid detection of Mecistocirrus digitatus

Hematophagous activity of Mecistocirrus digitatus, which causes substantial blood and weight loss in large ruminants, is an emerging challenge due to the economic loss it brings to the livestock industry. Infected animals are treated with anthelmintic drugs, based on the identification of helminth species and the severity of infection; however, traditional methods such as microscopic identification and the counting of eggs for diagnosis and determination of level of infection are laborious, cumbersome and unreliable. To facilitate the detection of this parasite, a SYBR green-based real-time PCR was standardized and validated for the detection of M. digitatus infection in cattle and buffaloes. Oligonucleotides were designed to amplify partial Internal Transcribed Spacer (ITS)-1 sequence of M. digitatus. The specificity of the primers was confirmed by non-amplification of DNA extracted from other commonly occurring gastrointestinal nematodes in ruminants. Plasmids were ligated with partial ITS-1 sequence of M. digitatus, serially diluted (hundred fold) and used as standards in the real-time PCR assay. The quantification cycle (Cq) values were plotted against the standard DNA concentration to produce a standard curve. The assay was sensitive enough to detect one plasmid containing the M. digitatus DNA. Clinical application of this assay was validated by testing the DNA extracted from the faeces of naturally infected cattle (n = 40) and buffaloes (n = 25). The results were compared with our standard curve to calculate the quantity of M. digitatus in each faecal sample. The Cq value of the assay depicted a strong linear relationship with faecal DNA content, with a regression coefficient of 0.984 and efficiency of 99%. This assay has noteworthy advantages over the conventional methods of diagnosis because it is more specific, sensitive and reliable.

Comparative evaluation of two DNA isolation techniques for PCR-based diagnosis of gastrointestinal nematode infections in sheep

The specific diagnosis of gastrointestinal parasite infections in livestock is central to their control. PCR assays have been developed for routine diagnosis and to overcome limitations of classical methods. Central to the performance of such assays is the effective isolation of the nucleic acids from samples and the elimination of components that are inhibitory to PCR. Here, we directly compared two techniques for the isolation of DNA from strongylid nematode eggs from faecal samples from sheep, and assessed their performance in relation to the sensitivity and specificity of PCR, time required for DNA isolation and ease of use. The results showed differences in the performance of the two isolation techniques, subsequently effecting the PCR results. The main differences related to the time required for DNA isolation, and the elimination of inhibitory substances from the DNA isolated by one technique but not the other.

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.

Establishment of a robotic, high-throughput platform for the specific diagnosis of gastrointestinal nematode infections in sheep

The accurate diagnosis of strongylid nematode infections is central to investigating their epidemiology and for parasite control. To overcome major limitations in sensitivity or specificity of traditional methods, including faecal egg count (FEC) and/or larval culture (LC), we evaluated and established a semi-automated, high throughput multiplexed-tandem PCR (MT-PCR) platform for the diagnosis of gastrointestinal strongylid nematode infections in sheep, and established its diagnostic sensitivity (100%) and specificity (87.5%) based on the testing of 100 faecal DNA samples from helminth-free sheep and 30 samples from sheep with infections confirmed by necropsy. Subsequently, the platform was employed to test 219 faecal samples from sheep with naturally acquired infections from various geographical localities within Australia and the results compared with those from conventional LC using 139 of the 219 samples. The results obtained using both MT-PCR and LC correlated significantly for most nematodes examined, but revealed that Oesophagostomum venulosum and Chabertia ovina (parasites of the large intestine) were significantly under-represented in the LC results. The results showed that Trichostrongylus spp. (87%), Teladorsagia circumcincta (80%) and Haemonchus contortus (67%) had the highest prevalences, followed by O. venulosum (51%) and C. ovina (12%). The molecular-diagnostic platform established can be used for species- or genus-specific diagnosis of patent nematode infections within 24h (compared with 7-10 days for LC), and is a sensitive and cost effective tool for routine application in research and service laboratories.