Comparison of ITS-2 rDNA nemabiome sequencing with morphological identification to quantify gastrointestinal nematode community species composition in small ruminant feces

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.

Benzimidazole-resistance associated mutation in Haemonchus contortus in Norwegian sheep, as detected by droplet digital PCR

The aim of this study was to investigate the occurrence of benzimidazole-resistant Haemonchus contortus in Norwegian sheep flocks. Screening was based on detection of one of the resistance-conferring mutations in the β tubulin isotype 1 gene (F200Y, TAC) in larvae (L3) cultivated from H. contortus eggs from naturally infected sheep. Faecal samples were collected in 2021/2022 from flocks in the northern (n = 34), central (n = 7), eastern (n = 40), southern (n = 1), and western (n = 87) areas of Norway. In total, samples were taken from 169 flocks (spring-ewes samples: 167, autumn-lambs samples: 134). Individual faecal samples were collected from 10 randomly selected ewes (spring) and 10 randomly selected lambs (autumn) in each flock. Faecal samples collected from each flock on each occasion were pooled (lamb and ewe samples pooled separately) and cultured for L3 development. After harvest of larvae (Baermann method), DNA was extracted and then analysed using droplet digital PCR with primer/probe sets targeting the BZ-associated F200Y (TAC) mutation. Haemonchus was found in 60% (80/134) of samples from lambs, and in 63% (106/167) from ewes. Among these, the F200Y mutation was detected in 73% (58/80) of larval samples from lambs and 69% (73/106) of larval samples from ewes, respectively. Although regional differences were evident, the mutation was detected in all areas indicating a widespread distribution and a strong potential for an increasing problem with treatment-resistant haemonchosis in Norwegian sheep flocks.

Low-cost molecular methods to characterise gastrointestinal nematode co-infections of goats in Africa

BACKGROUND

Veterinary diagnostics aid intervention strategies, track zoonoses, and direct selective breeding programs in livestock. In ruminants, gastrointestinal nematode (GIN) parasites are a major cause of production losses, but morphologically similar species limit our understanding of how specific GIN co-infections impact health in resource-limited settings. To estimate the presence and relative abundance of GINs and other helminths at the species level, we sought to develop a low-cost and low-resource molecular toolkit applied to goats from rural Malawi smallholdings.

METHODS

Goats were subjected to health scoring and faecal sampling on smallholdings in Lilongwe district, Malawi. Infection intensities were estimated by faecal nematode egg counts with a faecal subsample desiccated for DNA analysis. Two DNA extraction methods were tested (low-resource magbead kit vs high-resource spin-column kit), with resulting DNA screened by endpoint polymerase chain reaction (PCR), semi-quantitative PCR, quantitative PCR (qPCR), high-resolution melt curve analysis (HRMC), and 'nemabiome' internal transcribed spacer 2 (ITS-2) amplicon sequencing.

RESULTS

Both DNA isolation methods yielded comparable results despite poorer DNA purity and faecal contaminant carryover from the low-resource magbead method. GINs were detected in 100% of samples regardless of infection intensity. Co-infections with GINs and coccidia (Eimeria spp.) were present in most goats, with GIN populations dominated by Haemonchus contortus, Trichostrongylus colubriformis, Trichostrongylus axei, and Oesophagostomum columbianum. Both multiplex PCR and qPCR were highly predictive of GIN species proportions obtained using nemabiome amplicon sequencing; however, HRMC was less reliable than PCR in predicting the presence of particular species.

CONCLUSIONS

These data represent the first 'nemabiome' sequencing of GINs from naturally infected smallholder goats in Africa and show the variable nature of GIN co-infections between individual animals. A similar level of granularity was detected by semi-quantitative PCR methods, which provided an accurate summary of species composition. Assessing GIN co-infections is therefore possible using cost-efficient low-resource DNA extraction and PCR approaches that can increase the capacity of molecular resources in areas where sequencing platforms are not available; and also open the door to affordable molecular GIN diagnostics. Given the diverse nature of infections in livestock and wildlife, these approaches have potential for disease surveillance in other areas.

Preliminary results of the recombinase polymerase amplification technique for the detection of Haemonchus contortus from Hungarian field samples

Haemonchus contortus is a parasitic nematode of small ruminants responsible for significant economic losses and animal health concerns globally. Detection of gastrointestinal nematode (GIN) infection in veterinary practice typically relies on microscopy-based methods such as the faecal egg count and morphological identification of larval culture. However, mixed co-infections are common and species-specific identification is typically time-consuming and expertise-intensive. Compounded by increasing anthelmintic resistance, there is an urgent need to implement the molecular diagnosis of GIN in the livestock industry, preferably in field settings. Advances in isothermal amplification techniques including recombinase polymerase amplification (RPA) assays could improve this. Yet, constraints in RPA kit availability and amplicon detection systems limit the use of this technology in point of care settings. In this study, we present an early-stage, proof-of-concept demonstration of RPA targeting the internal transcribed spacer (ITS2) region of H. contortus. Having tested against eight closely related nematodes and also against five farm isolates in Eastern Hungary, preliminary results derived from a comparative analysis of 3 primer sets showed the assay detects H. contortus DNA and has a limit of detection of 10^-5 ng/μl. We also tested an end-result naked eye detection system using various DNA binding dyes, of which EvaGreen® dye was successful for a qualitative RPA detection that could be adaptable at farm sites.

Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing

Basic knowledge on the biology and epidemiology of equine strongylid species still needs to be improved to contribute to the design of better parasite control strategies. Nemabiome metabarcoding is a convenient tool to quantify and identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA gene, with a limited investigation of its predictive performance for cyathostomin communities. Using DNA pools of single cyathostomin worms, this study aimed to provide the first elements to compare performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. Barcode predictive abilities were compared across various mock community compositions of two, five and 11 individuals from distinct species. The amplification bias of each barcode was estimated. Results were also compared between various types of biological samples, i.e., eggs, infective larvae or adults. Bioinformatic parameters were chosen to yield the closest representation of the cyathostomin community for each barcode, underscoring the need for communities of known composition for metabarcoding purposes. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types. However, imperfect correlations were found between relative abundances from infective larvae and other life-stages for Cylicostephanus species using the ITS-2 barcode. While the results remain limited by the considered biological material, they suggest that additional improvements are needed for both the ITS-2 and COI barcodes.

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.

Reflections and future directions for continued development and refinement of guidelines for anthelmintic efficacy studies

This reflection paper complements the WAAVP (World Association for the Advancement of Veterinary Parasitology) general anthelmintic efficacy guideline, which outlines the general principles of anthelmintic efficacy evaluation across all animal host species. It provides background to the recommendations made in the WAAVP general anthelmintic efficacy guideline, with insights into the discussions leading to specific recommendations in the general guideline or the absence thereof. Furthermore, this paper discusses recent technological advancements with potential value to the evaluation of anthelmintic efficacy that may be considered for future versions of the general or species-specific guidelines if supported by sufficient levels of evidence. Finally, it also identifies potential research questions, such as the statistical approach for comparing worm counts between groups of animals.

A new diagnostic approach to fast-track and increase the accessibility of gastrointestinal nematode identification from faeces: FECPAKG2 egg nemabiome metabarcoding

Effective gastrointestinal nematode (GIN) management in livestock industries is becoming increasingly difficult due to the rise of anthelmintic resistance and changes in the temporal and geographical distribution of major GINs. Underpinning the response to these challenges is the need for a fast-tracked diagnostic identification technique, making it easier for livestock producers to make informed GIN management decisions. The traditional 'gold-standard' approach, larval culture followed by morphological differentiation, is laborious and potentially inaccurate. We developed a new diagnostic approach to identify GINs that integrates a remote-location digital faecal egg count platform, FECPAK^G2, with internal transcribed spacer 2 (ITS2) nemabiome metabarcoding. The technique involves a quick and simple protocol to harvest concentrated strongyle eggs from the FECPAK^G2 cassette utilising a repurposed pipette tip, followed by DNA isolation and Illumina next generation amplicon sequencing. The GIN compositions and alpha diversity generated by our FECPAK^G2 egg nemabiome metabarcoding approach was not significantly different to traditional morphological larval differentiation and nemabiome metabarcoding of larval and faecal samples. We demonstrated that storing FECPAK^G2 harvested eggs in either DNA isolation lysis buffer or 80% ethanol (v/v) had no impact on GIN identification outcomes for at least 60 days; enabling the transport of biological samples from their remote origins to a molecular diagnostic facility for nemabiome metabarcoding, in the absence of a cold chain. We discovered that sustained GIN egg embryonation in the lysis buffer storage solution lead to higher yields of DNA compared with ethanol-stored GIN eggs or faeces with GIN eggs. Taking advantage of an already well-established platform such as FECPAK^G2, and providing the livestock producers that use it with the option to identify GINs in their samples and contribute to large-scale GIN distribution and/or anthelmintic resistance surveys, is an important future direction for the FECPAK^G2 egg nemabiome metabarcoding approach.

Practical guide for microscopic identification of infectious gastrointestinal nematode larvae in sheep from Sardinia, Italy, backed by molecular analysis

Background

Gastrointestinal nematodes (GIN) are ubiquitous in small ruminant farming, representing a major health and production concern. Given their differences in pathogenicity and the current problems regarding anthelmintic resistance, specific diagnosis of GIN is of significant importance. At present, the most widely applied method for this entails culture and microscopic analysis of third-stage larvae, allowing for identification at least to the genus level. Overall, a variety of keys for microscopic analysis have been published, showing substantial variation. Given this fact, this study aimed to produce a practical and updated guide for the identification of infective ovine GIN larvae.

Methods

Using existing keys and protocols, a total of 173larvae of the most common species/genera of ovine GIN from pooled faecal samples from Sardinia (Italy) were identified and extracted, and further individual molecular identification was performed. Morphometric and morphological data as well as high-quality photographs were collected and combined to produce the final guide.

Results

GIN microscopically and molecularly identified during this research include Trichostrongylus spp., Teladorsagia circumcincta, Haemonchus contortus, Cooperia curticei, and Chabertia ovina. Based on microscopic analysis, 73.5% of the larvae were correctly identified. Based on sheathed tail length, 91.8% were correctly classified into their respective preliminary groups.

Conclusions

It is crucial for the microscopic identification of infectious GIN larvae to examine each larva in its entirety and thus to take multiple characteristics into account to obtain an accurate diagnosis. However, a preliminary classification based on sheathed tail length (resulting in three groups: A, short; B, medium; C, long) was found to be effective. Further identification within group A can be achieved based on the presence of a cranial inflexion, caudal tubercles and full body measurements (Trichostrongylus spp. < 720 µm, T. circumcincta ≥ 720 µm). Larvae within group B can be differentiated based on sheathed tail morphometry (H. contortus > 65 µm, C. curticei ≤ 65 µm), the presence of cranial refractile bodies, total body length measurements (H. contortus ≤ 790 µm, C. curticei > 790 µm) and shape of the cranial extremity. Finally, all characteristics proposed for the differentiation between Oesophagostomum spp. and C. ovina larvae (group C) were found to have considerable restrictions.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-05013-9.

Molecular phylogenetic identification and morphological characteristics of Raillietina echinobothrida (Cestoda: Cyclophyllidea: Davaineidae) in commercial chickens in North China

Raillietina echinobothrida (R. echinobothrida) is one of the most pathogenic and prevalent tapeworms threat to the commercial chickens in China. However, there is a lack of research on their molecular identification and morphological characteristics. This study explored the molecular identification markers for R. echinobothrida in North China based on 18s ribosomal RNA (18s rRNA) gene and the ribosomal DNA second internal transcribed spacer (ITS-2) gene. The BLAST results of 18s rRNA (1643 bp) and ITS-2 (564 bp) gene sequences showed that the isolated intestinal tapeworms were R. echinobothrida. Phylogenetic trees obtained by maximum likelihood (ML) or neighbor-joining (NJ) method revealed that the R. echinobothrida in North China had the closest evolutionary relationship with the species found on the Qinghai-Tibet plateau, China. Morphological observations by hematoxylin staining and scanning electron microscope showed four round suckers and a retractable rostellum on the spherical scolex of R. echinobothrida. Two rows of alternately arranged hooks distributed around the rostellum. There were 30-40 testes in each mature segment. A well-developed cirrus pouch lied outside the excretory duct of mature segment. The gravid segment contained 200-400 eggs and there was a well-developed oncosphere in each egg. In addition, abundant ultrastructural features in mature proglottid of R. echinobothrida in North China were identified by transmission electron microscopy. In conclusion, the present study established ways of molecular phylogenetic identification for R. echinobothrida based on 18s rRNA and ITS-2 gene, and identified the morphological and ultrastructural characteristics of R. echinobothrida in North China.