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

Francis, Emily Kate; Šlapeta, Jan

doi:10.1016/j.ijpara.2022.01.002

Cited by 18 publications

(14 citation statements)

References 49 publications

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“…ITS-2 rDNA species assignments and phylogenetic analysis ITS-2 ASVs were assigned to the species level using an in-house bespoke database of local trichostrongylid nematode ITS-2 rDNA reference sequences curated from previously published datasets derived from the GINs of livestock in New South Wales, Australia (Francis et al, 2020;Francis and Šlapeta, 2022) (LabArchives: https://dx.doi.org/10.25833/h6a4-be50). The database was imported into DADA2 using the 'assignTaxonomy' function, which assigns ASVs to the nearest match using the Bayesian classifier method, with a bootstrapping approach to assess the confidence assignment at each taxonomic level (Wang et al, 2007).…”

Section: Illumina Miseq Nemabiome Metabarcoding and Data Handlingmentioning

confidence: 99%

Refugia or reservoir? Feral goats and their role in the maintenance and circulation of benzimidazole-resistant gastrointestinal nematodes on shared pastures

Francis

Šlapeta

2023

Parasitology

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Gastrointestinal nematodes threaten the productivity of grazing livestock and anthelmintic resistance has emerged globally. It is broadly understood that wild ruminants living in sympatry with livestock act as a positive source of refugia for anthelmintic-susceptible nematodes. However, they might also act as reservoirs of anthelmintic-resistant nematodes, contributing to the spread of anthelmintic resistance at a regional scale. Here, we sampled managed sheep and cattle together with feral goats within the same property in New South Wales, Australia. Internal transcribed spacer 2 (ITS-2) nemabiome metabarcoding identified 12 gastrointestinal nematodes (Cooperia oncophora, Cooperia punctata, Haemonchus contortus, Haemonchus placei, Nematodirus spathiger, Ostertagia ostertagi, Teladorsagia circumcincta, Oesophagostomum radiatum, Oesophagostomum venulosum, Trichostrongylus axei, Trichostrongylus colubriformis and Trichostrongylus rugatus). Isotype-1 β-tubulin metabarcoding targeting benzimidazole resistance polymorphisms identified 6 of these nematode species (C. oncophora, C. punctata, H. contortus, H. placei, O. ostertagi and T. circumcincta), with the remaining 3 genera unable to be identified to the species level (Nematodirus, Oesophagostomum, Trichostrongylus). Both ITS-2 and β-tubulin metabarcoding showed the presence of a cryptic species of T. circumcincta, known from domestic goats in France. Of the gastrointestinal nematodes detected via β-tubulin metabarcoding, H. contortus, T. circumcincta, Nematodirus and Trichostrongylus exhibited the presence of at least one resistance genotype. We found that generalist gastrointestinal nematodes in untreated feral goats had a similarly high frequency of the benzimidazole-resistant F200Y polymorphism as those nematodes in sheep and cattle. This suggests cross-transmission and maintenance of the resistant genotype within the wild ruminant population, affirming that wild ruminants should be considered potential reservoirs of anthelmintic resistance.

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Section: Illumina Miseq Nemabiome Metabarcoding and Data Handlingmentioning

confidence: 99%

Refugia or reservoir? Feral goats and their role in the maintenance and circulation of benzimidazole-resistant gastrointestinal nematodes on shared pastures

Francis

Šlapeta

2023

Parasitology

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“…agricultural producers). Using eggs, Francis & Šlapeta (2022) recently developed a quick and simple nemabiome protocol. Such a protocol may facilitate the parabiome approach to a wider range of host-parasite systems.…”

Section: Parabiomementioning

confidence: 99%

Population genomics of helminth parasites

et al. 2023

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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.

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“…The cost of managing diseases caused by gastrointestinal nematodes in ruminant animal production is a major pain for farmers globally (Francis and Šlapeta, 2022). The losses incurred are due to disease manifestation, low productivity and a higher susceptibility to other infections (Kamal et al, 2021;Khan et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Metagenomic Studies for the Detection of Parelaphostrongylus odocoilei, Ostertagia leptospicularis and Eimeria ahsata in Northern Cyprus Sheep for the First Time

Olaifa

Özgör

2022

IJAR

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Background: Gastrointestinal parasitism is considered one of the major health problems of ruminants in developing and undeveloped countries in the world. Despite the universal knowledge of these parasites, little is known about their prevalence and distribution in Northern Cyprus. This study is aimed at the microscopic and metagenomic study of gastrointestinal parasites across Cyprus sheep farms. Methods: A total of 200 sheep faecal samples were randomly collected across sheep farms in suburban regions of Northern Cyprus during 2021-22. Samples were analyzed using the centrifugal floatation technique. Data were subjected to chi-square test analysis on SPSS to determine the relationship between age, sex of animals and prevalence of gastrointestinal nematodes. Samples were randomly selected to extract DNA and subjected to metagenomic analysis after which DNA has been extracted from the samples. Result: Our investigations in the Northern Cyprus sheep farms allowed us to identify three species of gastrointestinal parasites namely Parelaphostrongylus odocoilei, Ostertagia leptospicularis and Eimeria ahsata which are new to this region. The GINs recovered are Haemonchus, Moniezia and Toxocara among others. A high prevalence (85%) of gastrointestinal parasites was recorded. Results showed a considerable significant relationship (P less than 0.05) between the age of animals and parasite prevalence.

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

Cited by 18 publications

References 49 publications

Refugia or reservoir? Feral goats and their role in the maintenance and circulation of benzimidazole-resistant gastrointestinal nematodes on shared pastures

Refugia or reservoir? Feral goats and their role in the maintenance and circulation of benzimidazole-resistant gastrointestinal nematodes on shared pastures

Population genomics of helminth parasites

Metagenomic Studies for the Detection of Parelaphostrongylus odocoilei, Ostertagia leptospicularis and Eimeria ahsata in Northern Cyprus Sheep for the First Time

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