Abstract
BackgroundA novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Herein we describe for the first time the nematode community structures (nemabiomes) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments.MethodsA total of 158 fecal samples were collected (n = 35 in 2007 and n = 123 in 2013–2016) and cultured from groups of sheep on 61 commercial farms in the south-central part of the country where most animals are grazed. Among the samples, 2 × 44 (56%) were paired collections from the same groups pre- and post-treatment with anthelmintics such as macrocyclic lactones, benzimidazoles or levamisole. Samples were analyzed for their nemabiome using the PacBio platform followed by bioinformatic sequence analysis with SCATA. Species richness and diversity were calculated and analyzed in R.ResultsNematode ITS2 sequences were found in all larval culture samples except two, even though the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded, on average, 1008 sequences per sample. In total, 16 operational taxonomical units (OTU), all with ≥ 98 % identity to sequences in the NCBI database, were recognized. The OTUs found represented nematode species of which ten are commonly associated with sheep. Multiple species were identified in all pre-anthelmintic treatment larval culture samples. No effects on nematode diversity were found in relation to host age. On the other hand, recent anthelmintic treatment lowered species richness, especially after use of ivermectin and albendazole. Interestingly, despite zero egg counts after use of levamisole, these samples still contained nematode DNA and especially H. contortus.ConclusionsOur findings provide evidence that nemabiome analysis combined with diversity index analysis provides an objective methodology in the study of the efficacy of anthelmintic treatment as both high and low abundant species were detected.Graphical
Highlights
A novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species
Adults were infected by fewer species compared to lambs (LM, F(1.110) = 2.721, P = 0.0036)
The species composition showed that the nematode community was dominated by a fewer species among ewes compared to lambs (LM, F(1.110) = 9.165, P = 0.0063)
Summary
A novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Infection with gastrointestinal nematode (GIN) parasites is well known globally as a major veterinary problem which contributes to a decline in the productivity of the Halvarsson and Höglund Parasites Vectors (2021) 14:114 different parasitic species present in sheep is driven by a wide range of factors These include external factors such as climate and managerial factors affecting the exposure to the free living stages [4] and, not least, selection reinforced by use of anthelmintic compounds [5]. Access to diagnostic instruments that could rapidly rank strongyle nematodes according to their relative contribution to mixed infections would represent a major advantage in terms of the understanding of how selection by anthelmintics shapes nematode communities This present need for new diagnostics is underscored by the increasing evidence of anthelmintic resistance (AR) and requests for evidence-based use of anthelmintic drugs in parasite control [10]. Effective parasite control in general can be achieved through a combination of grazing management strategies and treatment with anthelmintics, this practice is under threat due to the increasing spread of resistance to these veterinary drugs [11]
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