Sheep Nemabiome Diversity and Its Response to Anthelmintic Treatment in Swedish Sheep Herds

Abstract

Background: 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. Herein we describe for the first-time the nematode community structure (nemabiome) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments. Methods: A total of 158 larval cultures were collected (n=35 in 2007 and n=126 in 2014-2016) from groups of sheep on 61 commercial farms in the south-central part of country were most animals are grazed. Among the samples, 2 x 44 (56%) were paired collected from the same groups pre- and post-treatment with macrocyclic lactones, benzimidazoles or levamisole. The sequences 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.Results: Nematode ITS2 sequences were found in all samples except two, despite that the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded on average 1,011 sequences per sample. Totally 26 operational taxonomical units (OTU) among which 18 (69%) had ≥99 % identity to sequences in the NCBI database were recognized. The OTUs found represented nematode species among which 10 are commonly associated with sheep. Multiple species were identified in all pre anthelmintic treatment 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 IVM and ABZ. Interestingly, despite zero egg count after use of levamisole, these samples still contained nematode DNA and especially H. contortus. Conclusions: Our findings provide evidence for that nemabiome analysis combined with diversity index analysis provide a sensitive and objective methodology in the study of the efficacy of anthelmintic treatment.

Anthelmintic resistance in small ruminants in the Nordic-Baltic region

“…However, despite always having a high efficacy of treatment with LEV, H. contortus in particular survived at a low level. Similarly, T. circumcincta survived treatment with either IVM or BZ, but to a lesser extent than H. contortus, and not at all after LEV treatment [54]. In Denmark, AR was confirmed by the controlled efficacy test (CET) in H. contortus and T. colubriformis isolated from a farm with both sheep and goats [39].…”