The use of ITS-2 rDNA nemabiome metabarcoding to enhance anthelmintic resistance diagnosis and surveillance of ovine gastrointestinal nematodes

A lack of quantitative information on the species composition of parasite communities present in fecal samples is a major limiting factor for the sensitivity, accuracy and interpretation of the diagnostic tests commonly used to assess anthelmintic efficacy and resistance. In this paper, we investigate the ability of ITS-2 rDNA nemabiome metabarcoding to enhance fecal egg count reduction testing by providing information on the effect of drug treatments on individual parasite species. Application of ITS-2 rDNA nemabiome metabarcoding to fecal samples from ewes from over 90 flocks across western Canada revealed high gastrointestinal nematode infection intensities in many flocks with Haemonchus contortus being the most abundant species followed by Teladorsagia circumcincta and then Trichostrongylus colubriformis. Integration of ITS-2 rDNA nemabiome metabarcoding with pre- and post-treatment fecal egg counting revealed consistently poor efficacy of producer-applied ivermectin and benzimidazole treatments against H. contortus, but much better efficacy against T. circumcincta and T. colubriformis, except for in a small number of flocks. Integration of nemabiome ITS-2 rDNA metabarcoding with Fecal Egg Count Reduction Tests (FECRT), undertaken on farm visits, confirmed that ivermectin and fenbendazole resistance is widespread in H. contortus but is currently less common in T. circumcincta and T. colubriformis in western Canada. FECRT/nemabiome testing did not detect moxidectin resistance in any GIN species but suggested the early emergence of levamisole resistance specifically in T. circumcincta. It also revealed that although poor efficacy to closantel was relatively common, based on total fecal egg counts, this was due to its narrow spectrum of activity rather than the emergence of anthelmintic resistance. This study illustrates the value of ITS-2 rDNA nemabiome metabarcoding to improve fecal egg count resistance testing, perform large-scale anthelmintic resistance surveillance and direct more targeted rational anthelmintic use.