ITS2 rDNA and isotype-1 beta-tubulin nemabiome metabarcoding to investigate gastrointestinal nematode diversity and benzimidazole resistance in sympatric sheep, cattle and feral goats

Parasitic gastrointestinal nematodes threaten the productivity of grazing livestock and anthelmintic resistance has emerged globally. Many wild ruminant species live in sympatry with livestock and are susceptible to generalist nematodes that could be carrying either the susceptible or anthelmintic-resistant genotype. A better understanding of the occurrence of the resistant genotype in wild ruminants who have never been treated with anthelmintics is required for sustainable livestock management. We applied ITS2 rDNA and isotype-1 beta-tubulin deep amplicon sequencing to larval samples obtained from the faeces of feral goats and sympatric sheep and cattle. Our results show the power of this approach, providing the first molecular evidence of feral goats as reservoirs of benzimidazole-resistant generalist nematodes, and revealing a cryptic species of Teladorsagia circumcincta.