Deep amplicon sequencing screening benzimidazole resistance associated specific single nucleotide polymorphisms in isotype-1 β-tubulin from trichostrongyloids on ruminant farms in northeast Germany.

In many countries, widespread benzimidazole resistance in ruminant trichostrongyloids has severe effects on animal health and farm economy. In Germany, benzimidazole resistance occurs with high prevalence in sheep, but has barely been shown for cattle strongyles. In this study, the frequency of isotype-1 β-tubulin specific single nucleotide polymorphisms associated with benzimidazole resistance in trichostrongyloids on twelve sheep and nine cattle farms in northeast Germany was quantified using deep amplicon sequencing. On sheep farms, reliable data for Haemonchus contortus, Teladorsagia circumcincta, and Trichostrongylus colubriformis were obtained, while read numbers for Trichostrongylus axei and Trichostrongylus vitrinus were low and allowed only preliminary interpretation. For H. contortus, the most frequently detected SNPs were F167Y (mean allele frequency 18.6%) and F200Y (34.8%), both of which increased after fenbendazole treatment. The E198A SNP had a low mean frequency (4.6%) and was not widespread. In addition, the novel E198G SNP, found in H. contortus with a mean frequency of 1.1% on farm S7, may confer benzimidazole resistance, as it causes resistance in Neurospora crassa. In T. circumcincta, F200Y (21.3%) was the most common SNP, followed by E198L (5.7%), while no SNP at codon 167 was detected. Both E198L and F200Y increased after fenbendazole treatment. In T. colubriformis, the F200Y SNP was highly prevalent. For the most common cattle trichostrongyloids Cooperia oncophora and Ostertagia ostertagi no SNPs were detected. Overall, the evolution of benzimidazole resistance should be further controlled, especially for the trichostrongyloids in cattle, where evolution of resistant parasites might still be preventable.