First genetic characterization of gastrointestinal nematode communities and benzimidazole resistance in cattle from Argentina.

Anthropogenic selective pressures imposed by intensive anthelmintic use provide a powerful framework to investigate rapid evolutionary responses in natural populations. The study described here applied the deep amplicon sequencing of ITS2 rDNA and isotype-1 β-tubulin genes, alongside the Faecal Egg Count Reduction Test, to identify gastrointestinal nematode (GIN) species and assess benzimidazole (BZD) resistance, in six commercial beef cattle farms in Argentina. Seven nematode species were identified, with communities dominated by Haemonchus placei and Cooperia punctata. Screening for isotype-1 β-tubulin (tbb-isotype-1) polymorphisms identified four SNPs known to be associated with BZD resistance: F167Y(TTC>TAC), E198A(GAA>GCA), E198L(GAA>TTG), and F200Y(TTC>TAC), which were identified in C. punctata, Ostertagia ostertagi, H. contortus, and C. oncophora. Treatment failures following BZD administration were mainly associated with C. punctata and, to a lesser extent, O. ostertagi carrying 71.4% of β-tubulin resistance-associated ASVs, consistent with strong directional selection at this locus. Surprisingly, C. punctata survivors frequently carried predominantly susceptible alleles, revealing a marked discordance between genotype and phenotype. In contrast, under combined BZD + macrocyclic lactone treatments, surviving C. punctata predominantly harbored β-tubulin resistance-associated alleles, consistent with enhanced selection under multidrug pressure. Together, these patterns suggest that variation in treatment outcome cannot be fully explained by tbb-isotype-1 alone, and likely involves additional genetic mechanisms, ecological factors such as parasite niche, and/or pharmacokinetic interactions. This study provides the first genetic characterization of GIN communities and BZD resistance in large-scale cattle systems in Argentina, revealing complex resistance dynamics and underscoring the importance of molecular surveillance to guide sustainable parasite control.