Widespread benzimidazole resistance and β-tub-1 F200Y SNP in gastrointestinal nematodes of sheep across Portugal.

Anthelmintic resistance (AR) to benzimidazoles (BZs) in gastrointestinal nematodes (GINs) of sheep was assessed across 35 farms in northern (Trás-os-Montes, TM), north-central (Beira Interior, BI), central (Estremadura, ES), and southern (Alentejo, AL) Portugal. Pooled fecal samples were tested for AR by egg hatch tests (EHTs) with albendazole (ABZ) and thiabendazole (TBZ). Effective concentrations inhibiting 50% egg hatch (EC50) were calculated, with EC50 > 0.13 µg/mL (ABZ) and > 0.10 µg/mL (TBZ) indicating AR. ABZ resistance was detected on 69% of farms, while TBZ, never administered, showed resistance on 59% of farms, suggesting wide BZ cross-resistance. EC50 values ranged from 0.05 to 0.68 µg/mL (ABZ) and 0.03-0.70 µg/mL (TBZ). Nemabiome metabarcoding identified 10 GIN species, predominantly Haemonchus contortus (41%), Teladorsagia circumcincta (33%), and Trichostrongylus colubriformis (19%). Less common species included Bunostomum trigonocephalum and Oesophagostomum venulosum. Species richness (3-6 per farm) was highest in TM, with unique occurrences of B. trigonocephalum and Cooperia sp. H. contortus dominated in TM and BI, while T. circumcincta prevailed in AL, where AR was most severe. Higher EC50 values correlated with increased T. circumcincta and T. colubriformis prevalence. The BZ-resistance F200Y SNP in the isotype-1 β-tubulin gene of H. contortus was detected on 85% of farms, with resistant allele frequencies inferring predominantly homozygous resistant populations (A/A; > 90% resistant allele) on some farms, strongly correlating with higher EC50 values, particularly in AL. Widespread BZ resistance underscores the need for enhanced AR surveillance, prudent anthelmintic use, and integrated management to sustain sheep health in Portugal, especially in Alentejo.