A national survey of gastrointestinal nematodes in Australian dairy goats using faecal egg counts and deep amplicon sequencing

Gastrointestinal nematodes (GINs) constrain goat health, welfare and productivity worldwide. In Australia, GINs are recognised as the highest-priority endemic pathogens of goats; however, comprehensive national data documenting the prevalence of GINs in goats remain limited. Here, we investigated the prevalence, infection intensity, species diversity and risk factors for GINs in dairy goats. In a cross-sectional study (November 2023 and July 2024), faecal samples ( n = 1028) from 68 herds were analysed using the modified McMaster technique. Strongylid species were identified in 500 samples using deep amplicon sequencing of the nuclear ribosomal DNA second internal transcribed spacer. Animal-level prevalence estimates were adjusted for the effect of clustering of GIN positivity at the herd level, and risk factors associated with strongylid faecal egg counts (FEC) were evaluated using linear mixed-effects models. Overall, 92% (95% confidence interval, CI: 89–95%) of goats and 100% of herds were positive for at least one GIN taxon. Strongylids showed the highest adjusted animal-level prevalence (91%, 95% CI: 87–94%), followed by Trichuris spp. (13%, 95% CI: 10–17%) and Nematodirus spp. (5%, 95% CI: 3–8%). Strongylid FECs were markedly overdispersed, with 30% of goats contributing 80% of total egg output. Age, climatic zone, deworming history and coinfection with Eimeria were significantly associated with strongylid FECs. Metabarcoding identified 11 strongylid species, dominated by Haemonchus contortus , Teladorsagia circumcincta and Trichostrongylus colubriformis . Haemonchus contortus was most abundant and prevalent nationally, underscoring its central role in production loss and the dissemination of anthelmintic resistance. These findings provide nationally representative evidence to inform sustainable parasite control in goats.