Integrative use of conventional and DNA metabarcoding methods reveals high diversity, prevalence and intensity of gastrointestinal parasites in pigs from Victoria, Australia

This cross-sectional study provides the first integrated parasitological and molecular survey of gastrointestinal parasites in pigs from 69 commercial and backyard farms across Victoria, Australia. In total, 1222 faecal samples were tested using the modified McMaster technique to determine faecal egg and oocyst counts. Samples test-positive for strongylid nematode stages were characterised further using next-generation sequencing (NGS) targeting the second internal transcribed spacer (ITS-2) of ribosomal DNA as a species-specific genetic marker. Based on faecal egg/oocyst count, 39.1 % of farms tested positive for at least one parasite taxon. Coccidia were most prevalent (9.5 %) in samples, followed by Ascaris suum (5.2 %), Trichuris suis (4.5 %) and strongylid nematodes (1.8 %). Infection intensity was highest for coccidia, with notable burdens also for Ascaris suum and strongylid in individual samples. Eggs of Metastrongylus spp. were detected for the first time in Australian domestic pigs on an outdoor farm. Prevalence patterns varied substantially according to the production system and pig age group: coccidia dominated in mature breeders (17.8 %) and piglets (15.4 %) in backyard settings (33.7 %), whereas Ascaris peaked in mature breeders (9.1 %) and growers/finishers (up to 5 %) in semi-intensive systems (21.7 %). Strongylid eggs were most frequently detected in gilts and mature breeders from backyard and extensive systems. Notably, NGS revealed a diverse community of strongylid nematodes, including Oesophagostomum dentatum, O. quadrispinulatum and Trichostrongylus axei and Metastrongylus apri and M. salmi. This is the first molecular detection of Metastrongylus species in domestic pigs in Australia. These findings uncover a considerable and underappreciated parasitic burden in pig populations across multiple production systems in Victoria.