First molecular survey of pigs in Victoria, Australia, reveals widespread Cryptosporidium infection, limited Giardia duodenalis occurrence and genotypes with zoonotic potential

Abstract Background Cryptosporidium spp. and Giardia duodenalis are enteric protozoan parasites of veterinary and public health significance, yet molecular epidemiological data from Australian pig populations remain limited, and no study has previously been conducted in Victoria. This study estimated prevalences and investigated species composition and genotypic diversity of Cryptosporidium spp. and G. duodenalis in faecal samples collected from pigs across farms in Victoria, Australia. Methods In total, 626 faecal samples were collected from pigs representing multiple age groups across 37 farms in the State of Victoria, Australia. Molecular detection and characterisation were performed using nested PCR targeting the small subunit of the nuclear ribosomal rRNA gene ( SSU ) and gp60 loci for Cryptosporidium and the tpi locus for G. duodenalis , followed by Sanger sequencing. Results Cryptosporidium spp. were detected in 320 samples (51.1%) across 28 farms (76%), with C. scrofarum (77.5%) and C. suis (18.4%) predominating. C. ubiquitum DNA was detected in three faecal samples from pigs on a single farm. Subtyping identified C. suis subtype XXVa-1 and C. ubiquitum subtype XIIa, both previously identified in humans. Giardia duodenalis was detected in seven samples (1.1%) from three farms, with assemblage E ( n = 5) and assemblage A ( n = 2) identified. Cryptosporidium prevalence estimates varied significantly by age group and farming system, being highest in weaners (68.6%) and semi-intensive systems (78.2%) and absent in adult pigs. Conclusions These findings establish the first molecular baseline for Cryptosporidium spp. and G. duodenalis in Victorian pigs, demonstrate the widespread occurrence of Cryptosporidium in pig production systems, identify genotypes with zoonotic potential and highlight the need for ongoing surveillance and targeted parasite management in Australian pig production.