Longitudinal prevalence, faecal shedding and molecular characterisation of Campylobacter spp. and Salmonella enterica in sheep

• This is the first comprehensive study of faecal excretion of Campylobacter and Salmonella spp. by sheep across Australia.
• A multiplex qPCR for detection of Campylobacter and Salmonella spp. in faecal samples from sheep was developed and the prevalence, bacterial shedding and species were analysed.
• In a longitudinal study, 3412 faecal samples from sheep were tested over three sampling times.
• The overall prevalences of Campylobacter spp. and S. enterica were 13.3% and 5.0%, respectively, with the highest prevalence for Campylobacter spp. in South Australia and the highest prevalence for S. enterica in New South Wales.
• Campylobacter jejuni was the only Campylobacter sp. identified from a subset of 120 positive samples sequenced at the 16S locus and S. enterica serovar Typhimurium was the only serovar of S. enterica identified from a subset of 120 positive samples sequenced at the ompF locus.
• Campylobacter spp. had the highest median bacterial concentration in faeces at weaning and post-weaning (medians of 3.4 × 106 and 1.1 × 105, respectively), whereas S. enterica had the highest median bacterial concentration at pre-slaughter (1.8 × 105/g faeces).

Faecal excretion of Campylobacter spp. and Salmonella enterica in sheep in Australia was determined using a quantitative multiplex PCR (qPCR) targeting the Campylobacter spp. purine biosynthesis gene (PurA) and the S. enterica outer membrane protein (ompF). The mutiplex qPCR was specific and Campylobacter spp. and S. enterica were each detected with a sensitivity of 5 organisms/µL faecal DNA extract. This multiplex qPCR was used to determine the prevalence and concentration of Campylobacter spp. and S. enterica in 3412 faecal samples collected from 1189 lambs on eight farms across South Australia (n = 2 farms), New South Wales (n = 1), Victoria (n = 2) and Western Australia (n = 3) at three sampling periods (weaning, post-weaning and pre-slaughter). The overall prevalences of Campylobacter spp. and S. enterica were 13.3% and 5.0%, respectively, with the highest prevalence for Campylobacter spp. in South Australia and the highest prevalence for S. enterica in New South Wales. Campylobacter jejuni was the only Campylobacter sp. identified from a subset of 120 positive samples sequenced at the 16S locus. S. enterica serovar Typhimurium was the only serovar of S. enterica identified from a subset of 120 positive samples sequenced at the ompF locus. Across all states, Campylobacter spp. had the highest median bacterial concentration in faeces at weaning and post-weaning (medians of 3.4 × 106 and 1.1 × 105, respectively), whereas S. enterica had the highest median bacterial concentration at pre-slaughter (1.8 × 105/g faeces).