There has been a rapid rise in the prevalence of cases of monophasic Salmonella Typhimurium (mST) in both humans and farm animals, and it has been found in pigs, cattle and poultry. It is therefore vital to have a good understanding of how to efficiently detect infected farms. The objective of this project was to determine sample type sensitivity in the detection of Salmonella to detect infected groups of animals on both pig (breeder, grower and finisher sites) and cattle (beef and dairy) farms, using data collected from a study investigating farms that were positive for mST, and to explore any variation between different age groups and management practices. A Bayesian approach in the absence of a gold standard was adopted to analyse the individual and pooled faecal sample data collected from each epidemiological group on each of the farms. The sensitivity of pooled sampling depended on the prevalence of infection in the group being sampled, with a higher prevalence leading to higher sensitivity. Pooled sampling was found to be more efficient at detecting positive groups of animals than individual sampling, with the probability of a random sample from a group of animals with 5% prevalence testing positive being equal to 15·5% for immature pigs (3·6% for an individual faecal sample, taking into account the sensitivity and infection prevalence), 7·1% for adult pigs (1·2% for individual sampling), 30% for outdoor cattle (2% for individual sampling) and 34% for indoor cattle (1% for individual sampling). The mean prevalence of each epidemiological group was higher in outdoor farms than indoor for both pigs and cattle (mean within-farm prevalence of 29·4% and 38·7% for outdoor pigs and cattle, respectively, compared to 19·8% and 22·1% for indoor pigs and cattle)

The objective of this study was to estimate the sensitivity of three different sampling/testing methodologies for the detection of Salmonella Enteriditis in commercial egg-laying flocks relative to the within-flock prevalence. The following methods were compared on 21 farms: (1) The European Union (EU) baseline survey method (five faecal and two dust samples); (2) an in-house method that involved collecting 10 dust and 10 faecal samples into jars with buffered peptone water, and (3) a method involving single samples of pooled faeces and dust that has been adopted as a monitoring method for the National Control Programme across the EU (the NCP method). Testing of individual bird ovaries/oviduct and caeca was carried out on each flock, and the sensitivity of each sampling method was estimated relative to the within-flock prevalence using Bayesian methods. Results showed that the sensitivity of all the sampling methods increased as the within-flock prevalence increased, and that all were more efficient than individual bird sampling for detection of S. Enteriditis in commercial flocks. The in-house method was the most sensitive of the methods compared, with a 98% power to detect a 0·1% prevalence, and the NCP method the least sensitive, with a 93% power to detect a prevalence of 20%.