Estimation of true Salmonella prevalence jointly in cattle herd and animal populations using Bayesian hierarchical...

The Finnish salmonella control program (FSCP) for beef production is based on both randomized and selective testing of herds and animals. Sampling of individual animals in abattoirs is randomized. Herds are selectively tested for salmonella on the basis of clinical symptoms and/or other factors. Risk assessment of FSCP is inherently difficult due to the complexity of the complete data set, especially if the detailed labeling of the testing types is lost. However, for a risk assessment of the whole production chain, methods for exploiting all available data should be considered. For this purpose, a hierarchical Bayesian model of true salmonella prevalence was constructed to combine information at different levels of aggregation: herds in geographical regions and individual animals arriving for slaughter. The conditional (municipality specific) probability of selection of a herd for testing was modeled given the underlying true infection status of the herd and information about the general sampling activity in the specific region. The model also accounted for the overall sensitivity of the sampling methods, both at the herd and at the animal level. In 1999, the 95% posterior probability intervals of true salmonella prevalence in the herd population, in individual cattle, and in slaughter animal populations were [0.54%, 1.4%] (mode 0.8%), [0.15%, 0.39%] (mode 0.2%), and [0.12%, 0.36%] (mode 0.2%), respectively. The results will be further exploited in other risk assessments focusing on the subsequent parts of the beef production chain, and in evaluation of the FSCP.