Generalised linear mixed models analysis of risk factors for contamination of Danish broiler flocks with Salmonella typhimurium.

We present a retrospective observational study of risk factors associated with the occurrence of Salmonella typhimurium (ST) in Danish broiler flocks. The study is based on recordings from 1994 in the ante-mortem database maintained by the Danish Poultry Council. The epidemiological units are the broiler flocks (about 4000 flocks) which are clustered within producers. Broiler flocks with ST-infected parent stocks show increased risk of salmonella infection, and also the hatchery affects the salmonella status significantly. Among the rearing factors, only the use of medicine as well as the time of rearing, and the sampling method are significant. Epidemiological control would seem most efficient on starting at the top levels of the production hierarchy from which a major part of the ST contamination is derived. A secondary purpose of the study is to evaluate different statistical approaches and software for the analysis of a moderately-sized data set of veterinary origin. We compare the results from five analyses of the generalised linear mixed model (GLMM) type. The first observation is that the results agree reasonably well and lead to similar conclusions. A closer look reveals certain patterns of bias and estimation accuracy that correspond well with theoretical findings and practical experience reported in the statistical literature.