Hierarchical Bayesian model for prevalence inferences and determination of a country's status for an animal pathogen

Certification that a country, region or state is "free" from a pathogen or has a prevalence less than a threshold value has implications for trade in animals and animal products. We develop a Bayesian model for assessment of: (i) the probability that a country is "free" of or has an animal pathogen; (ii) the proportion of infected herds in an infected country; and (iii) the within-herd prevalence in infected herds. The model uses test results from animals sampled in a two-stage cluster sample of herds within a country. Model parameters are estimated using modern Markov-chain Monte Carlo methods. We demonstrate our approach using published data from surveys of Newcastle disease and porcine reproductive and respiratory syndrome in Switzerland, and for three simulated data sets.