Sensitivity analysis to identify key parameters influencing Salmonella infection dynamics in a pig batch

In the context of managed herds, epidemiological models usually take into account relatively complex interactions involving a high number of parameters. Some parameters may be uncertain and/or highly variable, especially epidemiological parameters. Their impact on the model outputs must then be assessed by a sensitivity analysis, allowing to identify key parameters. The prevalence over time is an output of particular interest in epidemiological models, so sensitivity analysis methods adapted to such dynamic output are needed. In this paper, such a sensitivity analysis method, based on a principal component analysis and on analysis of variance, is presented. It allows to compute a generalised sensitivity index for each parameter of a model representing Salmonella spread within a pig batch. The model is a stochastic discrete-time model describing the batch dynamics and movements between rearing rooms, from birth to slaughterhouse delivery. Four health states were introduced: Salmonella-free, seronegative shedder, seropositive shedder and seropositive carrier. The indirect transmission was modelled via an infection probability function depending on the quantity of Salmonella in the rearing room. Simulations were run according to a fractional factorial design enabling the estimation of main effects and two-factor interactions. For each of the 18 epidemiological parameters, four values were chosen, leading to 4096 scenarios. For each scenario, 15 replications were performed, leading to 61440 simulations. The sensitivity analysis was then conducted on the seroprevalence output. The parameters governing the infection probability function and residual room contaminations were identified as key parameters. To control the Salmonella seroprevalence, efficient measures should therefore aim at these parameters. Moreover, the shedding rate and maternal protective factor also had a major impact. Therefore, further investigation on the protective effect of maternal or post-infection antibodies would be needed.