Model output. A. Effects of stay-time in retail markets on infection prevalence. Impact of stay-times on prevalence is most dramatic at stay-times less than 2 days. Simulations (N = 3528; for all possible combinations of parameters in Additional file 1: Table S1) were run under different combinations of parameter values (see Additional file 2: Figure S1) for each stay-time indicated on X-axis. Mean daily prevalence (over 1 year) was calculated for each parameter set. Each bar reflects an overall mean across parameter sets. These overall means were expressed as prevalence relative to the lowest stay-time (0.5 days; i.e., bars show ((mi – m0.5) / m0.5)×100, where m = mean prevalence across parameters sets, i = 1, 1.5, 2.5, 3, 3.5, 4 days). Absolute values of prevalence will depend on specific parameter values; qualitative results are robust; higher transmission rates lead to larger effects of stay-time (Additional file 2: Figure S1B). B. Impact of influx of chickens on effectiveness of decontamination in retail markets. Difference between mean prevalence of the ‘reference’ scenario (no disinfection routine) and mean prevalence under each treatment, divided by the reference and expressed as a percent. The frequency of disinfection is shown on X-axis. Efficacy of disinfection (i.e. 100, 90 and 50%) is indicated in the legend with a stay-time of 3 days. Left panel: Infected hosts were introduced only once at the start of the simulation (initial prevalence = 0.1%) and only susceptible or recovered hosts entered the market thereafter. Right panel: The number of infected hosts entering retail markets at each time step was chosen randomly from the distribution of prevalences in the wholesale market (Figure 2, red bars).