Saltelli sensitivity analysis to identify risk factors for beef carcass contamination with E. coli O157

Purpose: Escherichia coli O157 (STEC O157) is an important foodborne pathogen in humans, with cattle the main reservoir. Despite much microbiological research, it is still uncertain which risk factors most influence beef carcass contamination; therefore, it is difficult to determine the most effective mitigation strategies in the beef harvest chain. We address this gap using a stochastic, individual-animal based, computational model and Saltelli sensitivity analysis, a method not previously used in animal disease modelling.
Methods: Information from previous empirical studies was used to parameterise model inputs (18 risk factors). Saltelli global sensitivity analysis (GSA) - a variance-based method that can account for non-linearities and interactions between inputs, providing greater insight about the importance of inputs than traditional methods for sensitivity analysis - was used to identify risk factors with the greatest influence on variance of output (the prevalence of STEC O157 contaminated beef carcasses) and guided the stepwise introduction of interventions.
Results: The sum of total effect sensitivity indices (1.38) indicated that interactions between risk factors strongly influenced output in this model. Therefore, interventions were most effective when introduced in combination, when the reduction in STEC O157 contaminated carcasses was greater than that expected due to an additive effect. Improved abattoir hygiene - reduction of transfer of STEC O157 from both hide and gut to carcass - was the most effective combination. Interventions introduced subsequently, for example, vaccination, had relatively small impact on output.
Conclusions: This model and Saltelli GSA provided insight with practical application; improving abattoir hygiene is likely to be the most effective mitigation strategy, and targeting interventions at individual risk factors is likely to be ineffective in reducing the prevalence of STEC O157 contaminated carcasses.
Relevance: Implementation of effective combinations of interventions might reduce the incidence of STEC O157 associated disease in humans. Saltelli GSA shows promise for analysing complex modelling data.