Inferring fruit infestation prevalence from a combination of pre-harvest monitoring and consignment sampling data

Abstract

International trade in horticultural produce happens under phytosanitary inspection and production protocols. Fruit inspection typically involves the sampling and inspection of either 600-pieces or 2% of packed product within a single consignment destined for export, with the purpose of certification (typically with 95% confidence) that the true infestation level within the consignment in question doesn’t exceed a pre-specified design prevalence. Sampling of multiple consignments from multiple production blocks in conjunction with pre-harvest monitoring for pests can be used to provide additional inference on the prevalence of infested fruit within an overall production system subject to similar protocols. Here we develop a hierarchical Bayesian model that combines in-field monitoring data with consignment sample inspection data to infer the prevalence of infested fruit in a production system. The results illustrate how infestation prevalence is influenced by the number of consignments inspected, the detection efficacy of consignment sampling, and in-field monitoring effort and sensitivity. Uncertainty in inspection performance, monitoring methods, and exposure of fruit to pests is accommodated using statistical priors within a Bayesian modelling framework. We demonstrate that pre-harvest surveillance with a sufficient density of traps and moderate detection sensitivity can provide 95% belief that the prevalence of infestation is below $1\times {10}^{-6}$. In the absence of pre-harvest monitoring, it is still possible to gain high confidence in a very low prevalence of infestation ($<1\times {10}^{-5}$) on the basis of multiple clean samples if the inspection sensitivity during consignment sampling is high and sufficient consignments are inspected. Our work illustrates the cumulative power of in-field surveillance and consignment sampling to update estimates of infestation prevalence.