A new efficient sample pooling procedure for qualitative screening analysis. Application to the detection of salmonella spp and nut allergen by PCR

Abstract

Foodborne pathogens and allergens are a major concern for public health that determines food safety policy, and their screening could be improved using pooled samples.

The purpose of this paper is to propose a cost-effective and accurate pooling strategy for the unambiguous identification of foodborne pathogens and allergens, enabling laboratories to redouble testing capacity while saving time and making optimal use of resources.

Although a variety of pooling algorithms have been used in different fields, the strategy suggested here is a logical analysis of sample pooling aimed at qualitative analytical screening problems. It involves, on the one hand, a design matrix to make the pooled samples, which is a supersaturated-based design, particularly, a half-fraction of a Plackett-Burman. On the other hand, a logical (non-algebraic) modeling of the problem, as well as a logical procedure for the identification of the original positive samples, is included.

Regarding the efficiency of the proposal, it is higher than that of other pooling algorithms, with an expected number of tests per individual sample ranging between 0.10, for a prevalence below 1%, and 0.59, for a prevalence above 10%. In terms of accuracy, the pooling sensitivity reaches 0.9697 for a sensitivity of the analytical test about 0.99, while pooling specificity ranges from 0.9872 to 0.9999, provided that the sensitivity and specificity of the analytical test are equal to or greater than 0.90.

This pooling strategy has been applied to the detection of salmonella spp and nut allergen with complete identification of the contaminated samples. Furthermore, based on the EU reported food samples contaminated with salmonella, a comprehensive comparison between individual sampling and the applied pooling strategy has been conducted. For the specific case of salmonella, detailed calculations have been made on the expected efficiency gains induced by this pooling methodology for different types of food samples monitored in the EU.