Machine learning-enabled non-destructive paper chromogenic array detection of multiplexed viable pathogens on food

Fast and simultaneous identification of multiple viable pathogens on food is critical to public health. Here we report a pathogen identification system using a paper chromogenic array (PCA) enabled by machine learning. The PCA consists of a paper substrate impregnated with 23 chromogenic dyes and dye combinations, which undergo colour changes on exposure to volatile organic compounds emitted by pathogens of interest. These colour changes are digitized and used to train a multi-layer neural network (NN), endowing it with high-accuracy (91–95%) strain-specific pathogen identification and quantification capabilities. The trained PCA–NN system can distinguish between viable Escherichia coli, E. coli O157:H7 and other viable pathogens, and can simultaneously identify both E. coli O157:H7 and Listeria monocytogenes on fresh-cut romaine lettuce, which represents a realistic and complex environment. This approach has the potential to advance non-destructive pathogen detection and identification on food, without enrichment, culturing, incubation or other sample preparation steps. Fast and simultaneous identification of multiple viable pathogens on food is critical to public health. By integrating paper chromogenic arrays (PCAs) and machine learning, a system was developed to automatically recognize PCA patterns on multiplexed viable pathogens with strain-level specificity.