Strain-Level Food Surveillance of Escherichia coli Using a Specific-Nonspecific Hybrid Sensor Array Strategy

Array-based sensing platforms have advanced rapidly in recent years, offering strong potential for high-throughout and multiplexed detection. However, their practical translation in food safety remains constrained by insufficient selectivity in complex matrices. Here, we report a synergistic sensing strategy that integrates specific and cross-reactive recognition to construct a high-performance sensor array for rapid and accurate Escherichia coli analysis. A genus-specific aptamer is employed as a front-end module to selectively capture and pre-enrich E. coli, enabling bulk concentration quantification and effective suppression of non-E. coli interference prior to array-based discrimination. Strain-level differentiation is subsequently achieved by exploiting the cross-reactivity of a multivalent antibody targeting E. coli O157:H7 across related strains. To further amplify interstrain differences, boronate chemistry is incorporated through 4-mercaptophenylboronic acid and cysteamine, providing differential binding to cis-diol motifs on bacterial surface carbohydrates. The resulting sensor array generates multidimensional response fingerprints and enables the simultaneous identification of representative E. coli strains and complex mixtures within 1 h. Accurate bulk quantification and robust discrimination are demonstrated across a wide concentration range in buffer and in complex food matrices, including beef and milk. By benchmarking four machine-learning algorithms, the K-nearest neighbors (KNN) model delivered optimal performance, achieving 100% classification accuracy. Collectively, this work establishes a versatile and translatable sensing platform for rapid, precise detection of foodborne pathogenic E. coli, addressing a critical challenge in real-world food safety monitoring.