Metabolism-triggered sensor array aided by machine learning for rapid identification of pathogens

Chemical-nose strategy has achieved certain success in the discrimination and identification of pathogens. However, this strategy usually relies on non-specific interactions, which are prone to be significantly disturbed by the change of environment thus limiting its practical usefulness. Herein, we present a novel chemical-nose sensing approach leveraging the difference in the dynamic metabolic variation during peptidoglycan metabolism among different species for rapid pathogen discrimination. Pathogens were first tethered with clickable handles through metabolic labeling at two different acidities (pH = 5 and 7) for 20 and 60 min, respectively, followed by click reaction with fluorescence up-conversion nanoparticles to generate a four-dimensional signal output. This discriminative multi-dimensional signal allowed eight types of model bacteria to be successfully classified within the training set into strains, genera, and Gram phenotypes. As the difference in signals of the four sensing channels reflects the difference in the amount/activity of enzymes involved in metabolic labeling, this strategy has good anti-interference capability, which enables precise pathogen identification within 2 h with 100% accuracy in spiked urinary samples and allows classification of unknown species out of the training set into the right phenotype. The robustness of this approach holds significant promise for its widespread application in pathogen identification and surveillance.