Metabolic reprogramming enhances the susceptibility of multidrug- and carbapenem-resistant bacteria to antibiotics

Carbapenem-resistant Enterobacteriaceae and extended-spectrum β-lactamase-resistant bacterial pathogens are a major threat to human and global health. Alternative antibiotics are therefore used to treat infections caused by these pathogens, and approaches to increase their efficacy are needed. Here we used metabolomics, mutant Escherichia coli strains and whole-genome sequencing to examine the metabolic profiles of clinical carbapenem-resistant (CR-ECO), multidrug-resistant (MDR-ECO) and antibiotic-sensitive E. coli (S-ECO) isolates in response to antibiotics in vitro including micronomicin, an aminoglycoside. Downregulation of pyruvate formate-lyase (PFL) alters membrane permeability and reduces the efficacy of micronomicin, the most potent antibiotic, in CR-ECO and MDR-ECO. The metabolism of pyruvate to formate is required to potentiate the effects of micronomicin across multiple bacterial pathogens. Mice infected with CR-ECO and treated with formate plus micronomicin had reduced pathogen growth and spread, and increased survival, compared with mice treated with micronomicin or formate alone. Finally, elevated activity or expression of PFL and increased intracellular CO₂, a product of PFL- and formate dehydrogenase-dependent catabolism of formate, are required for antibiotic uptake and pathogen killing. The findings reveal a mechanism of metabolic reprogramming in MDR and CR bacteria for enhanced sensitivity to micronomicin.