Purine nucleotide limitation undermines antibiotic action in clinicalEscherichia coli

Abstract Metabolic variation across pathogenic bacterial strains can impact their susceptibility to antibiotics 1–4 and promote evolution of antimicrobial resistance (AMR) 5,6 . However, little is known about which metabolic pathways contribute to AMR, and the underlying mechanisms. Here, we measured antibiotic resistance of 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins. Most of the mutant strains that showed resistance to either of the two tested antibiotics carried mutations in metabolic genes. Resistance mutations against a β-lactam antibiotic (carbenicillin) were associated with purine nucleotide biosynthesis and limited the supply of ATP. We show that ATP limitation confers both resistance and tolerance against β-lactam antibiotics by upregulating the purine nucleoside transporter PunC. These results are clinically relevant, because an E. coli strain isolated from a clinical specimen had a purine nucleotide limitation, which reduced its susceptibility to antibiotics.