Molecular pharmacodynamics of amoxicillin-clavulanic acid for urinary tract infections caused by Escherichia coli

Amoxicillin-clavulanic acid (AMX-CLV) is a widely used oral β-lactam/β-lactamase inhibitor combination against Escherichia coli. Clinical success is largely confined to urinary tract infections. The mechanistic basis for this site-specific efficacy remains unclear. Using a hollow-fibre infection model to replicate human plasma and urinary pharmacokinetics, we show that plasma-like exposures rapidly select for pre-existing resistant subpopulations; whereas, urinary exposures produce sustained bactericidal activity without resistance emergence. Genomic and transcriptomic analyses following plasma drug exposure reveal that treatment selectively enriches pre-existing resistant lineages already harbouring oxidative-stress-associated mutations that activate the SOS response and drive IS-mediated amplification of blaTEM-1, leading to β-lactamase hyperproduction and treatment failure. In contrast, the high urinary concentrations of clavulanic acid exert direct antibacterial activity, eradicating these subpopulations. Our findings demonstrate that local pharmacokinetic environments fundamentally shape evolutionary trajectories under β-lactam/β-lactamase inhibitor therapy, explaining the restricted efficacy of AMX-CLV and revealing a dynamic interplay between stress responses, genome plasticity, and drug partitioning that governs treatment outcome.