Growth-mediated negative feedback shapes quantitative antibiotic response

Slow growth and persistence are common strategies bacteria use to survive antibiotic treatment. Bacterial growth responses to antibiotics are quantitatively characterized by dose-response curves. The shape of the dose-response curve varies drastically between antibiotics and plays a key role in drug treatments, interactions, and resistance evolution. Understanding the mechanisms that shape the dose-response curve is a major challenge. Here we show in Escherichia coli that the distinctly shallow dose-response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that target upregulation is not a specific response to trimethoprim but a general response to slower growth, regardless of cause. Quantitatively, folA expression follows a universal trend line that only depends on growth rate and converges to a fixed maximum value at zero growth. Synthetically breaking the negative feedback loop or reversing it to positive feedback drastically steepens the dose-response curve; a similar steepening occurs under conditions of slower growth. A general mathematical model that captures growth-mediated feedback explains these phenomena. Our results indicate that growth-mediated feedback loops shape drug responses and could be exploited to design evolutionary traps that enable selection against drug resistance.