Common regulatory mutation increases single-cell survival to antibiotic exposures in Pseudomonas aeruginosa

Typical antibiotic susceptibility testing (AST) of microbial samples is performed in homogeneous cultures in steady environments, which does not account for the highly heterogeneous and dynamic nature of antibiotic responses. The most common mutation found in P. aeruginosa lineages evolved in the human lung, a loss of function of repressor MexZ, increases basal levels of multidrug efflux MexXY, but does not increase resistance by traditional MIC measures. Here, we use single cell microfluidics to show that P. aeruginosa response to aminoglycosides is highly heterogeneous, with only a subpopulation of cells surviving exposure. mexZ mutations then bypass the lengthy process of MexXY activation, increasing survival to sudden drug exposures and conferring a fitness advantage in fluctuating environments. We propose a simple “Response Dynamics” assay to quantify the speed of population-level recovery to drug exposures. This assay can be used alongside MIC for resistance profiling to better predict clinical outcomes.