Engineering solutions to persistent bacteria

Abstract

Bacterial persistence is a state in which a sub-population of dormant cells, 'persisters', tolerates antibiotic treatment. Bacterial persisters have been implicated in biofilms and in chronic and recurrent infections. Despite this clinical relevance, persister formation is not well understood and, at the time of this research, there were no viable means for eradicating persisters. Here we show that specific metabolic stimuli enable killing of both Gram-negative (Escherichia coli) and Gram-positive (Staph lollccus aureus) persisters with aminoglycosides. This potentiation is aminoglycoside specific, it does not rely on growth resumption and it is effective in both aerobic and anaerobic conditions. It proceeds by the generation of a proton-motive force that facilitate aminoglycoside uptake. Our results demonstrate that persisters, although dormant are primed for metabolite uptake, central metabolism and respiration. We show that aminoglycosides can be used in combination with specific metabolites to treat E. coli and S. aureus biofilms. Furthermore, we demonstrate that this approach can improve the treatment of chronic infections in a mouse urinary tract infection model. This work establishes a strategy for eradicating bacterial persisters that is based on "tuning" metabolism, and highlights the importance of the metabolic environment to antibiotic treatment. Additionally, we also find that a bacterial population can "tune" the frequency of persisters through chemical signaling. We show that bacterial communication through indole signaling induces persistence in E. coli. We monitor indole-induced persister formation using microfluidics and identify the role of oxidative-stres and phage-shock pathways in this phenomenon. We propose a model in which indole signaling 'inoculates' a bacterial subpopulation against antibiotics by activating stress responses, leading to persister formation.