Bacteria can become resistant to antibiotics by acquiring mutations in genes encoding the physiologically relevant proteins targeted by the drugs. Consequently, resistance mutations can cause growth defects (fitness cost) in the absence of antibiotics. The cost thus, can hinder maintenance and dissemination of resistances, by enabling sensitive bacteria to outcompete resistant clones upon reducing the amount of antibiotics. Besides its paramount importance, the causes of the cost of resistance

more »

... re poorly understood. Here we show that DNA breaks explain 73% of the variation in the cost caused by resistance mutations affecting transcription, translation, and their coupling, in Escherichia coli. We also reveal that the RNase HI, responsible for the specific degradation of R-loops, is a key determinant of resistance costs and thus a novel target for antimicrobials specific against resistant bacteria, which we validated using a repurposed drug. Accordingly, we show that lack of RNase HI rapidly drives resistant clones to extinction in polymorphic populations with high resistance levels. These results reveal a key cause of the cost of resistance, and provide a conceptual framework for the development of novel strategies to lower the alarming levels of resistance currently observed in the human microbiome.