A small regulatory RNA controls antibiotic adaptation in Staphylococcus aureus by modulating efflux pump expression

Staphylococcus aureus is an opportunistic pathogen that poses a considerable burden to healthcare settings worldwide, aided by its ability to thrive in different environmental growth conditions and survive exposure to antibiotics. Small regulatory RNAs (sRNAs) are decisive in enhancing bacterial fitness by modulating gene expression in response to changing environmental conditions. We investigated the role of sRNAs in the adaptation of S. aureus to antibiotics. By assessing the fitness of a library of sRNA mutants, we identified that RsaA sRNA is required for optimal bacterial growth when exposed to low concentrations of fluoroquinolone, a class of antibiotics targeting DNA replication. We also found that in the absence of RsaA, S. aureus is less susceptible to β-lactam antibiotics, which act on the cell wall. RsaA has been reported to prevent the expression of MgrA, a master regulatory protein controlling the expression of efflux pumps. Here, we show that RsaA affects the sensitivity of S. aureus to fluoroquinolone and β-lactam antibiotics through MgrA. RsaA has two forms, a short one commonly referred to in RsaA studies, and a long form about twice the length, of which less is known. Interestingly, our phenotype was only restored when complemented with the long form of the gene or when it was supplied in two parts, the short form and the missing part to obtain the long form. This work demonstrates the role of regulatory RNAs in the adaptation of S. aureus to antibiotic resistance and highlights their value as potential therapeutic targets for manipulating individual sRNA responses to promote the efficacy of existing antibiotics.