Conservation and divergence of ciprofloxacin persister survival mechanisms between Pseudomonas aeruginosa and Escherichia coli

Studies have shown that DNA damage repair systems, including homologous recombination (HR) and the SOS response, are important for fluoroquinolone (FQ) persistence of Escherichia coli, which has been the workhorse organism of persister research. We sought to explore whether those systems are also important for FQ persistence of Pseudomonas aeruginosa, a common cause of lung infections in cystic fibrosis patients, which can be treated with FQs such as ciprofloxacin (CIP). Notably, P. aeruginosa has important differences in its DNA damage repair capabilities compared to E. coli that include the machinery needed to conduct non-homologous end-joining (NHEJ), Ku and LigD. Using a genetic approach, we found that loss of HR significantly depressed persister levels of P. aeruginosa to CIP during stationary-phase, but not in exponential-phase. This differed from E. coli grown in identical conditions, where loss of HR reduced survival in both stationary- and exponential-phase populations. Similarly, an inability to induce the SOS response reduced survival during both growth phases for E. coli but only in stationary-phase for P. aeruginosa. Loss of NHEJ machinery in P. aeruginosa did not impact persister levels during stationary- or exponential-phase, whereas overexpression of NHEJ machinery in P. aeruginosa had toxic effects. In addition, the generality of findings to another FQ, levofloxacin, and a recent clinical isolate, MRSN 1612, were confirmed. These results demonstrate that HR and the SOS response are important to CIP persistence of stationary-phase P. aeruginosa, dispensable to CIP persisters in growing P. aeruginosa cultures, and that the contributions of systems to E. coli persistence do not directly translate to persisters of P. aeruginosa.