TisB enables antibiotic tolerance in Salmonella by preventing prophage induction through ATP depletion

Persisters are phenotypically antibiotic-tolerant cells which can survive antibiotic exposure without acquiring antibiotic resistance. A proposed important factor in persistence is low intracellular ATP levels, which are thought to reduce the activity of antibiotic targets. However, previous studies demonstrated that persisters have comparable DNA damage as drug-sensitive bacteria after fluoroquinolone treatment. Furthermore, recent studies reported that endogenous prophages can reduce levels of antibiotic persistence in Salmonella after fluoroquinolone treatment. In this study, we examined prophage induction and persister cell survival of a prophage-free variant of Salmonella Typhimurium and strains harbouring a deletion of the tisAB genes, with tisB encoding the toxin from the tisB/istR-1 toxin-antitoxin system, known to reduce the intracellular ATP concentration. Treatment of the prophage-free variant with ciprofloxacin resulted in reduced killing and increased persistence as compared to the wild type. In addition, prophage induction and prophage mediated killing was significantly increased after deletion of tisAB following ciprofloxacin treatment. We also demonstrate that the recovery phase following the removal of ciprofloxacin, is crucial for the induction of endogenous prophages. Our results suggest that ATP-dependent prophage activation plays a significant role in DNA damage-mediated killing of bacteria. Low ATP levels can dampen the induction of prophages and increase the fraction of bacterial survivors after ciprofloxacin treatment.