Post-fluoroquinolone treatment molecular events and nutrient availability modulate Staphylococcus aureus antibiotic persistence

Staphylococcus aureus is a bacterial pathogen associated with about one million deaths per year. S. aureus infects diverse host sites including skin and the airway. At nutrient-limited infection sites, S. aureus cells become increasingly metabolically quiescent. While lower metabolic activity may help contain growth of the pathogen, it can enhance S. aureuss persistence to antibiotic treatment. Here, we focus on starved S. aureuss response to fluoroquinolones (FQs), which inhibit topoisomerases necessary for DNA and RNA synthesis and lead to double-stranded DNA break (DSB) formation. We show that although FQs accumulate in stationary-phase S. aureus during treatment, DSBs form and cells start to die during the post-treatment period when nutrients are replenished. We found that most persisters suffer DNA damage and rely on RecA to repair DSBs post-treatment. We discovered that persisters frequently pass on damaged chromosomes to their progeny, causing many of their progeny to stall. Given that persister resuscitation and death of non-persisters occur during the post-FQ treatment period, we asked how nutrient availability during this critical time impacts S. aureus survival. We show that continued starvation after treatment ends enhances S. aureus survival, even in populations lacking DSB-repair mechanisms. We demonstrate that post-treatment starvation delays the resumption of nucleic acid synthesis, presumably limiting topoisomerase activity, and allows the cells time to remove some intracellular FQs before they can trap active topoisomerases. Collectively, our findings highlight DSB repair processes and environmental conditions that can be targeted to improve treatment outcomes for staphylococcal infections. Significance StatementS. aureuss ability to overcome antibiotic treatment makes it a formidable pathogen. Since nutrients are often limited at infection sites, understanding how starved S. aureus responds to clinically relevant antibiotics, including DNA-damaging FQs, is essential for improving treatment outcomes. We show that DNA damage accumulates during the post-treatment period when nutrients are replenished. Continuing to starve the cells after treatment limits the incidence of DSBs, helping some cells survive even if they are incapable of DSB repair. Finally, we show that offspring stemming from cells that survive FQ treatment often experience damage and stress for several generations. Our work highlights strategies S. aureus deploys to recover from FQ treatment that can be targeted to enhance antibiotic efficacy.