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Persister cells are drug-tolerant bacteria that can survive lethal antibiotic exposure despite lacking genetic resistance mechanisms. Various pathways are involved in the formation of persisters, including the energy balance of the bacteria.To test the involvement of ATP in the formation of persister cells after treatment with antibiotics, the ATP-synthase was deleted in Salmonella Typhimurium. However, the resulting reduced ATP concentration did not increase the tolerance of the mutant, on the contrary, treatment with ciprofloxacin, a fluoroquinolone, resulted in fewer persistent cells compared to the corresponding wild type. Furthermore, the involvement of prophages in terms of persister cell formation of Salmonella Typhimurium was investigated. Deletion of the endogenous prophages, designated Gifsy-1, Gifsy-2, Gifsy-3, and ST63B, resulted in slowed initial killing and increased formation of persistent cells after the bacteria were exposed to ciprofloxacin. In particular, Gifsy-1 and the prophage-mediated lysis process were largely responsible for the reduced formation of persister cells in the prophage-carrying wild type.