Growth arrest or drug target inactivity is not sufficient for persister formation in E. coli

Persisters are a subpopulation of slow-growing or nondividing cells that are tolerant to antibiotics and are thought to be involved in persistent infections. The development of antibiotic tolerant phenotype is thought to be due to antibiotic target inactivity and is closely associated with growth arrest. While growth arrest and antibiotic target inactivity are widely believed to be important for persister formation, there have been inconsistent results and it has been difficult to determine whether growth arrest or antibiotic target inactivity is necessary or sufficient for persister formation. To address these questions, we used a novel approach to create antibiotic target inactivation via promoter swap to knock down quinolone drug target DNA gyrase subunit A (GyrA), as well as growth arrest via CRISPR interference to block key cell division protein (FtsZ) and a key ribosomal protein L28 (RpmB). Growth dynamics, relative target gene expression, cellular ATP levels and persister formation in the GyrA, FtsZ, and RpmB knockdown strains were compared with the control growing bacteria. Surprisingly, we found that the strains that had growth arrest induced by FtsZ or RpmB knockdown did not induce persister formation. Similarly, knockdown of GyrA, a quinolone drug target, did not induce persister cells tolerant to levofloxacin. In addition, ATP levels, a measure of cellular metabolism, were not reduced but increased in the GyrA, FtsZ, and RpmB knockdown strains compared with the control strain. Thus, we conclude that growth arrest or target inactivation is not sufficient to produce persister phenotype as commonly assumed and that cellular ATP levels did not correlate with persister formation. Further studies are needed to better understand how persisters are formed for improved treatment of persistent infections.