An isogenic E. coli population gives rise to multiple persister phenotypes.

Bacterial persisters are a multidrug-tolerant subpopulation capable of surviving and resuscitating after lethal antibiotic treatment, leading to relapsing infections and the emergence of antibiotic resistance. We challenge the conventional wisdom of one persister population and show strong evidence that multiple persister subpopulations are within an isogenic Escherichia coli population, allowing them to survive lethal antibiotic stress. We conducted transcriptomic analyses at multiple time points with lethal ampicillin (Amp) antibiotic, and as expected, several genes were differentially expressed over time. We identified a subset of genes consistently upregulated by comparing transcription levels at different time points of Amp-treated to untreated. Some genes had previously been associated with persisters, while others were new. Subsequently, network analysis showed the gene response between networks but could not map hypothetical genes. Overexpressing seven hypothetical genes resulted in slow or no growth, indicating that high production harmed the cell. We then made single gene knockouts, which dramatically reduced persister level by ∼4-6 fold at 3 h and ∼10-15 fold at 6 h of Amp treatment. However, no significant difference in survival rates was observed at 24 h, indicating the presence of multiple persister subpopulations. Our mathematical model demonstrated a 20-fold decrease in the slow-decaying fraction in the mutant, suggesting the importance of decay kinetics in bacterial survival. These results support the existence of multiple persisters subpopulations, each characterized by distinct decay rates. Also, challenges the idea of complete dormancy, suggest the presence of intricate, multifaceted survival mechanisms, and indicate that the persister population itself is heterogeneous.