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

Bacterial persisters are a subpopulation of multidrug-tolerant cells capable of surviving and resuming activity after exposure to bactericidal antibiotic concentrations, contributing to relapsing infections and the development of antibiotic resistance. We challenge the conventional view that persisters are metabolically dormant by providing compelling evidence that an isogenic population of Escherichia coli remains metabolically active in persistence. Our transcriptomic analysis, conducted at various time points following exposure to bactericidal concentrations of ampicillin (Amp), revealed a number of genes with differential expression over time. Some genes were consistently upregulated in Amp treated persisters compared to the untreated controls, a change that can only occur in metabolically active cells capable of increasing RNA levels. Some of these genes have been previously linked to persister cells, while others have not been associated with them before. If persister cells were metabolically dormant, we would expect minimal changes in the gene network across different time points of Amp treatment. However, network analysis revealed major shifts in gene network activity at various time points of antibiotic exposure. These findings reveal that persisters are metabolically active, non-dividing cells, thereby challenging the notion that they are dormant. Significance statementBacterial persisters are a subpopulation renowned for their multidrug tolerance and remarkable ability to survive bactericidal antibiotic treatments; understanding their formation and long-term survival presents significant challenges. These persisters play a critical role in driving antibiotic resistance, underscoring the urgency of deepening our knowledge about them as the threat of resistance continues to escalate. Our study challenges the long-held assumption that persisters are metabolically inactive and that persisters are not as dormant as previously thought.