Escherichia coli Transcriptome or Gene expression

Bacterial persisters, a subpopulation known for their multidrug tolerance and ability to survive lethal antibiotic treatments, have long posed challenges in understanding their formation and long-term survival. In our study, we conducted transcriptomic analyses at various time points following lethal ampicillin (Amp) antibiotic exposure. As anticipated, we observed differential gene expression over time. By comparing transcription levels between Amp-treated and untreated conditions, we identified a subset of consistently upregulated genes. Some of these genes were previously associated with persisters, while others were novel findings. Further experimentation involved creating single gene knockouts, which significantly reduced persister levels. Interestingly, no significant difference in survival rates was observed at 24 hours, suggesting the presence of multiple persister subpopulations. Overall design: RNA-sequencing from three different E. coli populations: (1) Stationary phase cells were diluted 1:100 times in pre-warmed MMB+ media and treated with Amp (0.1 mg/mL) for 24 h, and samples were isolated for RNA sequencing before antibiotic treatment (0 h) and after antibiotic treatment at 3 h, 6 h, and 24 h.