Revealing Transcriptomic Responses in Escherichia coli During Early Antibiotic Exposure

The earliest stages of bacterial adaptation to antibiotics are critical for survival, as the responses initiated in these moments shape the path toward tolerance and resistance. While long-term adaptations have been extensively studied, much less is known about the immediate, complex transcriptional changes that unfold in the first moments after antibiotic exposure. Here, we applied iModulon analysis to time-resolved transcriptomic data from Escherichia coli exposed to subinhibitory concentrations of two antibiotics, capturing regulatory changes within the first 30 minutes of exposure. This analysis reveals an integrated, three-phase framework of adaptation: an immediate and sustained primary response that broadly activates stress programs, a transient secondary response that restores redox balance, and a tertiary response that supports long-term survival through metabolic remodeling and antibiotic-specific defenses. This model provides new insight into how metabolic, redox, and stress responses are integrated to manage the physiological challenges of antibiotic stress, revealing a highly coordinated and dynamic regulatory strategy. By disentangling these overlapping transcriptional programs, our work offers a systems-level understanding of early bacterial adaptation and highlights new opportunities to investigate how survival mechanisms unfold during the critical moments following antibiotic exposure. Overall design: RNA-seq profiling of E. coli MG1655 in the first 30 minutes after exposure to ampicillin and ciprofloxacin