Revealing Transcriptomic Responses in Escherichia coli During Early Antibiotic Exposure

Abstract

The earliest responses of pathogenic bacteria to antibiotics can affect the outcome of an infection. While long-term adaptations have been extensively studied, the immediate transcriptional changes that unfold immediately following antibiotic exposure remain poorly understood. Here, we applied iModulon analysis to time-resolved transcriptomic data from Escherichia coli exposed to subinhibitory concentrations of two antibiotics (ampicillin and ciprofloxacin), capturing transcriptional regulatory changes occurring within the first 30 minutes of exposure. This analysis reveals an integrated, three-phase response: 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. These results highlight a coordinated and dynamic regulatory strategy describing how metabolic, redox, and stress responses are integrated to manage the physiological challenges of antibiotic stress. By disentangling these overlapping transcriptional regulatory programs, this work offers a genome-scale understanding of how survival mechanisms unfold during the critical moments following antibiotic exposure. The study opens new directions for investigating early survival mechanisms and the possible identification of new targets to disrupt the initial adaptation process. ImportanceInitial bacterial responses to antibiotics are important for survival and can influence the development of tolerance and resistance. Yet this period remains poorly understood, in part because the transcriptional responses that unfold within minutes of antibiotic exposure are complex and difficult to interpret. In this study, we applied novel data generation and data analytics approaches to untangle the complexity of the initial response of Escherichia coliI to two antibiotics. We reveal a three-phase process that explains how E. coli coordinates stress responses, maintains redox homeostasis, and establishes longer-term defenses. The novel transcriptomic analytics elucidate independently regulated sets of genes that constitute cellular processes. By identifying all such cellular processes that react over the initial time scale, we can deconvolute the response based on first principles of cellular physiology.