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. RNA-seq profiling of E. coli MG1655 in the first 30 minutes after exposure to ampicillin and ciprofloxacin

细菌对抗生素的早期适应阶段对其存活至关重要，此阶段启动的应答反应将决定细菌走向耐受与耐药的路径。尽管长期适应过程已得到广泛研究，但人们对于抗生素暴露后最初时刻所发生的即时、复杂的转录变化仍知之甚少。本研究针对暴露于两种亚抑制浓度抗生素的大肠杆菌（Escherichia coli）的时间分辨转录组数据，开展iModulon分析(iModulon analysis)，捕捉了抗生素暴露后前30分钟内的调控动态。该分析揭示了一套整合的三阶段适应框架：一是即时且持续的初级应答，可广泛激活应激程序；二是短暂的次级应答，用于恢复氧化还原平衡；三是三级应答，通过代谢重塑与抗生素特异性防御机制支持细菌长期存活。该模型为代谢、氧化还原与应激应答如何协同应对抗生素胁迫带来的生理挑战提供了全新视角，揭示了一套高度协调且动态的调控策略。通过解析这些相互重叠的转录程序，本研究实现了对细菌早期适应过程的系统层面认知，并为探索抗生素暴露后关键时刻的存活机制提供了新的研究方向。本数据集包含大肠杆菌MG1655（E. coli MG1655）在暴露于氨苄青霉素（ampicillin）与环丙沙星（ciprofloxacin）后前30分钟的RNA-seq谱数据。