Pre-treatment bacterial cell states shape antibiotic-induced transcriptional reprogramming and survival

Bacteria can survive antibiotic treatment through phenotypic adaptation, a process that is often transient and involves heterogeneous transcriptional reprogramming. However, how this transcriptional heterogeneity is generated and how it influences antibiotic survival remains unclear. Here, we use bacterial single-cell RNA sequencing and functional assays in Klebsiella pneumoniae to characterize transcriptional heterogeneity and examine how pre-treatment cell states are associated with antibiotic-induced responses and survival outcomes. Using growth phase as a biologically meaningful axis of transcriptional variation, we reveal that even within an isogenic population, distinct transcriptional responses can be induced and co-contribute to survival. These responses are shaped by the cell’s pre-treatment transcriptional state and the mechanism of antibiotic action. Genetic and environmental perturbations, such as rpoS deletion and nutrient supplementation, shift pre-treatment cell states and alter survival frequencies. Our findings establish the biological significance of transcriptional heterogeneity shaped by pre-treatment cell states, providing a systems-level framework for understanding bacterial antibiotic response and suggesting strategies to enhance antibiotic efficacy by modulating cell states. Bacteria can survive antibiotic treatment through transient, heterogeneous transcriptional reprogramming. Here, Liu et al. use bacterial single-cell RNA sequencing and functional assays to show that bacterial responses to antibiotics are shaped by pre-treatment cell states, revealing how transcriptional heterogeneity drives survival.