Metabolic reprogramming enables transient survival and envelope remodelling in Staphylococcus aureus under dalbavancin treatment

Abstract

Clinical failure of antibiotic therapy can occur in the absence of measurable resistance, yet the biological basis of this discordance remains poorly understood. Here, we identify a transient survival phenotype that limits dalbavancin efficacy and may contribute to treatment failure in the absence of stable resistance in Staphylococcus aureus . Survival-curve profiling revealed delayed killing across genetically and phenotypically diverse strain backgrounds, including vancomycin-susceptible and vancomycin-intermediate isolates. This phenotype persisted under pharmacokinetic-mimicking exposure conditions, demonstrating sustained survival during clinically relevant declining drug concentrations. Integrated metabolomic and transcriptomic analyses during the defined early survival window uncovered coordinated metabolic reprogramming centered on peptidoglycan biosynthesis, lipid carrier dynamics, and envelope stress regulation. These molecular changes translated into pronounced structural remodelling, including heterogeneous cell wall thickening, revealed by transmission electron microscopy and cryo-electron tomography. Functional interrogation of envelope-associated regulatory and biosynthetic pathways reduced survival under dalbavancin exposure, attenuated peptidoglycan accumulation, and partially restored autolysis, supporting a link between metabolic adaptation and transient survival rather than fixed genetic resistance. Importantly, this adaptive survival state was temporally constrained and pharmacologically suppressible. Disruption of late-stage peptidoglycan assembly reduced survival under dalbavancin exposure across multiple strain backgrounds. These findings establish a metabolically associated cell-envelope remodelling programme that transiently limits dalbavancin efficacy and provides a mechanistic framework for early treatment failure in the absence of stable resistance.