Decoding biofilm tolerance in clinical infections: Matrixome architecture, metabolic zonation, and therapeutic implications

Biofilm-associated infections continue to pose a major challenge in clinical and public health due to their high tolerance to antimicrobial agents and host immune defences. Accounting for up to 80% of chronic human infections, unlike genetic resistance, biofilm tolerance is a reversible, phenotypic condition caused by the organised matrixome. Biofilm tolerance arises from structural protection conferred by the extracellular matrix and metabolic heterogeneity within the community. This review covers the structural and physiological factors of tolerance, emphasising metabolic zonation, stress-induced dormancy (persister cells), and transport-based protection through increased efflux systems. We explore emerging ideas such as tolerance memory, host-driven selective pressures, and the pharmacokinetic (PK) mismatch caused by spatial drug gradients within the biofilm structure. Despite advances in understanding mechanisms, a significant gap remains in translation due to the reliance on planktonic-based diagnostics and standard susceptibility measures (e.g., MIC) that do not reflect biofilm recalcitrance. We suggest shifting toward "biofilm-aware" clinical approaches that incorporate spatial transcriptomics, AI-driven predictive models, and matrix-disrupting adjunct therapies, including nanotechnology, phage therapy, and AI–guided interventions. To promote global equity in managing these infections, interdisciplinary collaboration and accessible diagnostics are essential. Eradicating pathogens through a tolerance-informed control strategy is crucial for sustainably managing chronic and recurrent infections.