Optimising disinfection conditions to cover antimicrobial resistance: mechanistic insights, safe dosage threshold and genomic indicators

Disinfection is essential for pathogen control in engineered water systems, yet growing evidence suggests that conventional disinfection processes do not effectively address antimicrobial resistance (AMR). Therefore, AMR mitigation is not adequately reflected by conventional microbial inactivation metrics. This review synthesises current understanding of how widely used disinfection technologies (chlorination, ozonation, and UV irradiation) affect AMR dissemination through oxidative and photochemical stress, membrane injury, DNA damage, release of extracellular antibiotic resistance genes (eARGs), and altered horizontal gene transfer. Across these mechanisms, AMR responses are highly non-linear and strongly dependent on operational conditions. Insufficient exposure permits survival and regrowth, sublethal exposure can stimulate stress responses and gene exchange, and intensive treatment may lyse cells while leaving intracellular and extracellular resistance determinants insufficiently degraded. We propose a process optimisation framework in which disinfection performance is evaluated not only by microbial inactivation but also by the control of resistance genes and their transfer potential. We further challenge the reliance on culturable indicators or viable cell counts as single metrics of disinfection efficiency, as treated effluents can retain a distinct extracellular resistome that remains mobile or transformable after disinfection. To address this gap, we introduce the concept of genomic disinfection, whereby treatment performance is defined by the destruction or functional inactivation of intracellular and extracellular ARGs and associated mobility markers. Together, this review provides a unified framework linking disinfection mechanisms, process optimisation and genomic monitoring, and highlights the need to redefine treatment targets for AMR control in water and wastewater systems.