Metagenomic assessment of full-scale wastewater treatment plants identifies sentinel antibiotic resistance genes for monitoring reclaimed wastewater and sludge.
The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural biosolids. However, existing global data largely focus on secondary effluents, providing little actionable evidence for reuse-oriented systems. Here, we present the first integrated framework combining targeted antibiotic residue analysis with shotgun metagenomics of the resistome, mobilome, and microbiome across full-scale reuse oriented wastewater treatment plants (WWTPs) in Southern Europe to identify sentinel ARGs for monitoring.