Shotgun metagenomic surveillance of airport wastewater reveals microbial community restructuring and persistence of antimicrobial-resistance determinants after treatment

Airport wastewater has emerged as a valuable matrix for wastewater-based epidemiology, providing insights into microbial circulation and antimicrobial resistance (AMR) among highly mobile populations. However, the effects of wastewater treatment on the microbial community structure and resistome of airport wastewater have not been comprehensively characterized. Here, we present the first comprehensive metagenomic assessment of paired influent and effluent airport wastewater, enabling characterization of treatment-induced changes in microbial community composition and antimicrobial resistance determinants. Paired influent and effluent wastewater samples were collected from the wastewater treatment plant serving Catania–Fontanarossa Airport (Sicily, Italy). Wastewater treatment significantly reduced microbial richness and induced a consistent shift in community composition, as demonstrated by paired beta-diversity analyses. Proteobacteria became the dominant phylum after treatment, whereas Bacteroidetes and Firmicutes markedly declined. Differential abundance analyses showed enrichment of treatment-associated taxa, including Thauera, Aliiarcobacter and Pseudomonas , accompanied by depletion of gut-associated genera such as Bacteroides, Prevotella and Alistipes . Qualitative resistome profiling indicated partial reduction of several ARG classes but persistence of clinically relevant resistance determinants, particularly those associated with beta-lactams, aminoglycosides, macrolides and sulphonamides. Functional profiling indicated treatment-associated metabolic restructuring; however, no functional features remained statistically significant after correction for multiple testing. Overall, these findings demonstrate that airport wastewater treatment acts as an ecological filter that substantially restructures microbial communities without completely eliminating antimicrobial resistance signatures. Shotgun metagenomic surveillance of airport wastewater may therefore provide valuable complementary information for monitoring AMR dissemination and microbial dynamics within a One Health framework.