Metagenomic profiling reveals distinct signatures of pathogens, antibiotic-resistance genes and human viruses in urban river mouths of the north-western Adriatic coast

Coastal ecosystems are increasingly threatened by microbiological risk due to urban wastewater discharges, which might affect public health and have important economic consequences on the blue tourism. Here, we examine the changes in water and sediment microbiomes at the mouths of three urban-draining rivers (Marecchia, Marano, Rio Melo) and at the Santa Giustina wastewater treatment plant, situated in one of the most densely urbanized and touristic areas of the Adriatic Sea. During the peak summer season, water and sediment samples were analysed through 16S rRNA metabarcoding and shotgun metagenomics to identify the presence of pathogenic bacteria, human viruses, and antibiotic resistance genes (ARGs). Results revealed that impacted river mouths hosted distinct microbial fingerprints, with seawater showing higher levels of pathogenic bacteria (including Vibrio, Enterococcus, Escherichia-Shigella, and Streptococcus) than sediments. Several human viruses of risk groups 2 and 3, such as coronaviruses, herpesviruses, and hepatitis viruses, were detected, along with 99 ARGs, 82 of which were classified by the World Health Organization (WHO) as critically important. Our data suggest the persistence of pathogens in treated effluents and reveal a specific combination of bacterial taxa, viruses, and ARGs, with site-specific profiles. Overall, our findings underscore the need for systematic genomic-based monitoring to safeguard bathing water quality and mitigate risks to human and environmental health, in line with One Health principles.