Mobile resistome of microbial communities and antimicrobial residues from drinking water supply systems in Rio de Janeiro, Brazil

Antibiotic resistance genes (ARGs) are widespread in the environment due to the overuse of antibiotics and other pollutants, posing a threat to human and animal health. In this study, we evaluated antimicrobial residues, bacterial diversity and ARGs in two important watersheds, Guandu and Sao Joao, that supply drinking water to Rio de Janeiro city, Brazil. In addition, tap water samples were collected from three different cities in Rio de Janeiro State, including the metropolitan area of Rio de Janeiro city. Clarithromycin, sulfamethoxazole and azithromycin were found in untreated water and drinking water in all samples. A greater abundance of Proteobacteria was observed in Guandu and Sao Joao watersheds, with most of the sequences belonging to the Gammaproteobacteria class. A plasmidome-focused metagenomics approach revealed 4881 (Guandu), 3705 (Sao Joao) and 3385 (drinking water) ARGs mainly associated with efflux systems. The genes encoding metallo-beta-lactamase enzymes (bla(AIM), bla(GIM), bla(IMP), and bla(VIM)) were detected in the two watersheds and in drinking water samples. Moreover, we demonstrated the presence of the colistin resistance genes mcr-3 and mcr-4 (both watersheds) and mcr-9 (drinking water and Guandu) for the first time in Brazil. Our data emphasize the importance of introducing measures to reduce the disposal of antibiotics and other pollutants capable of promoting the occurrence and spread of the microbial resistome on aquatic environments and predicting possible negative impacts on human health.

Automated summary

This study evaluated antimicrobial residues, bacterial diversity, and antibiotic resistance genes (ARGs) in two important watersheds and tap water samples in Rio de Janeiro, Brazil. The presence of various antimicrobial residues and a wide range of ARGs was observed in the water sources. Specific bacterial populations and multiple antibiotic resistance genes were also detected. The study emphasizes the need to reduce the discharge of antibiotics and other pollutants to prevent potential negative impacts on human health.