Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings

Abstract

Aquatic ecosystems harbor a vast pool of antibiotic resistance genes (ARGs), which can suffer mutation, recombination and selection events. Here, we explored the diversity of ARGs, virulence factors and the bacterial community composition in water samples before (surface raw water, RW) and after (disinfected water, DW) drinking water conventional treatment, as well as in tap water (TW) and ultrafiltration membranes (UM, recovered from hemodialysis equipment) through metagenomics. A total of 852 different ARGs were identified, 21.8% of them only in RW, which might reflect the impact of human activities on the river at the sampling point. Although a similar resistance profile has been observed between the samples, significant differences in the frequency of clinically relevant antibiotic classes (penam and peptide) were identified. Resistance determinants to last resort antibiotics, including sequences related to mcr, optrA and poxtA and clinically relevant beta-lactamase genes (i.e. blaKPC, blaGES, blaIMP, blaVIM, blaSPM and blaNDM) were detected. 830 coding sequences (CDSs - related to 217 different ARGs) were embedded in contigs associated with mobile genetic elements, specially plasmids, of which 68% in RW, DW and TW, suggesting the importance of water environments in resistance dissemination. Shifts in bacterial pathogens genera were observed, such as a significant increase in Mycobacterium after treatment and distribution. In UM, the potentially pathogenic genus Halomonas predominated. Its draft genome was closely related to H. stevensii, hosting mainly multidrug efflux pumps. These results broaden our understanding of the global ARGs diversity and stress the importance of tracking the ever-expanding environmental resistome.