Metagenomic profiling of bacterial resistomes in full-scale wastewater treatment plants in Spain

Investigating the resistome of activated sludge communities is critical to understand the spread of antimicrobial resistances. Here, the resistomes of five full-scale wastewater treatment plants (WWTPs) in Spain were analyzed using a metagenomic approach. 888, 1361 and 1062 unique antibiotic resistance genes (ARGs) were identified in the aerated bioreactors, the anoxic/anaerobic bioreactors, and the treated effluents, respectively. The core resistome comprised 25 ARGs conferring resistance to betalactams (penP, blaI), fosmidomycin (fsr), tetracycline (tetA), thiopeptides (tipA), and vancomycin (vanJ, vanR, vanW, vanX, vanY). The cumulative coverages of ARGs for betalactams, cationic antimicrobial peptides (CAMPs), mercury, lincomycin, quaternary ammonia, and multidrug resistance mechanisms decreased in the effluents. In contrast, the ARGs for ethionamide, methylenomycin, thiopeptides, and vancomycin increased their relative abundances in the effluents of some WWTPs. Proteobacteria were the major putative hosts of ARGs in all samples, followed by Bacteroidetes in the bioreactors and Actinobacteria in the effluents. The genera making bigger contributions to the cumulative coverage of ARGs shifted across the different WWTPs and sample types, showing that different groups of bacteria hosting the resistome were enriched in each case. Many genera identified as putative hosts of ARGs are key players of biological wastewater treatment, including filamentous bacteria, nitrifiers, denitrifiers, and polyphosphate-accumulating organisms. These findings point to the optimization of the tertiary treatment of effluents and management of sludge as the most suitable approaches to mitigate the dissemination of ARGs from WWTPs globally.