Integrated metagenomic, culture-based, and whole genome sequencing analyses of antimicrobial resistance in wastewater and drinking water treatment plants in Barcelona, Spain

Abstract

The misuse and overuse of antimicrobials drive the emergence of antimicrobial resistance (AMR), a critical global health concern. While wastewater treatment plants (WWTPs) are essential for removing microorganisms and contaminants, they also serve as hotspots for antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), facilitating their persistence and dissemination. This study investigated AMR in two WWTPs and one drinking water treatment plant (DWTP) in the Baix Llobregat area of Barcelona, Spain. Four sampling campaigns were conducted during winter and summer 2023 across different treatment stages. Due to drought conditions, reclaimed water from the Baix Llobregat WWTP was discharged upstream of the DWTP intake to supplement water resources for indirect potable reuse. A total of 991 cultivable ARB were obtained, enabling phenotypic and genotypic characterisation. The most prevalent included Aeromonas spp. (44.3 %), Enterobacterales (27.9 %), Pseudomonas spp. (19.1 %), Acinetobacter spp. (4.8 %), Shewanella spp. (2.2 %), Stenotrophomonas spp. (1 %), and others (0.7 %). Among these, 57.3 % were multidrug-resistant and 2.7 % were extensively drug-resistant. Furthermore, 34.6 % produced extended-spectrum beta-lactamases, 14.1 % harboured carbapenemase genes, and 2.9 % exhibited colistin resistance. Shotgun metagenomic analysis revealed high taxonomic diversity, without dominant genera across treatment stages. The resistome was dominated by ARGs conferring resistance to beta-lactams, aminoglycosides, and macrolides, alongside genes linked to biocide resistance and heavy metal tolerance. Spearman correlation analysis of selected sequenced strains suggested a weak to moderate co-occurrence between ARGs and biocide or heavy metal tolerance genes. These findings underline WWTPs as AMR hotspots and reinforce the need to monitor DWTP source water within the One Health framework.

Keywords: Antibiotic-resistant bacteria; Antimicrobial resistance; Drinking water treatment plant; Heavy metal tolerance genes; Resistome; Wastewater treatment plant.