Multi-site wastewater metagenomics reveals geographically distinct microbial communities and plasmid-mediated antimicrobial resistance co-selection in Zambia

Abstract

Antimicrobial resistance (AMR) poses a disproportionate burden in low- and middle-income countries, yet comprehensive environmental surveillance, particularly for plasmid-mediated resistance, remains critically limited in sub-Saharan Africa. Wastewater systems harbour diverse microbial communities with a high potential to mobilise antibiotic resistance genes (ARGs), thereby driving the environmental dissemination of resistance. Here, we present a multi-site wastewater metagenomics analysis in Zambia, profiling the microbiome and resistome across 114 samples collected between October 2023 and August 2025 from five districts spanning three provinces. We identified distinct geographic AMR niches, with Chipata exhibiting significantly higher taxonomic and ARG diversity than multiple other sites. Clinically relevant enteric pathogens, including Escherichia coli and Klebsiella pneumoniae , were associated with broad multidrug resistance. Plasmid analysis identified disinfectant resistance genes ( qacEΔ1 ) as central hubs, co-occurring with sulfonamide and aminoglycoside resistance determinants, suggesting biocide-mediated co-selection. These findings demonstrate that wastewater surveillance can monitor AMR patterns in the community and reveal mobile reservoirs of resistance not routinely captured by clinical surveillance alone, supporting the integration of wastewater genomics into national action plans to monitor and mitigate AMR transmission.