The role of heavy metals in the co-selection of plasmid-borne metal and antibiotic resistance genes from industrially contaminated sediments

A comprehensive understanding of the sources and drivers of antimicrobial resistance is essential for effective antimicrobial stewardship. Co-selection is now recognised as a significant driver of antimicrobial resistance, with established links between heavy metal exposure and the presence of bacteria with antimicrobial resistance. The precise mechanisms that drive this process in the environment are co-resistance, cross-resistance, and co-regulation, but their respective impacts remain largely unexplored. Here, we investigated whether heavy metal contamination in freshwater sediments selects for bacteria harbouring plasmids that carry both metal and antibiotic resistance genes, or genes encoding cross-resistance mechanisms. A diverse set of plasmids was recovered from metal-impacted sites at Lake Macquarie (New South Wales, Australia), which carried resistance genes particularly to copper, zinc, cobalt, cadmium, and arsenic. Two-thirds of these plasmids also carried one or more antibiotic resistance genes, indicating co-selection through the co-resistance mechanism. Functional assessment confirmed that the multi-metal and polymyxin resistance plasmid genotype was linked to the corresponding bacterial phenotype. The metagenome of the metal-impacted sediments was also examined to explore evidence of co-selection, and a broad range of incomplete plasmid sequences containing homologues of both metal- and antibiotic-resistance genes was detected. This study demonstrates the important link between anthropogenic heavy metal contamination and potentially clinically relevant antibiotic resistance genes. It highlights the importance of approaching the management of antimicrobial resistance from a One Health perspective.