Freshwater snail faecal metagenomes reveal environmental reservoirs of antimicrobial resistance genes across two continents

The transfer of antimicrobial resistance genes (ARGs) from environmental microbes to pathogens is a critical but underexplored One Health driver of antimicrobial resistance (AMR). Here, we evaluate freshwater snails, which are geographically widespread aquatic invertebrates, as environmental reservoirs of ARGs. We collected faeces from eight gastropod genera at 15 freshwater locations across Malawi, Uganda, Zanzibar, and the United Kingdom, and conducted the first freshwater snail faecal metagenomic sequencing study. Proteobacteria dominated the faecal microbiomes, within which Aeromonadales were strongly associated with the total ARG load. We detected putative ARGs conferring resistance to 13 distinct antibiotic classes, including carbapenem resistance genes in all countries. In Malawi, we linked blaOXA-181 (blaOXA-48-like), a putatively mobile carbapenemase gene, to Shewanella xiamenensis - the gene's known progenitor - in a metagenome-assembled genome. We detected another blaOXA-48-like variant by read-mapping from a sample in the United Kingdom and identified mobile colistin resistance (mcr)-like genes at 11 of 15 locations. Our findings highlight freshwater snail microbiomes as One Health-relevant, environmental reservoirs of clinically important ARGs.