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. 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 UK and conducted the first freshwater snail faecal metagenomic study. We detected putative ARGs predicted to confer resistance to 13 antibiotic classes, including carbapenems. All ARGs that could be assembled into metagenome-assembled genomes (MAGs) were found within Proteobacteria, which dominated the faecal microbiomes and were strongly associated with the total ARG load. In Malawi, we linked bla_OXA-181 (bla_OXA-48-like), a previously mobilized carbapenemase gene, to Shewanella xiamenensis, the gene’s known progenitor. We detected another bla_OXA-48-like gene by read mapping from a sample in the UK. We identified mobile colistin resistance (mcr)-like genes at 11 of 15 locations, with two mcr-7-like genes being found in an Aeromonas jandaei MAG in Uganda. Our findings highlight freshwater snail faeces as a One Health-relevant environmental reservoir of clinically important ARGs.