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

Abstract

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 metagenomics study. We detected putative ARGs predicted to confer resistance to 13 antibiotic classes, including carbapenems in all countries. 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 blaOXA-181 (blaOXA-48-like), a previously mobilised carbapenemase gene, to Shewanella xiamenensis, the genes known progenitor. We detected another blaOXA-48-like gene by read-mapping from a sample in the United Kingdom. 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. Data SummaryShort reads from all samples sequenced in this study have been deposited in the Sequence Read Archive (SRA) under BioProject PRJNA1211045, with accession numbers SRX27371064 - SRX27371078. Data and code used to carry out analyses in R are available at https://github.com/amoreo71/freshwater_snail_faecal.