Antimicrobial resistant (AMR) bacteria in soil microbiomes 

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Soil microbiota represent a potential ancient evolutionary origin of antibiotic resistance and are considered a reservoir of resistance genes available for exchange with clinical pathogens. In a previous study with collaborators from the UK, we aimed to identify bacteria capable of growing in the presence of several antibiotics, including the ultra-broad-spectrum antibiotic meropenem, in agricultural soil using DNA stable isotope probing (SIP). Our exciting results indicate that uncultured bacteria within the poorly characterised phylum Acidobacteria are multi-drug resistant. This could suggest a role for uncultivated Acidobacteria as vectors of antimicrobial resistance (AMR) to pathogens that transit through the soil environment—an insight we anticipate could have a significant impact on the field.

 

Additionally, AMR has been found in soils across diverse ecosystems, including remote areas such as the Arctic. Together with collaborators from France, we have recently demonstrated variation in AMR with soil age in recently deglaciated Arctic soils using a space-for-time chronosequence approach. We observed that AMR increases over time, and its temporal spread is influenced by competitive and facilitative interactions among microbes for nutrients.