Dietary antibiotics can select genes encoding extended-spectrum ß-lactamases and carbapenemases in the human gut microbiome

Antimicrobial resistance (AMR) is a serious global health threat, yet the drivers of its spread among humans are not fully understood . Antibiotics can enter the human gastrointestinal tract through the food chain , but their role in promoting AMR in the gut microbiome has never been explored. Using an in vitro model of the human gut microbiota, we tested whether traces of antibiotics, alone or in combination, select for genes encoding resistance to last-resort antibiotics, originating from epidemic Gram-negative pathogens. We found that fluoroquinolones, trimethoprim, and a mixture of veterinary antibiotics, at levels similar to those measured in the feces of healthy individuals, enriched the human gut microbiota with gene encoding extended-spectrum ?-lactamases and carbapenemases. AMR enrichment relies on strain co-selection and shift in microbial flora composition. Overall, these data shed new light on the role of dietary antibiotics as facilitators of AMR implantation in the human gut.