Multidrug-resistant organisms (MDRO) are a major threat to public health. MDRO infections, including those caused by vancomycin-resistant Enterococcus (VRE), frequently begin by colonization of the intestinal tract, a crucial step that is impaired by the intestinal microbiota. However, the specific members of the microbiota that suppress MDRO colonization and the mechanisms of such protection are largely unknown. Here, using metagenomics and mouse models that mimic the patients’ exposure to antibiotics, we identified commensal bacteria associated with protection against VRE colonization. We further found a consortium of five strains that was sufficient to restrict VRE gut colonization in antibiotic treated mice. Transcriptomics in combination with targeted metabolomics and in vivo assays indicated that the bacterial consortium inhibits VRE growth through nutrient depletion, specifically by reducing the levels of fructose, a carbohydrate that boosts VRE growth in vivo. Finally, in vivo RNA-seq analysis of each strain of the consortium in combination with ex vivo and in vivo assays demonstrated that a single bacterium (Olsenella sp.) could recapitulate the effect of the consortium. Our results indicate that nutrient depletion by specific commensals can reduce VRE intestinal colonization, which represents a novel non-antibiotic based strategy to prevent infections caused by this multidrug-resistant organism.

Conjugative plasmids can transfer both vertically and horizontally in bacterial communities, playing a key role in the dissemination of antimicrobial resistance (AMR) genes across bacterial pathogens. AMR plasmids are widespread in clinical settings, but their distribution is not random, and certain associations between plasmids and bacterial clones are particularly successful. However, knowledge remains limited about the contribution made by vertical and horizontal transmission dynamics to plasmid distribution and maintenance in clinically relevant bacterial communities. In this study, we used a collection of wild type enterobacterial strains isolated from hospitalized patients to perform a comprehensive analysis of the transmission dynamics of the globally spread carbapenem resistance plasmid pOXA-48. We combined in vitro and in vivo experimental approaches to quantify key traits responsible for vertical (the level of AMR) and horizontal (conjugation frequency) plasmid transmission. Our results reveal significant variability in these traits across different bacterial hosts, with Klebsiella spp. strains showing higher pOXA-48-mediated AMR and conjugation frequencies than Escherichia coli strains. Using experimentally determined parameters, we developed a simple mathematical model to interrogate the contribution of vertical and horizontal transmission to plasmid distribution in bacterial communities. These simulations revealed that a small subset of clones, combining high vertical and horizontal plasmid transmission ability, play a critical role in stabilizing the plasmid in different polyclonal microbial communities. Our results indicate that strain-specific differences in plasmid transmission dynamics dictate successful associations between plasmids and bacterial clones, shaping AMR evolution.