Microbiome-mediated fructose depletion restricts murine gut colonization by vancomycin-resistant Enterococcus

Sandrine Isaac (), Alejandra Flor-Duro, Gloria Carruana, Leonor Puchades-Carrasco, Anna Quirant, Marina Lopez-Nogueroles, Antonio Pineda-Lucena, Marc Garcia-Garcera and Carles Ubeda ()
Additional contact information
Sandrine Isaac: Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - FISABIO
Alejandra Flor-Duro: Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - FISABIO
Gloria Carruana: Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - FISABIO
Leonor Puchades-Carrasco: Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe
Anna Quirant: Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - FISABIO
Marina Lopez-Nogueroles: Analytical Unit Platform, Instituto de Investigación Sanitaria La Fe
Antonio Pineda-Lucena: Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe
Marc Garcia-Garcera: University of Lausanne
Carles Ubeda: Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - FISABIO

Nature Communications, 2022, vol. 13, issue 1, 1-19

Abstract: Abstract 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.

Date: 2022
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DOI: 10.1038/s41467-022-35380-5

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