Promoting gut decolonization of multi-drug resistant bacteria via the microbiome

The fight against multi-drug resistant Enterobacteriaceae (MDR-E) has been declared as a high priority by the WHO. Colonization of the human gut with MDR-E, including MDR E. coli, is associated with an increased risk of infection and dissemination within the community. Probiotics developed to selectively decolonize the microbiota of carriers from MDR strains are a promising treatment alternative. We hypothesize that the human gut is a great resource for probiotics, which show the potential to selectively decolonize MDR-E. As a novel resource for the identification of potentially probiotic bacteria, a strain collection of Enterobacteriaceae was generated from 630 donors from four cohorts. As it is of great interest to screen as many strains as possible due to the high genetic diversity of bacterial isolates, we established an ex vivo assay to identify strains with protective properties. Specifically, candidate probiotics and a MDR E. coli strain were spiked into cecum content of mice representing the nutritional environment in vivo. Furthermore, we developed in vivo models for gut (de)colonization of MDR-E and characterized the decolonization properties of specific probiotic candidates. For this approach we selected a panel of commensal isolates which displayed different competitive abilities in the ex vivo assay and observed decolonization of MDR E. coli after precolonization with competitive isolates. To gain mechanistic insights into the competition between protective isolates and the MDR E. coli strain, we conducted growth curves and competition assays in minimal media supplemented with a single carbon source. We observed a general fitness advantage of the protective strain and reduced CFUs of the MDR E. coli strain after co-cultivation in minimal media with specific carbon sources. We could further demonstrate the competition for carbon sources in vivo. For promising candidates we intend to use loss-of-function genetic screens for genes, which may be crucial for the protective effect. We also want to identify potential cooperation partners and microbiome signatures, which are relevant for the protective effect.