Bacterial Community Barrier to Vancomycin Resistant Enterococcus

Current strategies to prevent resistance to specific antibiotics focus predominantly on reducing inappropriate use of those antibiotics. However, colonization with vancomycin-resistant Enterococci (VRE) in immunocompromised children is not predicted by prior vancomycin treatment. This observation, also seen for other multidrug resistant organisms (MDRO), suggests that other host and pathogen factors are pivotal drivers of the spread of antibiotic resistance. Using VRE as a model MDRO, the objective of this study is to discover drivers on both sides of the equation. On the host side—how human intestinal microbiome environment selects VRE—and the pathogen side—which genes allow VRE to outcompete in microbial communities. Using a combination of molecular, bioinformatic and population-level approaches, the proposed experiments will test the central hypothesis that VRE colonization and domination in humans requires disruption of both microbe-microbe and host-microbe interactions. This proposal builds upon preliminary observations that human microbiome communities differ in their ability block VRE colonization, and that VRE strains vary in their ability to overcome the bacterial community barrier. The first aim will focus on identifying intestinal community microbes that modulate VRE colonization. This will be evaluated using a priori bioinformatic predictions and validated in community culture experiments. These experiments will pinpoint the contributions of specific microbial community members by comparing VRE colonization in diverse communities and sub-communities. Identification of microbiome interactions that regulate MDRO colonization will enable exploration and discovery of new mechanisms to stop spread of antibiotic resistance. The second aim will focus on identifying which bacterial genes facilitate VRE colonization, persistence, and dominance. Genetic contribution to community colonization will be tested in community cultures, utilizing both genetic knockouts of predicted carriage genes and a broader survey with transposon-insertion libraries. This will yield fundamental insight into how VRE persists in the absence of direct antibiotic selection. Overall, this work will: i) identify microbiome disruptions that facilitate MDRO colonization for potential amelioration, ii) inform infection prevention efforts by identifying strains likely to spread drug resistance and uncover new microbiome interactions as novel anti-infective drug targets.