Temporal dynamics of MDRO eradication after FMT

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PROJECT SUMMARY The World Health Organization and U.S. Centers for Disease Control and Prevention have designated antimicrobial resistance a major threat to Global Health with over 23,000 annual deaths related to antimicrobial resistant infections in the U.S. alone. However, the drug pipeline to develop new antibiotics is dry. Small studies support the safety and efficacy of fecal microbiota transplantation (FMT) to eliminate intestinal colonization with antibacterial resistant organisms but its mechanisms are not well understood. We will leverage patient-linked samples from a clinical trial PREMIX (NCT02922816) to test our overarching hypothesis that anaerobic bacteria, viruses, and their gene-predicted functions are causally associated with decreased MDRO colonization after FMT. The Specific Aims of this proposal include: Aim 1: Use the clinical gold standard of bacterial culture to estimate efficacy of FMT in MDRO eradication. Aim 2A: Establish a novel metagenomic analytic pipeline (MAP) to quantify abundance of bacterial and viral taxa, AR, virulence, and colonization resistance genes. Aim 2B: Use 16S rRNA sequencing to estimate temporal dynamics of difficult to culture bacterial taxa in FMT vs controls. Aim 2C: Use metagenomic whole-genome sequencing and the MAP to estimate temporal dynamics of AR, virulence, and colonization resistance genes in FMT vs controls. Aim 3: Use environmental virome NGS techniques to test the association of viral (including bacteriophage) taxa with abundance of MDRO after FMT. We expect that completion of these aims and related training will lead to clinically applicable preliminary data and next steps in translational microbial therapeutic development for MDRO colonization. My long-term career goal is to become a collaborative leader in ID microbiome data science focusing on: 1) mechanisms of microbial therapeutics such as FMT in reducing colonization with multi- drug resistant organisms (MDRO), and 2) translating these findings into clinical and public health interventions to reduce MDRO colonization and infection. Emory and Georgia Tech are ideal and highly-collaborative research environments, which are both national leaders in biomedical research. Both institutions provide rich resources to complete the described aims and progress in career development to become an independent translational ID microbiome data scientist. In addition, Emory is an active site of microbial therapeutic investigation with 7 clinical trials of microbial therapeutics and a clinical FMT program that has completed over 300 treatments for refractory Clostridioides difficile.