Ahmed Babiker, MBBS, MSc.
Assistant Professor, Dept of Medicine, Division of Infectious Diseases
Emory University School of Medicine
About my role in the ARLG
I received ARLG’s Early Faculty Seedling Award to study how novel microbiome-based approaches lead to multidrug-resistant organism (MDRO) decolonization. Using combined anaerobic culturing and next generation sequencing, my team and I are working to identify the specific taxa that confer long-term MDRO decolonization among fecal microbiota transplantation (FMT)-treated individuals. In addition, we are working to establish a strain biobank to support the development of novel microbiome diagnostics and therapies for MDRO decolonization.
About my research
An overarching theme of my clinical and research interests is utilizing -omics techniques to directly address challenges posed by antimicrobial resistance (AMR). My research interests include the clinical and molecular epidemiology of MDROs within healthcare and low- or middle-income country settings, the role of the microbiome in colonization resistance, and the integration of novel diagnostics and -omics technology into clinical microbiology workflows.
In the future, I plan to apply the skills and knowledge obtained during my ARLG award period to collaborative projects to study innovative methods for MDRO therapies and decolonization techniques. I also intend to develop an independent line of translational AMR investigation.
Why is this research important?
As ARLG’s scientific agenda indicates, the current landscape of AMR and the antibiotic pipeline have created a critical need for new therapies. Microbiome therapeutics, such as FMT, offer a novel approach to improve dysbiotic microbiome states associated with MDRO colonization. While mounting evidence indicates that FMT is effective at eradicating MDRO intestinal colonization, the precise mechanisms by which FMT reduces MDRO colonization and enhances long-term colonization resistance are not well elucidated. To realize the full potential of microbiome therapies, more work is needed to determine the ecological dynamics that lead to long-term MDRO decolonization.
Impact of the ARLG mentoring and funding on my career
As an early-stage physician scientist, the Early Faculty Seedling Award has provided me with protected time and funds for practical training in genomic and metagenomic analysis and advanced anaerobic culturing methods. I am extremely grateful for this opportunity especially given the limited funding opportunities for non-U.S. citizens. Being part of the ARLG network has allowed me to connect with AMR thought leaders and has given me the opportunity to expand my mentoring and collaborative relationships in the areas of AMR and microbial therapeutics.