Understanding mobile element mediated spread of antibiotic resistance within gut microbial communities

• Applicant: Supriya Khedkar, Ph.D.
• Subject Area: Bioinformatics and Theoretical Biology ; Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology ; Microbial Ecology and Applied Microbiology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 555128266

The spread of antibiotic resistance in pathogens is a leading cause of untreatable infections and millions of deaths worldwide. Antibiotic resistance genes can be found in abundance in the gut microbial communities i.e., gut microbiome. These resistance genes can spread to pathogens which transiently co-exist in the gut. A leading mechanism for rapid dissemination of molecular functions such as antibiotic resistance amongst pathogens is Horizontal Gene Transfer (HGT -intercellular transfer of DNA) mediated by Mobile Genetic Elements (MGEs). Studying MGEs and their HGT potential in the human gut microbiome is important for enabling the design of intervention strategies that can prevent MGE-mediated spread of high-risk antibiotic resistance. MGE is an umbrella term that describes diverse MGE types such as transposable elements, phages, integrons and plasmids. These co-exist within a microbial genome and their interactions with the host bacterium and with each other influence their spread. A recent methodological advancement in the field of mobile DNA research has enabled annotation, comparative analysis and exploration of interactions between distinct MGE types at a go. This project aims to leverage this advancement to investigate MGE-mediated spread of antibiotic resistance amongst pathogens in the gut microbiome. It aims to achieve this by gaining insights into the gene flux and evolutionary arms race that orchestrates MGE-mediated HGT by (1) determining antibiotic resistance carrying capacity of mediators of horizontal gene transfer i.e, the MGEs; (2) identification of the known barriers of HGT and (3) studying the outcome of the interplay between the mediators and barriers. Thus, this proposal will answer both basic and translational questions at the interface of mobile DNA and microbiome research to address the healthcare issue of spread of antibiotic resistance amongst pathogens.

• DFG Programme: Research Grants