A Transposon-based Gene Drive to Combat Antimicrobial Resistance

About This Grant

This proposal outlines a research and career development plan to develop a transposon-based gene drive to combat antimicrobial resistance (AMR). AMR is an existential threat to modern medicine and global public health, causing over 2.8 million infections and 35,000 deaths annually in the U.S. alone. E. coli ST131 exemplifies this threat as a globally disseminated pathogen driving the epidemic spread of AMR. Limited development of new antibiotics coupled with rapidly emerging resistance creates an urgent need for novel approaches to combat AMR in this pathogen. Dr. Basta will address this challenge by harnessing the prolific spread of plasmids and transposons, the primary mobile genetic elements mediating AMR, to develop a transposon-based gene drive (TnDrive) for rapid elimination of resistance genes from bacterial populations, focusing on E. coli ST131 as a model pathogen. The central hypothesis is that the natural gene drive properties of plasmids and transposons creates an ideal solution to AMR that can be deployed in both medical and ecological settings. In preliminary work, Dr. Basta engineered a TnDrive proof-of-concept by combining a self-transmissible plasmid with a programmable transposon targeting an aminoglycoside resistance gene. Starting at a frequency of 1:20,000, TnDrive spread to virtually all cells within one day and eliminated the targeted AMR gene from over 99% of the population. To optimize TnDrive, Dr. Basta will: (1) enhance transmission by identifying and circumventing bacterial defenses and metabolic barriers to plasmid spread and evaluating alternative plasmid chassis for improved environmental and in vivo efficacy; and (2) improve AMR elimination by multiplexing highly efficient targeting guides, establishing guide design rules for minimizing off-target effects, protecting against native transposon- mediated inactivation, and modulating host factors controlling transposition. The long-term goal is to develop TnDrive into a clinically and ecologically viable solution to combat AMR while advancing our understanding of transposon biology, plasmid transfer dynamics, and genome engineering. The candidate, David Basta, MD, PhD, is completing clinical pathology residency at Brigham and Women’s Hospital (BWH) and working with Dr. Matthew Waldor, a leading pathogen geneticist who has trained over 30 independent investigators. The project builds upon novel high-throughput functional genetic tools developed by Dr. Basta in the Waldor lab during his pathology residency. This work will be conducted at BWH, which provides exceptional training resources and access to a large collection of genetically characterized clinical isolates through its pathogen genomics program. Dr. Basta is supported by an advisory committee with expertise in transposon biology, AMR, bacterial genetics and genomics, gene drives, and animal models of infection. This career development award will enable Dr. Basta’s transition to independence as a physician-scientist integrating expertise in clinical pathology, molecular microbiology, genome engineering, and synthetic biology.