Introduction
Microbes are remarkably adaptive—they evolve defenses, engage in constant arms races, and respond dynamically to environmental, chemical, and material stressors. Antimicrobial resistance (AMR) is a direct consequence of this adaptability. Our goal is to reverse-engineer these processes, using an evolution-informed approach to guide and direct microbial adaptation in beneficial ways. We combat AMR through three integrated research thrusts:
i) informing next-generation antimicrobial design,
ii) developing rapid detection methods, and
iii) mitigating transmission in natural and engineered water systems.
To do so, we study both pure cultures and complex microbial communities, combining traditional culture-based microbiology with advanced molecular and genomic techniques. Leveraging experimental microbial evolution and principles from evolutionary microbiology, we investigate how microbial fitness and adaptation can be harnessed to inform antimicrobial design and to improve the speed and accuracy of AMR detection, identification, and quantification in both clinical and environmental settings.
Read more about each of these research thrusts below.
Informing Nano-Enabled Antimicrobial Design
- Establish structure–property–activity relationships linking physicochemical parameters to antimicrobial efficacy.
- Elucidate mechanisms of action at the nano–bio interface.
- Quantify how nanoparticle properties influence bacterial stress responses and adaptive evolution.
- Identify design features that minimize resistance development while maintaining antimicrobial performance.
- Integrate mechanistic and evolutionary insights to develop predictive design rules for next-generation antimicrobial nanomaterials.
Developing Mechanism-Informed Diagnostic Tools for AMR Detection
- Link phenotypic resistance profiles with underlying genotypic signatures under defined antimicrobial stress conditions.
- Track evolutionary trajectories of bacterial adaptation to identify early and stable markers of resistance emergence.
- Discover and validate novel genetic targets for AMR detection.
- Differentiate transient adaptive responses vs. stable resistance mechanisms to improve diagnostic specificity.
- Integrate experimental evolution with sequencing to develop predictive markers of resistance development.
AMR Transmission in Engineered Water Systems
- Characterize microbial community composition and dynamics in engineered water systems under varying environmental conditions.
- Quantify how antibiotics, heavy metals, and other stressors shape community structure and select for resistant populations.
- Investigate horizontal gene transfer (HGT) pathways (e.g., plasmids, integrons) driving the spread of resistance genes.
- Examine co-selection mechanisms, where metal exposure promotes antimicrobial resistance.
- Track evolutionary adaptation of microbial communities under combined chemical and environmental pressures.