Heteroresistance & Antibiotic Susceptibility Testing

Overall theme of the projects revolve around studying cell-to-cell variation in growth rates and how they are related to antibiotic resistance of various kinds. We are developing various tools to identify genetic reasons for complex phenotypes at single cell level and do ultra-fast diagnostics of complex bacterial infections. These tools involve employing advanced microfabrication techniques, machine learning (cell detection and tracking), optics (fast imaging and tweezing single cells) and software development (for real-time analysis).

a. (Main-Project) Heteroresistance detection and mechanism identification

Heteroresistance has been recently identified as a major caveat to the antibiotic susceptibility testing(AST) using minimum inhibitory concentration(MIC) measurements[1]. The presence of a small resistant subpopulation of cells in the main population of susceptible cells can’t be detected on the fast ASTs[2] due to their low frequencies (1 in 103-107 ) and their exact mechanisms are relatively unstable and hard to study. In this project we develop microfluidic chips that can be used for large scale (~100,000) single cell phenotype and growth measurements and optical tweezing technique[3] to pick single cells for heteroresistance mechanism identification by single-cell sequencing.