Research Projects

Antimicrobial resistance in bacteria arises due to chromosomal or horizontally acquired genes. Among chromosomal genes, mutations in two-component signalling systems are frequently associated with antibiotic resistance in several bacterial pathogens. Given the role of two-component systems as regulators of global gene expression, understanding the impact of resistance-conferring mutations in these signalling pathways at the molecular, transcriptional and phenotypic levels is vital to design novel strategies for reversing antibiotic resistance. The PhoQ-PhoP two component system (PhoQP) confers resistance to colistin, carbapenems and trimethoprim in nosocomial enterobacterial pathogens such as Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae. Mutations in the PhoQ gene that are implicated in drug resistance are thought to lead to activation of PhoQP signalling, though there is little experimental data rigorously testing this prediction. Further, the molecular mechanism of PhoQ activation by resistance-conferring mutations as well as its effect on bacterial gene regulation and fitness are poorly understood. In this project, I propose to exploit my expertise in the area to develop tools to quantitate PhoQP activity across bacterial strains. Using these tools, I will ask, firstly, how PhoQP modulates intrinsic antibiotic resistance in E. coli. A panel of 100 E. coli strains isolated by my group from natural and clinical sources, as well as genome sequences of E. coli strains available in the public domain will be used to understand the basis for inter-strain variation in PhoQP activity, and its effect on multi-drug resistance and tolerance. Next, using experimental evolution and comparative transcriptomics approaches, I propose to explore how the PhoQP signalling pathway evolves under drug pressure, and whether divergence in sequence and function alters the importance of this pathway for antibiotic resistance in two Enterobacteria, i.e. E. coli and K. pneumoniae. Finally, by reconstructing PhoQ mutations from clinical isolates in a laboratory strain of E. coli I plan to investigate the molecular mechanisms of PhoQ activation and their impact on bacterial physiology. This work will bridge the knowledge gap required for rational design of novel inhibitors of PhoQ and result in the development of a facile model to screen novel resistance breakers.