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Project I
Microbial Stress Response and AMR. Pathogens undergo extensive physiological changes during the transition from their natural habitats to the human host. We investigate the underlying signal transduction pathways and the emergence of antimicrobial resistance (AMR) during this process. We have shown that the chromosomal resistance genes encoding the multidrug efflux pump MdtEF is up-regulated during anaerobic adaptation in E. coli to protect the bacterium from nitrosative stress. This and evidence from others suggests that AMR determinants such as efflux pumps have extensive physiological roles in bacteria, especially during the stress response. We aim to uncover the molecular mechanisms underlying the link of stress response and emergence of AMR in the common Gram-negative pathogens E. coli, S. Typhimurium, P. aeruginosa (In collaboration with Prof. Kunihiko Nishino, Osaka University).

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Project II
MDR in clinical Pseudomonas aeruginosa isolates and the interplay of resistance with pathogenesis, virulence, and quorum sensing. The Gram-negative bacterium Pseudomonas aeruginosa is a prevalent and pernicious pathogen that causes several notorious infectious diseases in humans. It is a leading cause of nosocomial infections and is the most common pathogen isolated from patients who have been hospitalized longer than 1 week. The pathogen is notorious for its intrinsic and acquired multidrug resistance owing to its poor membrane permeability, presence of multidrug efflux pumps, and adaptive resistance acquirement. We have acquired a broad collection of clinical P. aeruginosa strains isolated from the Queen Mary Hospital Hong Kong and identified several multidrug resistant isolates. We are systematically exploring their resistance mechanisms and interplay with virulence using a series of interdisciplinary tools and techniques, including multi-omics, CRISPR-Cas, LC/MS/MS, and imaging etcs.

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Xu et al, Cell Rep 2019

Project III
Development of native CRISPR-Cas-mediated genome editing in genetically recalcitrant, “non-model” strains of pathogens with clinical significance. Genetic analysis is crucial to the understanding, exploitation, and control of microorganisms. The advent of CRISPR-Cas-based genome-editing techniques, particularly those mediated by the single-effector (Cas9 and Cas12a) class 2 CRISPR-Cas systems, has revolutionized the genetics in model eukaryotic organisms. However, their applications in prokaryotes are rather limited. Remarkably, CRISPR-Cas systems belonging to different classes and types are continuously identified in prokaryotic genomes and serve as a deep reservoir for expansion of the CRISPR-based genetic toolkits. ~90% of the CRISPR-Cas systems identified so far belong to the class 1 system. We aim to harness these widespread native CRISPR-Cas systems for “built-in” genome editing for functional genomics in the genetically recalcitrant “non-model” species and strains.

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Xu et al, Environ. Microbiol


Project IV 
Metal homeostasis and heavy metal resistance. Transition metal ions are essential for bacterial physiology due to the key roles they play in many biological processes. However, high concentrations of metals are cytotoxic due to metal displacement of protein functional site, Fe-S clusters damage, oxidative stress, etc. As a consequence, bacteria have evolved sophisticated metal homeostasis systems to maintain physiological levels of metals in the cell. Efflux is a major means of metal detoxification and mechanism of metal resistance in bacteria. We have shown that Cu/Ag efflux system is up-regulated during O2 limitation and amino acid deprivation conditions, resulting in Cu and Ag resistance. We also investigated the cross-talk of metal homeostatic processes and showed that Zn stress led to increased cellular demands for Fe and decreased sensitivity to Cu. Currently, we are exploring metal homeostasis in other physiologically or clinically relevant stress conditions.

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