IMIB - Institute for Molecular Infection Biology

Applications and outcomes of genome targeting by CRISPR-Cas systems in bacteria

CRISPR-Cas systems are made of RNA-guided nucleases and they are used for programmable DNA and RNA targeting. These systems can be engineered to efficiently target and kill bacteria, which have poor non-homologous recombination mechanisms. The aim of my thesis is to characterize and engineer CRISPR-Cas systems as antimicrobials, with a focus on the gram-negative bacterium Klebsiella pneumoniae. This pathogen belongs to the so-called “ESKAPE” bacteria, which are the main responsible for nosocomial infections and easily develop antibiotic resistance. These characteristics make them a real threat for human health, so it is necessary to find alternative treatments to antibiotics. For this reason, I am working as part of a collaborative project to kill K. pneumoniae using CRISPR-based antimicrobials delivered through phage-based vehicles. I am focusing on improving the antimicrobial activity by characterizing different nucleases. Moreover, I am interested in escape mechanisms of gram-negative bacteria from CRISPR-based targeting to develop counteractive strategies to boost the killing. Specifically, I am characterizing the escape mechanisms from type V Cas12a nucleases and type VI Cas13a nucleases. With my project, I hope to contribute to the development of an effective CRISPR-based method to fight multi-drug resistant infections.