Decoding bacterial immunity to enhance antimicrobial action

The rise of antibiotic resistance demands new strategies to combat bacterial infections. With renewed interest in phage-bacteria interactions, over 150 novel phage defence systems were recently identified, most of which protect bacteria from propagating phages via host-regulated death or growth arrest in an abortive infection process (Abi). Abi systems, encoded primarily on mobile genetic elements, exhibit diverse mechanisms and are pervasive in bacteria. However, despite significant mechanistic progress, critical aspects of their regulation in native bacterial hosts remain unclear, such as the impact of genetic background on their maintenance or how autoimmunity (erroneous activation without phages) is avoided. This project aims to systematically uncover genetic and environmental regulators of Abi systems to harness them for antimicrobial applications. We previously demonstrated that antifolate antibiotics trigger autoimmunity of the Abi system CBASS by disrupting allosteric regulation of a system component, causing bacterial cell death. Moreover, we found that autoimmunity is influenced by genetic background and strongly dependent on antifolate resistance genes. Building on these findings, we will experimentally map genetic drivers of Abi systems in the Escherichia coli pangenome using high-throughput genetics across native hosts. To understand the contribution of the cell environment, we will use high-throughput screening to profile autoimmunity and transcriptional regulation of Abi systems across environments. The applicability of these findings will be piloted by combining conditions that trigger autoimmunity or overexpress Abi systems with phages, natural system triggers. This project will provide new insights into Abi regulation and function paving the way towards approaches to tackle bacterial infections.