Genetic engineering of <i>Staphylococcus haemolyticus</i> : Overcoming Restriction-Modification Barriers and Targeting Virulence Genes

<i>Staphylococcus haemolyticus</i> is a multidrug-resistant opportunistic pathogen which causes disease in vulnerable patients. Previously, genetic modification of this pathogen was prevented due to the prevalence of strain-specific restriction modification systems, which use DNA methylation to identify and foreign DNA (including plasmids) when it enters the cells, and then destroy it using restriction enzymes. We analysed the methylomes of a selection of <i>S. haemolyticus</i> strains and used this data to tailor molecular tools to evade the RM systems. This enabled us to improve transformation efficiency and perform genome editing, including large-scale chromosomal modifications and targeted deletion of suspected virulence genes (a first for <i>S. haemolyticus</i> ). Beyond its immediate relevance to researchers studying this pathogen, the tools and approaches developed here have broader utility for genetic engineering of other coagulase-negative staphylococci and bacteria with similar RM barriers. Additionally, we found that two RM systems were enriched in clinical strains, suggesting they may have a function in virulence, in addition to their roles as bacterial phage defence systems.