Anti-plasmid defense in hypervirulent Klebsiella pneumoniae involves Type I-like and Type IV restriction modification systems

Hypervirulent Klebsiella pneumoniae (hvKp) and classical multidrug-resistant (MDR) strains belong to distinct lineages and hvKp are typically characterized by hypermucoid capsules that have been shown to limit horizontal gene transfer (HGT), including plasmid acquisition. However, the convergence of hypervirulence and MDR is increasingly common worldwide. When we profiled 127 antibiotic-susceptible hvKp strains, we found that most (86%) are highly permissive to plasmid transfer despite their capsules. In the few strains that showed low permissiveness, we identified two restriction modification (RM) systems: the Type IV restriction system McrBC that targets bacteriophage, and a unique Type I RM system. Both systems effectively inhibit plasmid uptake in recipient strains. Further analysis reveals that L-arginine and spermidine metabolism regulates the Type I-like RM system through S-adenosyl methionine. Strains lacking these RM systems were highly receptive to plasmids, and clinical isolates worldwide often lack these systems, correlating with their antibiotic resistance. Collectively, our study provides the first report on the susceptibility of hvKp strains to plasmid transfer and evidence of unusual RM systems restricting plasmid acquisition. It reveals an arms race between plasmids evolving to bypass RM systems and host strains developing new defenses. This dynamic and the rarity of these RM systems help explain the emergence of MDR hvKp strains in clinical settings driven by antibiotic pressure.