Association between Type IV-A CRISPR/Cas system and plasmid-mediated transmission of carbapenemase genes in Klebsiella pneumoniae

The global rise of carbapenem-producing K. pneumoniae is largely attributed to plasmid-mediated transmission of carbapenemase genes. Type IV-A CRISPR/Cas system is mainly located on plasmids in K. pneumoniae and involved in plasmid competition. However, the role of Type IV-A system in the dissemination of carbapenemase genes in K. pneumoniae remains unclear. Here, we comprehensively investigated the relationship between Type IV-A system and plasmid-mediated transmission of carbapenemase genes based on 152 K. pneumoniae clinical strains and 46226 K. pneumoniae public genomes available in NCBI database. We found that the presence of Type IV-A system was positively associated with bla_NDM-1, bla_NDM-5, bla_OXA-48, and bla_VIM-1 but negatively related to bla_KPC-2, bla_KPC-3, bla_IMP and bla_OXA-181. Additionally, plasmids carrying Type IV-A system were predominantly the vehicles of bla_NDM-1 gene. Protospacer search revealed that Type IV-A system frequently matched conjugation transfer region of bla_KPC-2-related IncF plasmids, especially IncFIB(K)/IncFII(K), IncFII(pHN7A8)/IncR, and IncFIB(pQil)/IncFII(K) plasmids. The prevalence of self-targeting event further highlighted the interference mechanism of transcriptional repression proposed by Type IV system. Despite frequent targeting of IncF plasmids by Type IV-A system, different types of IncF plasmids displayed varying distribution between CRISPR-positive and -negative genomes, thereby suggesting a differentiated response of Type IV-A system to IncF plasmids. Our results underscore complex interactions between Type IV-A system and plasmid-mediated carbapenemase genes, revealing its significant role in shaping the transmission dynamics of carbapenemase-encoding plasmids.