CRISPR-Cas3 and type I restriction-modification team up against blaKPC-IncF plasmid transfer in Klebsiella pneumoniae
Yang Yang, Peiyao Zhou, Dongxing Tian, Weiwen Wang, Ying Zhou, Xiaofei Jiang
Abstract
Abstract Objective We explored whether the Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification (R-M) systems are compatible and act together to resist plasmid attacks. Methods 932 global whole-genome sequences from GenBank, and 459 K. pneumoniae isolates from six provinces of China, were collected to investigate the co-distribution of CRISPR-Cas, R-M systems, and bla KPC plasmid. Conjugation and transformation assays were applied to explore the anti-plasmid function of CRISPR and R-M systems. Results We found a significant inverse correlation between the presence of CRISPR and R-M systems and bla KPC plasmids in K. pneumoniae , especially when both systems cohabited in one host. The multiple matched recognition sequences of both systems in bla KPC -IncF plasmids (97%) revealed that they were good targets for both systems. Furthermore, the results of conjugation assay demonstrated that CRISPR-Cas and R-M systems in K. pneumoniae could effectively hinder bla KPC plasmid invasion. Notably, CRISPR-Cas and R-M worked together to confer a 4-log reduction in the acquisition of bla KPC plasmid in conjugative events, exhibiting robust synergistic anti-plasmid immunity. Conclusions Our results indicate the synergistic role of CRISPR and R-M in regulating horizontal gene transfer in K. pneumoniae and rationalize the development of antimicrobial strategies that capitalize on the immunocompromised status of KPC-KP.