The Role of Restriction-Modification Systems in the Horizontal Transfer of Carbapenem Resistance Genes in Klebsiella pneumoniae

The rising detection rates of carbapenem-resistant Klebsiella pneumoniae (CRKP) pose significant challenges to clinical anti-infection treatments. The horizontal transfer of antibiotic resistance genes (ARGs) via plasmids is one of the primary mechanisms of acquired bacterial resistance. However, data analysis regarding the genetic mobility of these resistance genes remains relatively scarce. In this study, we analyzed the genomic sequences of 428 K. pneumoniae strains from the GenBank database over the past three years, focusing on Restriction-Modification (RM) system typing, plasmid typing, and resistance gene assessment. Our findings revealed a consistent distribution of RM systems among the 428 K. pneumoniae strains across China and other countries, with Type II RM systems being predominant (98.7%). These systems recognize the methylation and restriction site CCWGG (W = A or T). In other clinically common carbapenem-resistant bacteria, such as Acinetobacter baumannii and Pseudomonas aeruginosa , the proportion of Type II RM systems is only 2%. However, in K. pneumoniae and Escherichia coli strains, the carriage rate of M.EcoRII methyltransferase is 100%. From the perspective of bacterial RM defense and the horizontal transfer of mobile genetic elements (MGEs), the methylation and restriction enzyme recognition sites in K. pneumoniae are characteristic of Type II RM systems, sharing the same recognition sequence CCWGG. This may suggests that the corresponding methylated MGEs in K. pneumoniae not only spread horizontally within the species but can also engage in gene exchange with carbapenem-resistant Escherichia coli (CREC) in clinical settings. There is no difference in the distribution types of RM systems between carbapenem-resistant and sensitive K. pneumoniae . However, further analysis of carbapenem-resistant plasmids shows that the prevalence of RM systems is 33.15%. Plasmids play a central role in the epidemiology of antibiotic resistance, and the increased prevalence of RM systems in resistant gene plasmids provides more opportunities for the horizontal transfer of MGEs. In K. pneumoniae , the bla _KPC−2 gene is primarily carried by IncF plasmids and is associated with multiple sequence types. However, compared to IncF, IncN, and IncH, IncA/C plasmids possess a more diverse repertoire of carbapenem ARGs. The findings of this study emphasize the key role of RM systems and plasmids in the spread of CRKP. They provide epigenetic insights into the horizontal gene transfer (HGT) of K. pneumoniae , thereby offering potential strategies for controlling the spread of ARGs.