Objective To analyze the drug resistance genes, virulence genes and homologies of carbapenem-resistant Klebsiella pneumoniae (CRKP) colonized and infected patients in surgical intensive care unit based on whole genome sequencing. Methods Whole genome sequencing analysis was performed on CRKP infected strains isolated from the Department of General Surgery Intensive Care Unit and the Department of Liver Surgery Intensive Care Unit of Zhongshan Hospital, Fudan University in March 2021 and CRKP colonized strains isolated from the above departments between January and March 2021. The drug resistance genes, virulence genes and homologies of the strains were analyzed. ResultsA total of 16 CRKP strains were included, including 10 colonized strains and 6 infected strains. Except for the β-lactamase drug resistance gene CTX (16.7% vs. 100.0%, P<0.05), there was no significant difference in the detection rate of other drug resistance genes between CRKP infected strains and colonized strains (P>0.05). The cluster analysis of drug resistance genes of some strains was relatively close. Whole genome sequencing analysis showed that CRKP strains carried a variety of virulence genes, and the detection rates of entB, irp2, iroN, and rmpA genes were 100.0%, 87.5%, 37.5%, and 62.5%, respectively. There was no significant difference in the detection rate of virulence genes between CRKP infected strains and colonized strains (P>0.05). Homology analysis showed that some strains had close homologous relationships, and there was the possibility of cross transmission. Conclusions Some of CRKP infection strains and colonization strains in surgical intensive care unit patients have the risk of cross transmission. In the future, we should strengthen the prevention and control of nosocomial infection to reduce the incidence of infection.