Abstract:[Background] Pulmonary flora is closely associated with host health and respiratory diseases. Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a common opportunistic pathogen in clinical practice, while its impact on pulmonary flora after infection remains unclear. [Objective] To explore the perturbation of carbapenem-resistant K.pneumoniae CRKP2 on the pulmonary flora of C57BL/6 mice. [Methods] The C57BL/6 mice were randomly assigned into 3 groups which were intranasally inoculated with CRKP2, carbapenem-sensitive K.pneumoniae KP2044, and sterile PBS solution, respectively. The structure of pulmonary flora was analyzed via 16S rRNA high-throughput sequencing. [Results] Compared with those in healthy mice, the alpha diversity and beta diversity of the pulmonary flora in the mice after KP2044 and CRKP2 strain infection significantly changed. Specifically, the infection with strain CRKP2 and KP2044 significantly increased the relative abundance of Proteobacteria and decreased that of Lactobacillus. Compared with KP2044, CRKP2 showed decreased biofilm formation and caused low mortality of infected mice, which indicated that CRKP2 infection led to weaker alteration of pulmonary flora than KP2044 infection.[Conclusion] Although K.pneumoniae is an opportunistic pathogen, high-dose carbapenem-resistant K.pneumoniae CRKP2 significantly affects the pulmonary flora of healthy mice. Although stain CRKP2 has multi-drug resistance, it leads to lower disturbance on the pulmonary flora than strain KP2044. Therefore, we hypothesize that the degree of disturbance of the pulmonary flora by K.pneumoniae infection may be related to strain virulence.