Investigation of the resistance and virulence of carbapenem-resistant Klebsiella pneumoniae based on whole-genome sequencing

Objective To investigate the clinical characteristics and molecular epidemiological features of resistance and virulence in carbapenem-resistant Klebsiella pneumoniae (CRKP) within this region, thereby providing a scientific basis for the prevention, treatment, and epidemiological research of CRKP.Methods A total of 60 non-repetitive CRKP clinical isolates were retrospectively analyzed from November 2023 to September 2024 at Puyang Oilfield General Hospita. Antimicrobial susceptibility testing was performed using VITEK 2 Compact analyzer, Kirby-Bauer disk diffusion method and broth microdilution method. The mucoid phenotype was identified via the string test, and carbapenemase production was detected using the carbapenemase inhibitor enhancement test. Whole-genome sequencing and bioinformatics analysis were performed to determine the molecular characteristics, such as multilocus sequence typing (MLST), capsular serotypes, resistance genes, virulence factors and plasmid replicon types, as well as to elucidate the phylogenetic relationships among isolates.Results The CRKP isolates were primarily recovered from elderly male inpatients, with sputum specimens constituting the majority of samples (71.67%, 43/60), predominantly from the respiratory medicine department (30.00%, 18/60). All isolates exhibited high resistance to multiple common antibiotics, with sensitivity retained only to ceftazidime/avibactam, polymyxin B and tigecycline (>60.00%).Two isolates tested positive in the string test, and carbapenemase inhibitor enhancement test revealed that 95.00%(57/60) isolates produced class A serine carbapenemase. Allisolates harbored resistance genes to fluoroquinolones, fosfomycins,β-lactam antibiotics and aminoglycosides,virulence genes related to enterobactin, ECP fimbriae, and outer membrane proteins,and IncF-family plasmids.The predominant carbapenemase gene and capsule serotype were blaKPC-2 (95.00%,57/60) and KL19 (43.33%, 26/60), respectively. MLST identified ST11 (51.67%, 31/60) as the predominant clonal group, with the ST11-KL62 subclone (38.71%, 12/31) being the most frequent.Conclusion CRKP in this hospital exhibits high resistance to multiple common antibiotics, with carbapenems resistance primarily mediated by blaKPC-2. Multiple drug resistance genes and virulence genes coexist in all isolates and showe polyclonal dissemination. ST11 is the dominant clonal group and ST11-KL62 is the dominant subclonal type.