Phenotypic and genotypic characterization of carbapenem resistant Klebsiella pneumoniae clinical isolates from Damietta, Egypt

The notable emergence of carbapenemase production is a critical problem threatening human health worldwide. Hence, this study aimed to monitor the prevalence of carbapenemase-producing Klebsiella pneumoniae in Damietta, Egypt. Additionally, the study investigated the association of carbapenemase producers and certain virulence traits, including biofilm formation and colibactin genotoxin. This study included 86 clinical isolates of Klebsiella pneumoniae collected from various clinical analytical laboratories and private clinics in Damietta, Egypt, between June 2023 and May 2024. Carbapenemase production was determined by various phenotypic assays (CarbaNP/mCIM/eCIM). Genotypic detection of carbapenemase-encoding genes (blaNDM, blaKPC, blaVIM, blaIMP, and blaOXA-48) and certain virulence genes (clbA, clbB, mrkD, and fimH) was performed using multiplex PCR. Chi-square and Fisher’s exact tests were used for statistical analysis. In the current study, 44.2% (38/86) of Klebsiella pneumoniae were identified as carbapenemase producers. All carbapenemase-producing Klebsiella pneumoniae (38/38, 100%) were positive by mCIM, while 92.1% (35/38) were positive by CarbaNP, and 65.8% (25/38) were positive by eCIM. The blaNDM, blaOXA-48, and blaKPC genes were detected in 71%, 36.8%, and 5.2% of the tested isolates, respectively. No blaIMP or blaVIM were detected. Different biofilm formation capabilities were observed among carbapenemase producers: moderate (42.1%), strong (36.8%), weak (13.1%), and non-biofilm (7.8%). The capacity for biofilm formation differed significantly between carbapenemase-producing and non-producing Klebsiella pneumoniae. The mrkD gene was significantly associated with carbapenemase-producing Klebsiella pneumoniae in contrast to fimH and colibactin-encoding genes. This study provides valuable insights into the continuous emergence of carbapenemase-producing Klebsiella pneumoniae, which poses a serious clinical and public health concern. A significant association was observed between carbapenemase producers and certain virulence factors. This emphasizes the urgent need for ongoing monitoring, effective stewardship programs, intensive surveillance, and strict infection control policies to control the spread of such highly resistant strains.