Genomic characterization of an extensively drug-resistant Klebsiella pneumoniae co-harboring mcr-3.11, blaNDM-5 and blaCTX-M-27 isolated from pelvic effusion in a colon cancer patient

OBJECTIVE: This study aimed to characterize the genomic features and possible transmission mechanisms of an extensively drug-resistant (XDR) Klebsiella pneumoniae (KP2024). The isolate was recovered from pelvic effusion of a postoperative colon cancer patient in Hebei, China, with a focus on the rare mcr-3.11 gene as well as blaNDM-5 and blaCTX-M-27. RESULTS: Genetic analysis of key resistance determinants identified three epidemiologically important plasmids: an IncFIB plasmid carrying blaCTX-M-27 (pKP2024-1), an IncFII plasmid carrying mcr-3.11 (pKP2024-3), and an IncX3 plasmid carrying blaNDM-5 (pKP2024-4). Comparative genomic analysis indicated that blaCTX-M-27 was located within a highly conserved transposition unit mediated by ISEcp1. Additionally, mcr-3.11 and diacylglycerol kinase (dgkA) formed a conserved mobile genetic element, while blaNDM-5 was located within a typical Tn3-IS3000-IS5-blaNDM-5-bleMBL-trpF-IS26-ISKox3 structure on the IncX3 plasmid. All these plasmids harbored complete conjugative transfer systems or mobile genetic elements, indicating a high potential for horizontal gene transfer. CONCLUSION: This study reports an XDR K. pneumoniae co-harboring mcr-3.11, blaNDM-5, and blaCTX-M-27, isolated from the postoperative pelvic effusion of a colon cancer patient. Multiple key resistance genes are distributed on different types of plasmids, conferring resistance to "last-line" clinical agents such as carbapenems and colistin. The co-existence of multiple plasmids and the co-evolution of resistance genes may further increase the risk of resistance transmission, highlighting the importance of enhancing clinical surveillance for such highly resistant clones.