Clinical characteristics and molecular epidemiology of KPC-NDM co-producing carbapenem-resistant Klebsiella pneumoniae in China: a multicentre retrospective case-control study

Background KPC and NDM co-producing carbapenem-resistant Klebsiella pneumoniae (KN-CRKP) is an escalating global health threat with limited treatment options. Methods Here, we conducted a multicentre retrospective case-control study on KN-CRKP in China (2020–2025), collecting 3012 non-duplicated CRKP isolates, of which 71 (2.4%) were KN-CRKP. For clinical analysis, 39 patients with KN-CRKP infections were identified from 71 isolates and matched in a 1:2 ratio with 78 patients infected by KPC-2-producing CRKP. For global analysis, we retrieved 100,141 genomes from GenBank, of which 662 non-redundant KN-CRKP sequences were combined with our 71 KN-CRKP isolates. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), plasmid transfer and stability, fitness cost, transcriptomics and Bayesian phylogeography were used to investigate evolution mechanisms and molecular epidemiology of KN-CRKP strains. Findings Among the infected patients, hospital-acquired or ventilator-associated pneumonia was the most common (41.0%, 16/39). Patients with KN-CRKP infections had a non-significantly higher 28-day mortality (38.5%, 15/39) than the KPC-CRKP control group (24.4%, 19/78; p = 0.133), but a significantly higher in-hospital mortality (46.2%, 18/39 vs. 25.6%, 20/78; p = 0.036). Independent risk factors included diabetes, a history of CRO (carbapenem-resistant gram-negative organism) infection treated with ceftazidime-avibactam (CZA) treatment, and recent use of β-lactam/β-lactamase inhibitor combinations. All KN-CRKP isolates were resistant to carbapenems and CZA, but exhibited highly susceptible to colistin (98.6%), cefiderocol (94.4%), and aztreonam-avibactam (100%). The predominant KN-CRKP clones were ST11 (73.2%) and ST307 (15.5%). Global surveillance of 733 global KN-CRKP identified ST11 as a pandemic lineage diverging into China/Brazil subclusters, with emerging clones ST147/ST307 showing post-pandemic increases. Plasmid profiling revealed bla NDM mainly on IncX3/IncN plasmids and bla KPC on IncR/IncFII plasmids, with novel hybrid plasmids carrying both carbapenemases identified. bla NDM -carrying plasmids had higher transferability/stability than bla KPC -carrying ones. In vitro experiments confirmed bla NDM transfer from Citrobacter freundii to bla KPC -carrying K. pneumoniae , forming KN-CRKP. Interpretation The high mortality and global prevalence of KN-CRKP emphasise the need for enhanced surveillance and infection control globally. Funding National Natural Science Foundation of China (82472323 and 82172306), Zhejiang Province Natural Science Foundation of China (LQN26H200003, LR25H200001, LQN25H200002, MS25H190009), the "Pioneer" and "Leading Goose" R&D Program of Zhejiang Province (2025C02187), the Zhejiang Provincial Medical and Health Technology Project (2025HY0224) and Zhejiang Provincial Disease Prevention and Control Science and Technology Program (2025JK063). We appreciate the statistical support provided by Hui Liu (Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China).