Work

Comprehensive genomic analysis of carbapenem-resistant Citrobacter freundii and characterization of a co-carrying blaKPC−2 and blaNDM−1 isolate in Zhejiang Province， China

Year: 2026

Type: article

Abstract: Despite the clinical importance of carbapenem-resistant Citrobacter freundii (CRCF), its resistance genomics is poorly understood. This study systematically characterizes the genomic features and evolution of clinical CRCF isolates, with detailed analysis of a bla KPC−2 and bla NDM−1 co-harboring strain. Clinical CRCF isolates were collected from multiple tertiary hospitals in China, and their basic clinical data were obtained. Phenotypic characterization was performed through antimicrobial susceptibility testing and plasmid conjugation transfer assays. Bioinformatic analysis was conducted based on whole-genome sequencing data. Clinical data from 37 CRCF isolates in Zhejiang Province, China, revealed that infections primarily occurred among elderly patients (≥ 70 years, 65%) and in high-risk departments such as the ICU. The majority of isolates were recovered from urine samples (67%). Antimicrobial susceptibility testing indicated high resistance to carbapenems and most β-lactams, whereas susceptibility to amikacin remained moderate (21.6%) and no resistance against tigecycline and colistin was detected. Resistance mechanism analysis revealed that 97.3% of isolates carried bla NDM , and bla CMY was present in all strains. IncX3 (59.5%), IncFIB (54.1%), and IncFII (51.4%) were the predominant plasmid types. MLST identified 17 sequence types, with ST22 and ST116 being most prevalent. Both STs carried bla NDM−1 , clustered phylogenetically, and were persistently isolated from 2019 to 2024, indicating long-term clonal circulation. Complete genome analysis of a rare bla KPC−2 and bla NDM−1 co-harboring strain (T1001) confirmed that both genes were located on conjugative plasmids, with IS 26 and IS Kpn19 facilitating their integration. The dissemination of CRCF in Zhejiang Province, China, is driven by both clonal expansion of successful lineages (ST22, ST116) and horizontal transfer of resistance plasmids. These clones, persisting from 2019 to 2024, carry bla NDM−1 and show high carriage rates of IncX3 and IncFIB plasmids, suggesting a possible association between these replicon types and the dominant clones. Although amikacin, tigecycline, and colistin remain effective in vitro, the complex recombination mechanisms of resistance genes—particularly IS 26 /IS Kpn19 -mediated modular dissemination—pose a serious nosocomial threat. Enhanced infection control measures are urgently needed to curb the spread of these multidrug-resistant bacteria and their resistance plasmids.

Source: BMC Microbiology

DOI: 10.1186/s12866-026-05080-x