High transconjugation efficiency of fusion plasmid pNDM_KPC in carbapenem-resistant Citrobacter freundii and its formation driven by IS 26-mediated integration

Abstract

Carbapenem-resistant Enterobacteriales (CRE) are increasingly recognized as reemerging nosocomial pathogens due to the dissemination of dual carbapenemase production. This study investigates the coexistence of bla_KPC-2 and bla_NDM-1 in CRE isolates, harbored on plasmids either separately and integratively, and examines the underlying mechanisms of plasmid formation and resistance dissemination. Two Citrobacter freundii isolates co-producing Klebsiella pneumoniae carbapenemase (KPC) and New Delhi metallo-beta-lactamase (NDM) carbapenemases were analyzed. S1-PFGE, Southern blot, and mating conjugation experiments were conducted to determine gene location, transferability, and transconjugation efficiency. Whole-genome sequencing (WGS) was used to elucidate plasmid evolution mechanisms. Specific PCR followed by sequencing was performed to identify hotspot integration sites. Experiments of checkerboard microdilution and time-kill were completed to test the treatment option based on aztreonam. Three plasmids were identified in C. freundii, pNDM, pKPC, and a fusion plasmid (pNDM_KPC) co-harboring bla_KPC-2 and bla_NDM-1. All plasmids exhibited transconjugation capability, with significant differences in transfer efficiency (P < 0.05). pKPC demonstrated the highest efficiency (ranging from 10⁻¹ to 10⁻²), followed by pNDM_KPC (10⁻⁴ to 10⁻⁶) and then pNDM (around 10⁻⁸). IS26, located downstream of the intI site, was identified as a critical hotspot mediating the disintegration and integration of pNDM_KPC. Synergy effect and bactericidal activity were observed on aztreonam plus ceftazidime/avibactam or meropenem/vaborbactam or imipenem/relebactam. The presence of CRE isolates harboring fusion plasmid pNDM_KPC would pose a significant threat in nosocomial infections and should arise wide attention. IS26 downstream of IntI would be the hotspot driving the integration state of pNDM_KPC and contributing to complex resistance mechanisms.IMPORTANCEThe global rise of carbapenem-resistant Enterobacterales (CRE) poses a critical threat to public health. Our study identifies Citrobacter freundii strains co-harboring three distinct carbapenemase-encoding plasmids: pNDM, pKPC, and a novel fusion plasmid (pNDM_KPC). We reveal significant differences in conjugation efficiency among these plasmids, with the fusion plasmid demonstrating a moderate yet concerning ability to spread dual carbapenemase genes. This finding highlights the fusion plasmid as a potential vector for the co-dissemination of bla_NDM-1 and bla_KPC-2, emphasizing the need for enhanced surveillance. Furthermore, we identify the IS26 element downstream of the intI site as a potential recombination hotspot driving plasmid fusion. These insights deepen our understanding of carbapenemase gene transmission and call for global attention to the fusion plasmid-mediated resistance spread.

Keywords: Carbapenem-resistant; Citrobacter freundii; IS26; IntI; KPC-2; NDM-1; integration; pNDM_KPC; transconjugation efficiency.