Emergence and dissemination of an IncC plasmid co-harbouring blaKPC-2, blaNDM-1 and blaVIM-24 carbapenemase genes across multiple Gram-negative species in Colombia
Abstract
Abstract Objectives Carbapenem-resistant Gram-negative bacilli (CRGNB) pose a public health threat, increasingly driven by plasmid-mediated dissemination of carbapenemase genes. As part of a Colombian genomic monitoring programme, we aimed to characterize CRGNB co-harbouring multiple carbapenemase genes and determine their genetic context. Methods We screened 832 carbapenem-resistant isolates collected during 2011–2023 using carbapenemase-targeted qPCR. Ten isolates co-harbouring blaKPC, blaNDM and blaVIM underwent antimicrobial susceptibility testing, long-read whole-genome sequencing, comparative genomics and conjugation assays. Results Nine Enterobacterales isolates and one Aeromonas caviae isolate from unrelated patients in geographically distant Colombian hospitals carried closely related IncC plasmids ranging from 160 to 317 kb. These plasmids co-harboured blaKPC-2, blaNDM-1 and blaVIM-24 within three conserved multidrug resistance regions, including a Tn21-associated region carrying blaNDM-1 and blaVIM-24 and a Tn6454-associated blaKPC-2 platform, alongside class 1 integrons, insertion sequences and multiple additional antimicrobial resistance determinants. The ten isolates were resistant to multiple β-lactam/β-lactamase inhibitor combinations, and five were cefiderocol resistant. Aztreonam/avibactam remained active against all isolates; colistin resistance was confined to intrinsically resistant Providencia rettgeri and Serratia sarumanii. Conjugation assays demonstrated plasmid transfer to Escherichia coli J53, and sequencing confirmed transfer of a 179 kb IncC plasmid with functional conjugation machinery. Comparative genomic analysis showed a highly conserved IncC plasmid backbone across multiple species, supporting broad dissemination of this resistance platform. Conclusions This first report of a single plasmid co-harbouring three carbapenemase genes. This finding highlights a concerning mechanism for interspecies dissemination of MDR Gram-negative pathogens and underscores the importance of long-read genomic surveillance focused on high-risk plasmids.