Emergence and dissemination of an IncC plasmid co-harbouring bla KPC-2, bla NDM-1 and bla VIM-24 carbapenemase genes across multiple Gram-negative species in Colombia.

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 bla KPC, bla NDM and bla VIM 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 bla KPC-2, bla NDM-1 and bla VIM-24 within three conserved multidrug resistance regions, including a Tn21-associated region carrying bla NDM-1 and bla VIM-24 and a Tn6454-associated bla KPC-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.