Emergence of colistin-resistant ST290 Klebsiella pneumoniae lineages co-harboring blaKPC−2 and blaNDM−1 on novel IncR-bearing plasmids

The coexistence of bla KPC−2 and bla NDM−1 in Klebsiella pneumoniae , frequently mediated by mobile genetic elements, represents a critical public health threat. To investigate this threat, we characterized two clinical isolates harboring both genes, analyzing their antimicrobial resistance profiles, virulence potential, and genetic relatedness. In this study, we isolated two colistin-resistant K. pneumoniae strains that co-harbored bla KPC−2 and bla NDM−1 from different patients at separate time points. The isolates underwent antimicrobial susceptibility testing, serum killing, and biofilm formation tests. Their genetic characteristics were elucidated through comprehensive whole-genome sequencing and subsequent bioinformatic analysis. Both K. pneumoniae isolates, identified as sequence type ST290 with capsular serotype KL21. In addition to β-lactams, they were resistant to tetracyclines, quinolones, aminoglycosides. They also demonstrated intermediate serum resistance and strong biofilm formation. Genomic analysis identified two IncR‑bearing plasmids co‑carrying bla KPC‑2 and bla NDM‑1 , one of which was a multireplicon hybrid plasmid containing IncR along with additional replicons, whereas the other harbored only the IncR replicon. Colistin resistance was associated with pmrB mutations (V287M and E293K), as well as additional mgrB missense mutation. Both strains harbored diverse other antimicrobial resistance genes and virulence factors. Phylogenetic analysis confirmed their close relatedness and distinctness from other ST290 lineages. This study documents the emergence of ST290 K. pneumoniae strains carrying both bla KPC−2 and bla NDM−1 on a single IncR plasmid, accompanied by chromosomally encoded colistin resistance-associated mutations. Our findings highlight the diverse genetic backgrounds capable of fostering such pan-drug-resistant pathogens and underscore their potential for further resistance evolution.