Molecular and metabolic features of colistin-resistant ST11 carbapenem-resistant Klebsiella pneumoniae

Introduction. The emergence of colistin-resistant carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a critical threat to public health, a challenge that was exacerbated by the coronavirus disease 2019 (COVID-19) pandemic. Gap statement. The specific metabolic adaptations that underlie colistin resistance in high-risk sequence type 11 (ST11) CRKP clinical strains, particularly in direct comparison with their susceptible counterparts, remain poorly characterized. Aim. To explore metabolic features associated with colistin resistance in clinical CRKP isolates. Methodology. Twelve CRKP strains, encompassing both colistin-resistant and colistin-susceptible isolates, were analysed for antimicrobial resistance profiles, virulence-associated genes, sequence types and biofilm formation capacity. Comparative untargeted metabolomics was performed to map metabolic shifts between the resistant and susceptible groups. Results. All isolates belonged to the high-risk clone ST11, harboured the KPC-2 carbapenemase and carried multiple virulence genes, with K2 being the dominant serotype. All isolates formed biofilms, with resistant isolates showing enhanced capacity. Colistin resistance was chromosomally mediated by pmrB and mgrB mutations, with no plasmid-encoded mcr genes detected. Untargeted metabolomics identified 126 significantly differentially expressed metabolites (DEMs) between resistant and susceptible isolates. These DEMs were significantly enriched in lipids and lipid-like molecules. Colistin-resistant strains exhibited increased glycerophospholipids, sphingolipids and fatty acids, coupled with decreased metabolites from central carbon and amino acid pathways. Conclusion. In this exploratory study, colistin resistance in these ST11 CRKP strains was associated with chromosomal alterations in pmrB and mgrB and with marked shifts in membrane-associated lipid metabolites. While these metabolic changes suggested membrane remodelling, they remain associative and require functional validation. Beyond resistance, the co-carriage of these traits with robust virulence gene expression highlights a critical clinical challenge, supporting the need for further research into combination therapies targeting these adaptive lipid pathways.