Transferable IncX3-blaNDM-15 in an uncommon ST580 Klebsiella pneumoniae recovered during paediatric intensive-care surveillance

Abstract

Objective: Carbapenem-resistant Klebsiella pneumoniae harboring blaNDM poses a serious threat to public health; however, blaNDM-15 remains poorly characterized outside the dominant epidemic lineages. Methods: We characterized K. pneumoniae strain ETFK6090, isolated from a perianal surveillance swab of an 11-month-old immunocompromised child in a paediatric intensive care unit. Investigations included antimicrobial susceptibility testing, broth conjugation, S1 nuclease PFGE with Southern blotting, complete genome sequencing, and comparative genomic analysis against 465 curated blaNDM-positive K. pneumoniae genomes from 37 countries. Results: ETFK6090 belonged to ST580 and exhibited resistance to carbapenems, ceftazidime-avibactam, broad-spectrum cephalosporins, fluoroquinolones, gentamicin, chloramphenicol and trimethoprim-sulfamethoxazole; amikacin and fosfomycin retained low MICs. The complete genome comprised one chromosome and five plasmids, blaNDM-15 was localized on a 46,161-bp IncX3 plasmid, confirmed by Southern blotting. Conjugation into Escherichia coli EC600 transferred carbapenem and cephalosporin resistance, confirming in vitro mobility. The blaNDM-15 genetic environment retained a conserved blaNDM module, with IS-mediated rearrangements at the downstream boundary. In the global comparison, blaNDM-1 and blaNDM-5 predominated, the ST580-blaNDM-15 combination was exceedingly rare, and ETFK6090 constituted a distinct branch apart from major epidemic lineages. Conclusions: A transferable IncX3-blaNDM-15 plasmid can emerge in an uncommon ST580 background, underscoring the necessity to extend genomic surveillance of carbapenem-resistant K. pneumoniae beyond dominant epidemic clones, particularly in high-risk paediatric and intensive-care settings.