Genomic Epidemiology and Plasmid-Mediated Dissemination of Carbapenem-Resistant Klebsiella pneumoniae in a Tertiary Hospital
TL;DR
CRKP dissemination outside ICUs in this single tertiary hospital is described, driven by both ST11 clonal expansion and plasmid-mediated horizontal gene transfer and highlights the accumulation of resistance determinants and potential enhanced multidrug resistance transmission.
Abstract
Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a major threat to global public health. Although intensive care units (ICUs) are traditionally regarded as the main reservoirs for CRKP, CRKP has been widely reported across multiple hospital departments; however, department-specific molecular epidemiology and resistance gene dissemination remain incompletely characterized. Moreover, CRKP isolates co-harboring multiple carbapenemase genes, such as blaNDM-1 and blaOXA-232, are rare and insufficiently characterized. Methods Twenty K. pneumoniae isolates were collected from a teaching hospital in 2024. Antimicrobial susceptibility testing was performed to determine minimum inhibitory concentrations. Conjugation assays were conducted to evaluate the transferability of blaNDM-1 Whole-genome sequencing was performed using Illumina and Oxford Nanopore platforms, followed by hybrid assembly. Resistance genes, insertion sequences, and virulence factors were identified using ABRicate with ResFinder, ISFinder, and VFDB. MLST, plasmid replicon typing, cgMLST, and comparative genomic analyses were performed using BacWGSTdb. Results The isolates were mainly recovered from sputum and peritoneal drainage fluid, each accounting for 25% (5/20). Most isolates originated from the Surgery department (60%, 12/20), followed by the ICU (20%, 4/20). ST11 was the predominant clone (65%, 13/20), followed by ST15 (10%, 2/20), with ST638, ST1049, ST4573, ST23, and ST3332 detected at low frequencies. Thirteen isolates carried blaKPC-2, while two harbored blaNDM-1 Conjugation assays confirmed the transferability of blaNDM-1. Genomic analysis of the ST638 isolate KP1226 identified a 173,720-bp plasmid, pKP1226-1, carrying blaNDM-1, blaOXA-232, and multiple T4SS-related genes, suggesting a conjugative structure. Conclusion This study describes CRKP dissemination outside ICUs in this single tertiary hospital, driven by both ST11 clonal expansion and plasmid-mediated horizontal gene transfer. The rare blaNDM-1-positive plasmid co-harboring blaOXA-232 highlights the accumulation of resistance determinants and potential enhanced multidrug resistance transmission.