Global genomic epidemiology of carbapenemase-producing Klebsiella pneumoniae, 1996-2023.

OBJECTIVES

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as a significant global public healthchallenge.

METHODS

A total of 63,099 KP genomes was available in the NCBI Genome database, and assembly quality was further assessed using QUAST. Antibiotic resistance genes (ARGs), virulence factors (VFs), and plasmid replicons were identified with ABRicate. Multilocus sequence typing (MLST) was performed with MLST.

RESULTS

This study conducted a systematic and comprehensive global genomic analysis of 35,471 CRKP isolates collected from 101 countries from 1996 to 2023. The results showed that China (25.11%), the United States (21.63%) and the United Kingdom 101 countries from 1996 to 2023. The results showed that China (25.11%), the United States (21.63%) and the United Kingdom peaked in 2018, followed by a declining trend. Our analysis revealed that carbapenemases in CRKP were predominantly KPC (53.93%), followed by NDM (25.58%) and OXA-48-like (21.86%). The isolates were classified into 1,046 known sequence types (ST), with the most common types being ST11 (23.90%), ST258 (12.85%), ST147 (7.64%), ST15 (5.21%), and ST307 (4.03%). Notably, all CRKP isolates carried multiple ARGs, with the United States having the highest number of unique ARGs. Principal coordinate analysis (PCoA) revealed that the composition of ARGs among CRKP isolates from China differs significantly from that of isolates in other countries. Furthermore, CRKP isolates from China carried the highest number of VFs, highlighting a distinct profile compared to other regions.

CONCLUSIONS

This study provides comprehensive data on CRKP, underscoring the necessity for continued global surveillance to monitor the dissemination of resistance and virulence.