Genomic surveillance of carbapenem-resistant Klebsiella pneumoniae in the Republic of Moldova

Abstract

Antimicrobial-resistant Klebsiella pneumoniae poses a global threat to human, animal, and environmental health. The challenges of AMR surveillance have led to the development of advanced molecular biology techniques, such as genomic sequencing, to identify the resistance gene diversity and the factors contributing to the AMR emergence and spreading. In this study, a total of 99 Klebsiella pneumoniae strains suspected of producing ESBL or carbapenemases were collected between January 2020 and December 2023 from nine hospital laboratories, predominantly from hospital-associated infections/isolates. The strains were analysed using conventional methods as well as whole-genome sequencing. Phenotypic testing indicated very high resistance to key antibiotic classes, including third-generation cephalosporins (98%), fluoroquinolones (97%), aminoglycosides (95%), and carbapenems (68%). Subsequent bioinformatic analysis was performed using tools such as iTOL, the Center for Genomic Epidemiology platform, and Kleborate. Sixteen distinct MLST types were identified among the studied strains. The most common were ST395 (N=56), ST377 (N=12), and ST23 (N=5). Phylogenetic inference revealed two major ST395 clusters spanning multiple hospitals, consistent with inter-hospital dissemination. All ST395 strains carried the resistance genes blaOXA-48, blaCTX-M-15, blaOXA-1, blaNDM-1, and blaTEM-1B. Bioinformatic analysis of the sequences showed that most isolates contained 7 of the 8 Col group plasmid/replicon types and 5 of the 21 Inc group types. A high virulence score was observed in 37 strains, while 2 strains showed a very high score. This includes globally transmitted strains such as ST395 and ST23 (hypervirulent), as well as the regionally dominant ST377 lineage, which was highly resistant but not hypervirulent. Our study suggests several independent introductions of K. pneumoniae strains, including carbapenem resistant and hypervirulent strains into Moldova, followed by spread across several hospitals. This includes globally transmitted strains such as ST395 and ST23, as well as regionally dominant strains like ST377. Comprehensive genomic surveillance of AMR has offered crucial insights for tracking multidrug-resistant Klebsiella pneumoniae strains. These findings help shape surveillance priorities and underline the importance of whole-genome sequencing in both research and ongoing monitoring. Such efforts are essential for guiding effective prevention and control strategies to limit the spread of resistant K. pneumoniae in the Republic of Moldova.