Global Emergence and Genomic Epidemiology of bla_NDM-Carrying Klebsiella variicola

Abstract

Purpose

Klebsiella variicola has emerged as a human pathogen in the past decade. Here, we present findings related to a K. variicola strain carrying the bla_NDM-1 gene, which was isolated from a urinary tract infection in China. Global transmission dynamics and genomic epidemiology of bla_NDM-carrying K. variicola were further investigated.

Material and Methods

The complete genome sequence of the strain was determined using the Illumina NovaSeq 6000 and Nanopore MinION sequencer. Genomic features and resistance mechanisms were analyzed through diverse bioinformatics approaches. Additionally, genome sequences of K. variicola strains carrying bla_NDM were retrieved from the NCBI database, and a comprehensive analysis of the global dissemination trends of these strains was conducted.

Results

K. variicola strain 353 demonstrated resistance to multiple antimicrobials, including carbapenems. Within its genome, we identified fourteen antimicrobial resistance genes associated with β-lactam, aminoglycoside, fosfomycin, quinolone, trimethoprim, rifamycin, and sulfonamide resistance. The carbapenem-resistant gene bla_NDM-1 was located on an IncU-type plasmid spanning 294,608 bp and flanked by ISCR1 and IS26. Downstream of bla_NDM-1, we identified an Intl1 element housing numerous antibiotic resistance genes. A comprehensive search of the NCBI database revealed 72 K. variicola strains carrying bla_NDM from twelve different countries, predominantly from clinical sources, with the highest prevalence observed in the USA and China. A total of 28 distinct sequence types (STs) were identified, with ST115 being the most prevalent, followed by ST60.

Conclusion

In summary, this study presents the genomic characterization of a K. variicola strain carrying bla_NDM-1 on an IncU-type plasmid. The research highlights the global dissemination of bla_NDM-carrying K. variicola, observed in both healthcare settings and natural environments. Our data have revealed a diverse array of antimicrobial resistance determinants in K. variicola, providing valuable insights that could aid in the development of strategies for the prevention, diagnosis, and treatment of K. variicola infections.

Keywords:

• Klebsiella variicola
• bla_NDM-1
• whole-genome sequencing
• IncU type plasmid
• urinary tract infection

Acknowledgments

This work was supported by the Traditional Chinese Medicine Science and Technology Project of Zhejiang Province, China (Grant number 2024ZL253), and the Medicine and Health Science and Technology Project of Zhejiang Province, China (Grant number 2021KY475).

Disclosure

The authors report no conflicts of interest in this work.