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.