Comparative Genomics Revealing the Genomic Characteristics of Klebsiella variicola Clinical Isolates in China

<i>Klebsiella variicola</i> is an opportunistic pathogen often misidentified as <i>Klebsiella pneumoniae</i>, leading to misdiagnoses and inappropriate treatment in clinical settings. The genetic and molecular characteristics of clinically isolated <i>K. variicola</i> remain largely unexplored. We aim to fill this knowledge gap by examining the genomic properties of and evolutionary relationships between clinical isolates of <i>K. variicola</i>. The genomic data of 70 <i>K. variicola</i> strains were analyzed using whole-genome sequencing. A phylogenetic tree was generated based on the gene sequences from these <i>K. variicola</i> strains and public databases. Among the <i>K. variicola</i> strains, the drug resistance genes with the highest carrying rates were beta-lactamase and aminoglycoside. Locally isolated strains had a higher detection rate for virulence genes than those in public databases, with yersiniabactin genes being the most prevalent. The K locus types and MLST subtypes of the strains exhibited a dispersed distribution, with O3/O3a being the predominant subtype within the O category. In total, 28 isolates carried both IncFIB(K)_Kpn3 and IncFII_pKP91 replicons. This study underscores the importance of developing more effective diagnostic tools and therapeutic strategies for <i>K. variicola</i> infections. The continued surveillance and monitoring of <i>K. variicola</i> strains is essential for understanding the epidemiology of infections and informing public health strategies.