Comprehensive Genome Analysis of a Human-Derived β-Lactam-Resistant Klebsiella variicola Isolate from China

Klebsiella variicola is an emerging bacterial pathogen commonly associated with opportunistic human infections.

In this study, we characterized and analyzed the core genome of a β-lactam-resistant K. variicola subsp. variicola isolate from a human in Kunming, Yunnan, China.

The human-derived β-lactam-resistant K. variicola genome was assembled into 37 contigs, with a total genome size of 5,667,700 bp. K. variicola comprises multiple antimicrobial resistance (AMR) genes, including blaLEN-22, fosA, OqxA, and OqxB, as well as the virulence-associated factors fimH, nlpI, and iutA. The β-lactam-resistant K. variicola genome comprised K and O (KL30 and O3/O3a) serotypes. We also identified 29 SNPs from three different snpEff categories: 18 low, five moderate, and six modifiers. Subsequently, we identified five assembled replicons, including three plasmids. Plasmid pKp5-1, plasmid p15WZ-82_res, and plasmid pKP91, and two phage regions: phage region-1, which resembled Entero-phage-HK446, and phage region-2, which was questionable with phage-Erwini-vB-EhrS-59. Furthermore, secondary metabolites, such as redox-cofactor, butyrolactone, azole-containing-RiPP, terpene-precursors (two distinct clusters), NRP-metallophores, and RiPP-like gene clusters were also identified in the K. variicola genome.

Identifying key antibiotic resistance determinants, virulence factors, capsule serotypes, secondary metabolites, plasmids, and phage replicons emphasizes the zoonotic potential of this pathogen. Given the potential zoonotic implications, a multidisciplinary approach should be used to prevent the spread of β-lactam-resistant K. variicola.