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

Taif Shah,1 Jie Li,2,3 Zahir Shah,4 Yunlan Lu,2 Weihong Qin2 1State Key Laboratory of Conservation and Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, People’s Republic of China; 2Kunming Customs Port Outpatient Department, Yunnan International Travel Health Care Center, Kunming, Yunnan, People’s Republic of China; 3Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, People’s Republic of China; 4College of Veterinary Sciences, The University of Agriculture, Peshawar, KP, PakistanCorrespondence: Taif Shah, Email [email protected] Weihong Qin, Email [email protected]: Klebsiella variicola is an emerging bacterial pathogen commonly associated with opportunistic human infections.Methods: 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.Results: 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.Discussion: 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.Keywords: Klebsiella variicola, antimicrobial resistance, virulence, secondary metabolite genes, plasmids, phages