Genomic Characterization Reveals Infections and Silent Dissemination of Carbapenemase-Producing Klebsiella Oxytoca Complex Associated with ST2 Lineage in a Hospital Setting

Abstract

Our aim was to investigate lineages and resistome of carbapenemase-producing Klebsiella oxytoca Complex (KoC) strains isolated from 2019 to 2022 from colonization and infection samples to evaluate their potential dissemination. This prospective study showed the presence of eight multidrug-resistant K. oxytoca ST2 strains harboring bla_KPC-2, bla_KPC-3, or bla_IMP-8 genes among both colonized (n = 5) and infected (n = 3) patients isolated during this period. Genomic analysis revealed antimicrobial resistance genes, virulence loci, including kleboxymycin and yersiniabactin, highlighting their resistance and pathogenicity in clinical settings. CgSNP analysis revealed that five isolates, HA8pKo, HA10pKo, HA14pKo, HA21Ko and HA22pKo, were the same strain disseminating among colonized patients (n = 4) during two months in 2019. K. oxytoca HA8pKo, HA10pKo, HA14pKo, HA21Ko, and HA22pKo strains shared three replicon types (Col(pHAD28), IncM1, and IncFII (K) as well as the bla_KPC-2 gene. The bla_KPC-2 gene was contained in the IncFII (K) replicon (pDCVEA12-KPC) which harbored a mercury resistance (mer) gene locus. The silent dissemination of carbapenemase-producing KoC strains colonizing patients is a cause for concern, prompting questions about the most suitable approaches for asymptomatic patients to prevent the spread and potential outbreaks. Our findings reinforced the relevance of epidemiological surveillance programs to identify the reservoir of carbapenemase-producing strains.