Clonal dissemination and persistence of Carbapenem-resistant bla KPC-2 harbouring Klebsiella pneumoniae ST307 in a Tertiary Hospital in the Republic of Korea

Abstract

Objectives: We investigated the epidemiological patterns of carbapenem-resistant, bla _KPC-2 harbouring Klebsiella pneumoniae (K. pneumoniae) ST 307 isolates in a tertiary hospital in South Korea between 2019 and 2021 and compared them to isolates collected from 25 hospitals through a nationwide survey, using whole genome sequencing and phylogenetic analysis.

Methods: Whole genome sequences of 25 isolates from hospital GB2 and 45 isolates from 25 other hospitals were analysed for antibiotic resistance gene profiles, virulence gene profiles, plasmid replicons, and phylogenetic relationships.

Results: Core genome single nucleotide polymorphism (cgSNP)-based phylogenetic analysis categorized the 70 isolates into three distinct groups and 13 subgroups, supported by high bootstrap values and low SNP differences. Subgroup 1 comprised the 18 isolates from GB2 collected over 3 years, suggesting long-term persistence and repeated outbreaks within GB2. Region-specific dissemination was indicated by several subgroups containing isolates from different hospitals within the same province. Subgroup 7 comprised isolates from multiple provinces and years, suggesting potential long-distance transmission via patient transfers or community reservoirs. All isolates carried multiple β-lactam resistance genes; bla _CTX-M-15 was observed in 67 isolates (89.3%) and the OXA variants in 70 isolates (93.3%). None of the isolates carried the rmpA/rmpA2 or magA genes, while 58 of the 70 (82.9%) harboured yersiniabactin-encoding genes.

Conclusions: Our findings reveal both clonal persistence within a tertiary hospital and region-specific dissemination of bla _KPC-2 producing K. pneumoniae ST307 across South Korea. These results highlight the importance of continuous nationwide surveillance and genomic analysis to implement effective infection control measures to mitigate further dissemination.

Figure 1.

Phylogenetic tree of (a) bla_KPC-2 harbouring K. pneumoniae ST307 isolates sequenced in this study (n = 70) and complete sequences of K. pneumoniae ST307 downloaded from public databases (n = 71). The phylogeny was rooted at the midpoint, and numerical values on certain tree branches represent bootstrap support values based on 1000 replicates, expressed as percentages. The isolates of this study were categorized into three groups, group 1 to 3. (b) to (d) Highlight each clade, represented within differently colored boxes to indicate distinct subgroups (subgroups 1 to 13), along with detailed isolate information.