A novel sequence type of carbapenem-resistant hypervirulent Klebsiella pneumoniae strains from a county-level tertiary hospital in Southeastern China

The whole-genome sequencing of carbapenem-resistant Klebsiella pneumoniae (CRKP) strains is required for investigating the molecular epidemiology because of their diverse molecular types across geographical regions. CRKP strains were collected from a tertiary hospital in Southeastern China from January 2017 to December 2020. Following species identification, drug susceptibility phenotypes were determined based on minimum inhibitory concentrations using the VITEK 2 Compact system. In addition, whole-genome sequencing was performed to identify the resistance genes and high virulence genes (rmpA, rmpA2, iucA, iroB, and peg-344). Finally, a phylogenetic tree was constructed based on the core genes. Forty CRKP strains were identified, and 25% of the involved patients (n = 10) died during hospitalization. The dominant sequence type (ST) was ST11 (65%), followed by ST290 (n = 4, 10%) and a novel ST (n = 4, assigned as ST6242, 10%). CRKP strains with this new ST were resistant to amikacin but susceptible to sulfamethoxazole-trimethoprim, and the phylogenetic tree indicated that they were derived from ST11 strains. All ST6242 strains were classified as the hypervirulent type (positive for rmpA, rmpA2, iucA, and peg-344). CRKP strains with this novel ST harbored highly virulent genes and a unique resistance phenotype. Thus, they should be epidemiologically monitored.