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

Abstract

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.