Genomic Analysis of Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae in a Chinese Tertiary Hospital

Lan Chen; Ying Zhou; Shanshan Wang; Chunyang Wu; Peiyao Zhou; Bingjie Wang; Zhu Chen; Fangyou Yu

doi:10.2147/IDR.S425949

Genomic Analysis of Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae in a Chinese Tertiary Hospital

Infect Drug Resist. 2023 Sep 27:16:6385-6394. doi: 10.2147/IDR.S425949. eCollection 2023.

Authors

Lan Chen^#¹, Ying Zhou^#², Shanshan Wang¹, Chunyang Wu³, Peiyao Zhou⁴, Bingjie Wang², Zhu Chen⁵, Fangyou Yu²

Affiliations

¹ Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, People's Republic of China.
² Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200082, People's Republic of China.
³ Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, People's Republic of China.
⁴ Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China.
⁵ Department of Clinical Laboratory Medicine, Ningbo No. 2 Hospital, Ningbo, Zhejiang, 315010, People's Republic of China.

^# Contributed equally.

Abstract

Background: Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) has become a clinical crisis and is associated with significant morbidity and mortality. The prevalence of CR-hvKP has trended upward since 2010. This study aims to describe the clinical and genomic characteristics of CR-hvKP collected from a tertiary hospital in eastern China, from August 2020 to October 2021.

Methods: We tested the susceptibility to common antibiotics in these isolates to feature the antibiotic-resistant phenotypes. We also applied whole-genome sequencing and core-genome phylogenetic to analysis the genetic features of these isolates. Plasmid replicons were identified by using the PlasmidFinder database, and core-genome phylogenetic analysis by Parsnp database.

Results: All these strains isolated from the patients with serious underlying diseases and poor prognosis. We found all CR-hvKp isolates exhibited a multidrug-resistant (MDR) phenotype. These results revealed that bla_KPC-2 was the predominant carbapenemases gene (n = 53, 84.1%), and ST11-KL64 CR-hvKP strains dominated, forming a single cluster, and differed by an average of 26 core SNPs. We only found eight ST15 isolates containing KL24 and KL112 type capsules, with the main carbapenem resistance genes being bla_OXA-232 and bla_KPC-2. All ST11-KL64 strains had a series of resistance and virulence genes, along with IncHIB-FIB virulence plasmids and IncFII resistance plasmids, while the prevalence of resistance plasmids like the IncFII plasmid was absence in ST15 isolates.

Conclusion: This suggests that ST11-KL64 CR-hvKP has emerged as the most prevalent hypervirulence and carbapenem-resistant K. pneumoniae and may contribute to hospital outbreaks of infection, which required most clinical attention.

Keywords: Klebsiella pneumoniae; antimicrobial resistance; carbapenem-resistant; hypervirulence; virulence genes; whole-genome sequencing.

Grants and funding

This research is supported by Medical Scientific Research Foundation of Zhejiang Province, Grant No.2023KY1072. This research is also supported by Medical Scientific Research Foundation of Zhejiang Province, Grant No.2022KY1124.