Genomic epidemiology of hypervirulent carbapenem-resistant Klebsiella pneumoniae at Jinshan local hospital, Shanghai, during 2014-2018

Ming-Quan Guo; Yi-Ting Wang; Shan-Shan Wang; Li-Kuang Chen; Ying-Hua Xu; Gang Li

doi:10.1016/j.jmii.2023.10.012

Genomic epidemiology of hypervirulent carbapenem-resistant Klebsiella pneumoniae at Jinshan local hospital, Shanghai, during 2014-2018

J Microbiol Immunol Infect. 2024 Feb;57(1):128-137. doi: 10.1016/j.jmii.2023.10.012. Epub 2023 Nov 2.

Authors

Ming-Quan Guo¹, Yi-Ting Wang², Shan-Shan Wang³, Li-Kuang Chen⁴, Ying-Hua Xu⁵, Gang Li⁶

Affiliations

¹ Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200025, China.
² Department of Laboratory Medicine, Jinshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
³ Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, 102629, China.
⁴ Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200025, China; Department of Laboratory Medicine, Clinical Pathology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan.
⁵ Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, 102629, China. Electronic address: xuyh@nifdc.org.cn.
⁶ Department of Laboratory Medicine, Jinshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China. Electronic address: li_gang@fudan.edu.cn.

PMID: 37951801
DOI: 10.1016/j.jmii.2023.10.012

Abstract

Background: Hypervirulent carbapenem-resistant Klebsiella pneumoniae (Hv-CRKP) triggered a significant public health challenge. This study explored the prevalence trends and key genetic characteristics of Hv-CRKP in one Shanghai suburbs hospital during 2014-2018.

Methods: During five years, Hv-CRKP strains identified from 2579 CRKP by specific PCR, were subjected to performed short- and long-read sequencing technology; epidemiological characteristics, antimicrobial-resistance genes (ARGs), virulence determinants, detailed plasmid profiles and conjugation efficiency were comprehensively investigated.

Results: 155 Hv-CRKP and 31 non-Hv-CRKP strains were sequenced. Hv-CRKP strains exhibited significant resistance to six common antibiotic classes (>92%). ST11 steadily increased and became the most prevalent ST (85.2%), followed by ST15 (8.5%), ST65 (2.6%), ST23 (1.9%), and ST86 (0.6%). ST11-KL64 (65.2%) rapidly increased from 0 in 2014 to 93.9% in 2018. bla_KPC-2 was the primary carbapenemase gene (97.4%). Other ARGs switched from aac(3)-IId to aadA2 in aminoglycoside and from sul1 to sul2 in sulfanilamide. The time-dated phylogenetic tree was divided into four independent evolutionary clades. Clade 1 and 3 strains were mostly limited in the ICU, whereas Clade 2 strains were distributed among multiple departments. Compared to ybt14 in ICEKp12 in Clade 1, Clade 3 strains harbored ybt9 in ICEKp3 and bla_CTX-M-65. Hv-CRKP infected more wards than non-Hv-CRKP and showed greater transmission capacity. Three plasmids containing crucial carbapenemase genes demonstrated their early transmission across China.

Conclusion: The Hv-CRKP ST11-KL64 has rapidly replaced ST11-KL47 and emerged as the predominant epidemic subtype in various hospital wards, highlighting the importance of conducting comprehensive early surveillance for Hv-CRKP, especially in respiratory infections.

Keywords: Carbapenem resistance gene; Genomic epidemiology; Hypervirulent carbapenem-resistant Klebsiella pneumoniae; Virulence plasmid.

MeSH terms

Anti-Bacterial Agents / pharmacology
Carbapenem-Resistant Enterobacteriaceae* / genetics
Carbapenems / pharmacology
China / epidemiology
Genomics
Hospitals
Humans
Klebsiella Infections* / epidemiology
Klebsiella pneumoniae
Phylogeny

Substances

Anti-Bacterial Agents
Carbapenems