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Shi Q, Ruan Z, Zhang P, Hu H, Han X, Wang Z, Lou T, Quan J, Lan W, Weng R, Zhao D, Du X, Yu Y, Jiang Y. Epidemiology of carbapenem-resistant Klebsiella pneumoniae in China and the evolving trends of predominant clone ST11: a multicentre, genome-based study. J Antimicrob Chemother 2024:dkae227. [PMID: 38997220 DOI: 10.1093/jac/dkae227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024] Open
Abstract
OBJECTIVES Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major nosocomial infectious pathogen with rapidly increasing prevalence. The genomic epidemiological characteristics of CRKP nationwide, especially the evolving trends within the predominant clones, should be evaluated clearly. METHODS We collected 3415 K. pneumoniae strains from 28 hospitals across China. Antimicrobial susceptibility testing and WGS were performed. Subsequent genomic analyses, including sequence typing, K-locus (KL) identification, antimicrobial resistance gene screening, and virulence score assessment were performed. The phylogenetic relationship of clonal group 11 was determined based on core-genome analysis, and the presence of the pLVPK-like virulence plasmid in ST11 isolates was confirmed using plasmid core-gene analysis. Additionally, the trends of the ST11 lineage with different KL types on a global scale were investigated using Beast2. RESULTS Of the K. pneumoniae strains, 708 were identified as CRKP isolates (20.7%), of which 97.7% were MDR. ST11 was the predominant clone, and KPC-2 was the prevalent carbapenemase in China, although the prevalence of specific clones and carbapenemases varied by geographic region. Among ST11 isolates, KL47 and KL64 were the predominant KL types, and KL64 gradually replaced KL47, with a higher percentage of KL64 isolates harbouring the pLVPK-like plasmid. Global genome data showed a significant increase in the effective population size of KL64 over the last 5 years. CONCLUSIONS The prevalence of CRKP was very high in certain regions in China. The increasing convergence of virulence and resistance, particularly in ST11-KL64 isolates, should be given more attention and further investigation.
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Affiliation(s)
- Qiucheng Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Qingchun East Road, 310016 Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ping Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Qingchun East Road, 310016 Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huangdu Hu
- Center for General Practice Medicine, Department of Infectious Diseases, Zhejiang Provincial People's Hospital, Hangzhou Medical College Affiliated People's Hospital, Hangzhou, China
| | - Xinhong Han
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou, China
| | - Zhengan Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Qingchun East Road, 310016 Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tao Lou
- Department of Infectious Diseases, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Jingjing Quan
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Qingchun East Road, 310016 Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Lan
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Qingchun East Road, 310016 Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Rui Weng
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Qingchun East Road, 310016 Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Qingchun East Road, 310016 Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoxing Du
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Qingchun East Road, 310016 Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Qingchun East Road, 310016 Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Qingchun East Road, 310016 Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Li YT, Wang YC, Chen CM, Tang HL, Chen BH, Teng RH, Chiou CS, Lu MC, Lai YC. Distinct evolution of ST11 KL64 Klebsiella pneumoniae in Taiwan. Front Microbiol 2023; 14:1291540. [PMID: 38143864 PMCID: PMC10748404 DOI: 10.3389/fmicb.2023.1291540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Carbapenem-resistant ST11_KL64 Klebsiella pneumoniae emerged as a significant public health concern in Taiwan, peaking between 2013 and 2015, with the majority of isolates exhibiting OXA-48 as the sole carbapenemase. In this study, we employed whole-genome sequencing to investigate the molecular underpinnings of ST11_KL64 isolates collected from 2013 to 2021. Phylogenomic analysis revealed a notable genetic divergence between the ST11_KL64 strains in Taiwan and those in China, suggesting an independent evolutionary trajectory. Our findings indicated that the ST11_KL64_Taiwan lineage originated from the ST11_KL64 lineage in Brazil, with recombination events leading to the integration of ICEKp11 and a 27-kb fragment at the tRNAASN sites, shaping its unique genomic landscape. To further elucidate this unique sublineage, we examined the plasmid contents. In contrast to ST11_KL64_Brazil strains, which predominantly carried blaKPC-2, ST11_KL64_Taiwan strains exhibited the acquisition of an epidemic blaOXA-48-carrying IncL plasmid. Additionally, ST11_KL64_Taiwan strains consistently harbored a multi-drug resistance IncC plasmid, along with a collection of gene clusters that conferred resistance to heavy metals and the phage shock protein system via various Inc-type plasmids. Although few, there were still rare ST11_KL64_Taiwan strains that have evolved into hypervirulent CRKP through the horizontal acquisition of pLVPK variants. Comprehensive characterization of the high-risk ST11_KL64 lineage in Taiwan not only sheds light on its epidemic success but also provides essential data for ongoing surveillance efforts aimed at tracking the spread and evolution of ST11_KL64 across different geographical regions. Understanding the molecular underpinnings of CRKP evolution is crucial for developing effective strategies to combat its emergence and dissemination.
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Affiliation(s)
- Yia-Ting Li
- Division of Respiratory Therapy, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yao-Chen Wang
- Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Ming Chen
- Department of Internal Medicine, Tungs’ Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Hui-Ling Tang
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Bo-Han Chen
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ru-Hsiou Teng
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Chien-Shun Chiou
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Min-Chi Lu
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yi-Chyi Lai
- Department of Microbiology and Immunology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
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