Distinct evolution of ST11 KL64 Klebsiella pneumoniae in Taiwan

Yia-Ting Li; Yao-Chen Wang; Chih-Ming Chen; Hui-Ling Tang; Bo-Han Chen; Ru-Hsiou Teng; Chien-Shun Chiou; Min-Chi Lu; Yi-Chyi Lai

doi:10.3389/fmicb.2023.1291540

Distinct evolution of ST11 KL64 Klebsiella pneumoniae in Taiwan

Front Microbiol. 2023 Dec 8:14:1291540. doi: 10.3389/fmicb.2023.1291540. eCollection 2023.

Authors

Yia-Ting Li^#¹, Yao-Chen Wang^#^{2

3}, Chih-Ming Chen^#⁴, Hui-Ling Tang⁵, Bo-Han Chen⁶, Ru-Hsiou Teng⁶, Chien-Shun Chiou⁶, Min-Chi Lu^{5

7}, Yi-Chyi Lai^{8

2}

Affiliations

¹ Division of Respiratory Therapy, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan.
² Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan.
³ School of Medicine, Chung Shan Medical University, Taichung, Taiwan.
⁴ Department of Internal Medicine, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan.
⁵ Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan.
⁶ Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan.
⁷ Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan.
⁸ Department of Microbiology and Immunology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan.

^# Contributed equally.

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 tRNA^ASN 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 bla_KPC-2, ST11_KL64_Taiwan strains exhibited the acquisition of an epidemic bla_OXA-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.

Keywords: KL64_Clade I; Klebsiella pneumoniae; ST11; phylogenomic analysis; plasmids.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by Chung Shan Medical University Hospital, Taichung, Taiwan (grant no. CSH-2021-C-047), China Medical University Hospital, Taichung, Taiwan (grant no. DMR-112-186), and Ministry of Science and Technology, Taiwan (grant nos. MOST-109-2314-B-039-049-MY3 and NSTC 112-2320-B-040-025). The funders had no role in the study design, data collection, analysis, publication decision, or manuscript preparation.