Heterogeneous multicopy of blaCTX-M variants on the same plasmid enhances evolutionary adaptability in clinical Klebsiella pneumoniae

Rui Weng; Jingyi Zhu; Xueqing Wu; Qiucheng Shi; Yue Li; Junxin Zhou; Yanfei Wang; Yinping Wang; Weiyi Huang; Haiyang Liu; Sai Qiao; Ying Chen; Jinzheng Ren; Ping Zhang; Jingjing Quan; Dongdong Zhao; Xiaoting Hua; Xiaoxing Du; Jiawei Wang; Yunsong Yu; Yan Jiang

doi:10.1038/s41467-026-69266-7

Heterogeneous multicopy of blaCTX-M variants on the same plasmid enhances evolutionary adaptability in clinical Klebsiella pneumoniae

Rui Weng, Jingyi Zhu, Xueqing Wu, Qiucheng Shi, Yue Li, Junxin Zhou, Yanfei Wang, Yinping Wang, Weiyi Huang, Haiyang Liu, Sai Qiao, Ying Chen, Jinzheng Ren, Ping Zhang, Jingjing Quan, Dongdong Zhao, Xiaoting Hua, Xiaoxing Du, Jiawei Wang, Yunsong YuYan Jiang

Department of Life Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

Pathogenic bacteria continually evolve under antimicrobial pressure through acquired resistance genes, making it crucial to understand their evolutionary strategies. We identify a clinical Klebsiella pneumoniae isolate resistant to ceftazidime/avibactam (CZA), harboring heterogeneous multicopy blaCTX-M, among which a blaCTX-M-249 variant mediates CZA resistance. Both blaCTX-M-249 and its closely related allele blaCTX-M-65 are dominant within the clonal population and are located at two loci on the same plasmid, with their proportions shifting under antibiotic pressure. Using experimental and mathematical models, we demonstrate that the heterogeneous arrangement of blaCTX-M variants on the same plasmid confers greater stability and competitive advantage than that across separate plasmids, particularly during drug switching. Re-analysis of large genomic datasets supports the universality of this phenomenon. Our findings reveal an evolutionary strategy in which β-lactamase genes, through multicopy heterogeneity on a single plasmid, ensure stable inheritance of resistance and enhance bacterial adaptability under fluctuating clinical antibiotic pressures.

Original language	English
Article number	2460
Journal	Nature Communications
Volume	17
Issue number	1
Early online date	7 Feb 2026
DOIs	https://doi.org/10.1038/s41467-026-69266-7
Publication status	Published - 7 Feb 2026

Data Availability Statement

The novel variants of blaCTX-M we discovered in this study, blaCTX-M-247, blaCTX-M-248 and blaCTX-M-249, have been submitted and designated in GenBank under accession number MZ379780, MZ379781, and MZ379782, respectively. All raw genomic data for strains ICU-3 and ICU-18, under different antibiotic pressures, generated from the Illumina and Nanopore platforms, have been deposited in the SRA under BioProject accession number PRJNA1194354. The pICU-3 and pICU-18 sequences are available under GenBank accession numbers PX405700 and pX405701 [https://www.ncbi.nlm.nih.gov/nuccore/pX405701], respectively. Additionally, the genomic raw sequence data of K. pneumoniae from our laboratory were obtained from two surveillance projects (PRJNA1290706 [https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA1290706] and PRJNA1291361). Source data are provided with this paper.

Funding

This work was supported by the National Key Research and Development Program of China (No. 2023YFC2307100 to Y.Y.) and the National Natural Science Foundation of China (No. 82272373 to Y.J. and No. 82402666 to P.Z.). This work was presented as a Top Abstract in an oral report at ESCMID Global 2024, Barcelona. We thank Prof. Hangjin Jiang from the Center for Data Science, Zhejiang University, Hangzhou, China, for his valuable assistance with the mathematical models.

Funders	Funder number
Center for Data Science
Zhejiang University
National Key Research and Development Program of China	2023YFC2307100
National Natural Science Foundation of China	82272373, 82402666

ASJC Scopus subject areas

General Chemistry
General Biochemistry,Genetics and Molecular Biology
General
General Physics and Astronomy

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Cite this

Weng, R., Zhu, J., Wu, X., Shi, Q., Li, Y., Zhou, J., Wang, Y., Wang, Y., Huang, W., Liu, H., Qiao, S., Chen, Y., Ren, J., Zhang, P., Quan, J., Zhao, D., Hua, X., Du, X., Wang, J., ... Jiang, Y. (2026). Heterogeneous multicopy of blaCTX-M variants on the same plasmid enhances evolutionary adaptability in clinical Klebsiella pneumoniae. Nature Communications, 17(1), Article 2460. https://doi.org/10.1038/s41467-026-69266-7

Weng, R, Zhu, J, Wu, X, Shi, Q, Li, Y, Zhou, J, Wang, Y, Wang, Y, Huang, W, Liu, H, Qiao, S, Chen, Y, Ren, J, Zhang, P, Quan, J, Zhao, D, Hua, X, Du, X, Wang, J, Yu, Y & Jiang, Y 2026, 'Heterogeneous multicopy of blaCTX-M variants on the same plasmid enhances evolutionary adaptability in clinical Klebsiella pneumoniae', Nature Communications, vol. 17, no. 1, 2460. https://doi.org/10.1038/s41467-026-69266-7

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abstract = "Pathogenic bacteria continually evolve under antimicrobial pressure through acquired resistance genes, making it crucial to understand their evolutionary strategies. We identify a clinical Klebsiella pneumoniae isolate resistant to ceftazidime/avibactam (CZA), harboring heterogeneous multicopy blaCTX-M, among which a blaCTX-M-249 variant mediates CZA resistance. Both blaCTX-M-249 and its closely related allele blaCTX-M-65 are dominant within the clonal population and are located at two loci on the same plasmid, with their proportions shifting under antibiotic pressure. Using experimental and mathematical models, we demonstrate that the heterogeneous arrangement of blaCTX-M variants on the same plasmid confers greater stability and competitive advantage than that across separate plasmids, particularly during drug switching. Re-analysis of large genomic datasets supports the universality of this phenomenon. Our findings reveal an evolutionary strategy in which β-lactamase genes, through multicopy heterogeneity on a single plasmid, ensure stable inheritance of resistance and enhance bacterial adaptability under fluctuating clinical antibiotic pressures.",

author = "Rui Weng and Jingyi Zhu and Xueqing Wu and Qiucheng Shi and Yue Li and Junxin Zhou and Yanfei Wang and Yinping Wang and Weiyi Huang and Haiyang Liu and Sai Qiao and Ying Chen and Jinzheng Ren and Ping Zhang and Jingjing Quan and Dongdong Zhao and Xiaoting Hua and Xiaoxing Du and Jiawei Wang and Yunsong Yu and Yan Jiang",

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AU - Weng, Rui

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AU - Wu, Xueqing

AU - Shi, Qiucheng

AU - Li, Yue

AU - Zhou, Junxin

AU - Wang, Yanfei

AU - Wang, Yinping

AU - Huang, Weiyi

AU - Liu, Haiyang

AU - Qiao, Sai

AU - Chen, Ying

AU - Ren, Jinzheng

AU - Zhang, Ping

AU - Quan, Jingjing

AU - Zhao, Dongdong

AU - Hua, Xiaoting

AU - Du, Xiaoxing

AU - Wang, Jiawei

AU - Yu, Yunsong

AU - Jiang, Yan

PY - 2026/2/7

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N2 - Pathogenic bacteria continually evolve under antimicrobial pressure through acquired resistance genes, making it crucial to understand their evolutionary strategies. We identify a clinical Klebsiella pneumoniae isolate resistant to ceftazidime/avibactam (CZA), harboring heterogeneous multicopy blaCTX-M, among which a blaCTX-M-249 variant mediates CZA resistance. Both blaCTX-M-249 and its closely related allele blaCTX-M-65 are dominant within the clonal population and are located at two loci on the same plasmid, with their proportions shifting under antibiotic pressure. Using experimental and mathematical models, we demonstrate that the heterogeneous arrangement of blaCTX-M variants on the same plasmid confers greater stability and competitive advantage than that across separate plasmids, particularly during drug switching. Re-analysis of large genomic datasets supports the universality of this phenomenon. Our findings reveal an evolutionary strategy in which β-lactamase genes, through multicopy heterogeneity on a single plasmid, ensure stable inheritance of resistance and enhance bacterial adaptability under fluctuating clinical antibiotic pressures.

AB - Pathogenic bacteria continually evolve under antimicrobial pressure through acquired resistance genes, making it crucial to understand their evolutionary strategies. We identify a clinical Klebsiella pneumoniae isolate resistant to ceftazidime/avibactam (CZA), harboring heterogeneous multicopy blaCTX-M, among which a blaCTX-M-249 variant mediates CZA resistance. Both blaCTX-M-249 and its closely related allele blaCTX-M-65 are dominant within the clonal population and are located at two loci on the same plasmid, with their proportions shifting under antibiotic pressure. Using experimental and mathematical models, we demonstrate that the heterogeneous arrangement of blaCTX-M variants on the same plasmid confers greater stability and competitive advantage than that across separate plasmids, particularly during drug switching. Re-analysis of large genomic datasets supports the universality of this phenomenon. Our findings reveal an evolutionary strategy in which β-lactamase genes, through multicopy heterogeneity on a single plasmid, ensure stable inheritance of resistance and enhance bacterial adaptability under fluctuating clinical antibiotic pressures.

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Heterogeneous multicopy of blaCTX-M variants on the same plasmid enhances evolutionary adaptability in clinical Klebsiella pneumoniae

Abstract

Data Availability Statement

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