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Characterization and genome sequencing of a novel T7-like lytic phage, kpssk3, infecting carbapenem-resistant Klebsiella pneumoniae

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Abstract

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has spread globally and emerged as an urgent public health threat. Bacteriophages are considered an effective weapon against multidrug-resistant pathogens. In this study, we report a novel lytic phage, kpssk3, which is able to lyse CRKP and degrade exopolysaccharide (EPS). The morphological characteristics of kpssk3 observed by transmission electron microscopy, including a polyhedral head and a short tail, indicate that it belongs to the family Podoviridae. A one-step growth curve revealed that kpssk3 has a latent period of 10 min and a burst size of 200 plaque-forming units (pfu) per cell. kpssk3 was able to lyse 25 out of 27 (92.59%) clinically isolated CRKP strains, and it also exhibited high stability to changes in temperature and pH. kpssk3 has a linear dsDNA genome of 40,539 bp with 52.80% G+C content and 42 putative open reading frames (ORFs). No antibiotic resistance genes, virulence factors, or integrases were identified in the genome. Based on bioinformatic analysis, the tail fiber protein of phage kpssk3 was speculated to possess depolymerase activity towards EPS. By comparative genomics and phylogenetic analysis, it was determined that kpssk3 is a new T7-like virus and belongs to the subfamily Autographivirinae. The characterization and genomic analysis of kpssk3 will promote our understanding of phage biology and diversity and provide a potential strategy for controlling CRKP infection.

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Data availability statement

The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

We would like to thank Dr. Supeng Yin (Fourth Medical Center of PLA General Hospital) for English language editing.

Funding

This work was funded by the National Natural Science Foundation of China (No. 81571896 and no. 81772073), the Foundation of State Key Laboratory of Trauma, Burns and Combined Injury (no. SKLZZ201708), and the Technological Innovation Plan in Major Fields of Southwest Hospital, Key Projects (no. SWH2016ZDCX2001).

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Authors and Affiliations

  1. State Key Laboratory of Trauma, Burns and Combined Injury, Chongqing Key Laboratory for Proteomics Disease, Institute of Burn Research, Southwest Hospital, The Third Military Medical University (Army Medical University), Chongqing, 400038, China

    Yunlong Shi, Yu Chen, Zichen Yang, Yulong Zhang, Xinzhu Liu, Ping Chen, Meixi Liu, Cheng Zhang, Xiaoqiang Luo, Yajie Chen, Zhiqiang Yuan, Jing Chen, Yali Gong & Yizhi Peng

  2. Department of microbiology, College of Basic Medicine, Third Military Medical University (Army Medical University), Chongqing, China

    Zichen Yang

  3. Department of Plastic Surgery, No. 474 Hospital of PLA, Urumqi, China

    Yulong Zhang

  4. Department of Cardiothoracic Surgery, No. 958 Hospital of PLA, Chongqing, China

    Bo You

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  1. Yunlong Shi
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Contributions

YZP and YLG conceived and designed the experiments. YLS, YC, ZCY, YLZ, XZL and YJC performed the experiments. PC and BY analyzed the data. MXL, CZ, XQL, ZQY and JC contributed reagents and materials. YLS wrote the paper. All authors contributed toward revising the paper and agreed to be accountable for all aspects of the work.

Corresponding authors

Correspondence to Yali Gong or Yizhi Peng.

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All authors declare that they have no conflict of interest.

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No human participants or animals were used by any of the authors in this study.

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Handling Editor: T. K. Frey.

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Supplementary Fig. S1

(A) Plaque morphology of kpssk3; (B) transmission electron micrograph of kpssk3 (TIFF 1384 kb)

Supplementary Fig. S1

(A) Plaque morphology of kpssk3; (B) transmission electron micrograph of kpssk3 (TIFF 235 kb)

Supplementary Fig. S3

(A) Thermal stability of kpssk3; (B) pH stability of kpssk3 (TIFF 179 kb)

Supplementary material 4 (DOC 97 kb)

Supplementary material 5 (DOC 40 kb)

Supplementary material 6 (DOC 94 kb)

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Shi, Y., Chen, Y., Yang, Z. et al. Characterization and genome sequencing of a novel T7-like lytic phage, kpssk3, infecting carbapenem-resistant Klebsiella pneumoniae. Arch Virol 165, 97–104 (2020). https://doi.org/10.1007/s00705-019-04447-y

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