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Complete Genome Sequences of Leclercia sp. W6 and W17 Isolated from a Gastric Cancer Patient

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Abstract

Leclercia sp. W6 and W17, which belong to the Enterobacteriaceae, were isolated from a stomach sample from a 78-year-old female gastric cancer patient, and genomic sequencing and analysis were performed. The genome of Leclercia sp. W6 consists of one chromosome with a size of 4,945,486 bp, while that of Leclercia sp. W17 contains one chromosome and two plasmids with a total size of 5,125,645 bp. Average nucleotide identity (ANI) calculations indicated that strains W6 and W17 exhibited similarities < 91.0% to other strains within the Enterobacteriaceae, except for six Leclercia strains. Phylogenomic analysis based on core-genome showed that strains W6 and W17 belong to the genus Leclercia, and phylogenetic analysis based on ANI values revealed that strains W6 and W17 formed an independent clade from those six Leclercia strains. Furthermore, comparative genomic analysis revealed that strains W6 and W17 had 5086 orthologous clusters (OCs) in their pan-genomes, and 59 exclusive OCs which were absent in their closest relatives. Genomic annotations revealed that the genomes of strains W6 and W17 encoded genes related to multidrug resistance clusters, multiple antibiotic resistance loci, and multidrug efflux pumps and had an identical urease gene cluster and a dissimilatory nitrate reduction pathway. Bioinformatic analyses indicated that strains W6 and W17 represented a novel species within the genus Leclercia. Genomic annotations revealed that these strains encoded genes related to multidrug resistance, nitrate reduction, and urease activity, which contribute to gastric malignant transformation. This will broaden our knowledge of the genetic mechanisms of the Enterobacteriaceae and help improve the clinical conditions of gastric cancer patients.

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Abbreviations

ANI:

Average nucleotide identity

CARD:

Comprehensive antibiotic resistance database

COG:

Clusters of orthologous groups

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

OCs:

Orthologous clusters

ORFs:

Open reading frames

RAST:

Rapid annotation using subsystem technology

VFDB:

Virulence factors database

VDD:

Virulence, disease and defense

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Acknowledgements

This study is funded by the Zhejiang Provincial Department of Health (No. Y2017KY202), the Natural Science Foundation of Zhejiang Province (No. LQ19C010006), and the Scientific Research Foundation of Zhejiang Sci-Tech University (No. 17042187-Y).

Author information

Authors and Affiliations

  1. Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou, 310014, People’s Republic of China

    Yun-Yun Xu, Chao-Jie Huang & Xiao-Wu Xu

  2. Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People’s Republic of China

    Lin Xu & Xue-Wei Xu

  3. College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People’s Republic of China

    Lin Xu

  4. College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310012, People’s Republic of China

    Xia-Wei Jiang

  5. Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Xuhui District, 274th Dong’an Road, Shanghai, 200032, People’s Republic of China

    Xiao-Wu Xu

  6. Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China

    Xiao-Wu Xu

  7. Shanghai Pancreatic Cancer Institute, Shanghai, 200032, People’s Republic of China

    Xiao-Wu Xu

  8. Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, People’s Republic of China

    Xiao-Wu Xu

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  1. Yun-Yun Xu
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Correspondence to Xiao-Wu Xu.

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All authors declare that they have no conflicts of interest.

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The genome sequences of Leclercia sp. W6 and W17 have been deposited in DDBJ/EMBL/GenBank under accession number CP031104 for the chromosome of strain W6 and CP031101-CP031103 for the chromosome and two plasmids of strain W17.

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Our study was approved by the Ethics Committee of the Zhejiang Provincial People's Hospital (2019KY028).

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Xu, YY., Huang, CJ., Xu, L. et al. Complete Genome Sequences of Leclercia sp. W6 and W17 Isolated from a Gastric Cancer Patient. Curr Microbiol 77, 2775–2782 (2020). https://doi.org/10.1007/s00284-020-02075-3

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  • DOI: https://doi.org/10.1007/s00284-020-02075-3

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