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Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei

Author

Listed:
  • Leah W. Roberts

    (The University of Queensland
    The University of Queensland
    The University of Queensland)

  • Patrick N. A. Harris

    (The University of Queensland
    Pathology Queensland, Central Microbiology)

  • Brian M. Forde

    (The University of Queensland
    The University of Queensland
    The University of Queensland)

  • Nouri L. Ben Zakour

    (The University of Queensland
    The University of Queensland
    The University of Queensland)

  • Elizabeth Catchpoole

    (Pathology Queensland, Central Microbiology)

  • Mitchell Stanton-Cook

    (The University of Queensland
    The University of Queensland)

  • Minh-Duy Phan

    (The University of Queensland
    The University of Queensland)

  • Hanna E. Sidjabat

    (The University of Queensland
    The University of Queensland)

  • Haakon Bergh

    (Pathology Queensland, Central Microbiology)

  • Claire Heney

    (Pathology Queensland, Central Microbiology)

  • Jayde A. Gawthorne

    (The University of Queensland
    The University of Queensland)

  • Jeffrey Lipman

    (The University of Queensland
    The University of Queensland)

  • Anthony Allworth

    (Royal Brisbane & Women’s Hospital)

  • Kok-Gan Chan

    (University of Malaya
    Jiangsu University)

  • Teik Min Chong

    (University of Malaya)

  • Wai-Fong Yin

    (University of Malaya)

  • Mark A. Schembri

    (The University of Queensland
    The University of Queensland)

  • David L. Paterson

    (The University of Queensland
    The University of Queensland)

  • Scott A. Beatson

    (The University of Queensland
    The University of Queensland
    The University of Queensland)

Abstract

Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to characterise a hospital outbreak of blaIMP-4 carbapenemase-producing E. hormaechei. Using Illumina sequencing, we determined that all outbreak strains were sequence type 90 (ST90) and near-identical. Comparison to publicly available data linked all outbreak isolates to a 2013 isolate from the same ward, suggesting an environmental source in the hospital. Using Pacific Biosciences sequencing, we resolved the complete context of the blaIMP-4 gene on a large IncHI2 plasmid carried by all IMP-4-producing strains across different hospitals. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing. Finally, Oxford Nanopore sequencing rapidly resolved the true relationship of subsequent isolates to the initial outbreak. Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak.

Suggested Citation

  • Leah W. Roberts & Patrick N. A. Harris & Brian M. Forde & Nouri L. Ben Zakour & Elizabeth Catchpoole & Mitchell Stanton-Cook & Minh-Duy Phan & Hanna E. Sidjabat & Haakon Bergh & Claire Heney & Jayde A, 2020. "Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-019-14139-5
    DOI: 10.1038/s41467-019-14139-5
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    Cited by:

    1. Nenad Macesic & Jane Hawkey & Ben Vezina & Jessica A. Wisniewski & Hugh Cottingham & Luke V. Blakeway & Taylor Harshegyi & Katherine Pragastis & Gnei Zweena Badoordeen & Amanda Dennison & Denis W. Spe, 2023. "Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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