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Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain

Author

Listed:
  • Amandine Perrin

    (Institut Pasteur, Microbial Evolutionary Genomics
    CNRS, UMR 3525
    Institut Pasteur, Hub Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS)

  • Elise Larsonneur

    (Institut Pasteur, Microbial Evolutionary Genomics
    CNRS, UMR 3525
    CNRS, UMS 3601 IFB-Core)

  • Ainsley C. Nicholson

    (Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention)

  • David J. Edwards

    (Centre for Systems Genomics, University of Melbourne
    Bio21 Molecular Science and Biotechnology Institute, University of Melbourne)

  • Kristin M. Gundlach

    (Wisconsin State Laboratory of Hygiene)

  • Anne M. Whitney

    (Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention)

  • Christopher A. Gulvik

    (Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention)

  • Melissa E. Bell

    (Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention)

  • Olaya Rendueles

    (Institut Pasteur, Microbial Evolutionary Genomics
    CNRS, UMR 3525)

  • Jean Cury

    (Institut Pasteur, Microbial Evolutionary Genomics
    CNRS, UMR 3525)

  • Perrine Hugon

    (Institut Pasteur, Microbial Evolutionary Genomics
    CNRS, UMR 3525)

  • Dominique Clermont

    (CIP—Collection de l'Institut Pasteur, Institut Pasteur)

  • Vincent Enouf

    (Institut Pasteur, Pasteur International Bioresources network (PIBnet), Plateforme de Microbiologie Mutualisée (P2M))

  • Vladimir Loparev

    (Centers for Disease Control and Prevention)

  • Phalasy Juieng

    (Centers for Disease Control and Prevention)

  • Timothy Monson

    (Wisconsin State Laboratory of Hygiene)

  • David Warshauer

    (Wisconsin State Laboratory of Hygiene)

  • Lina I. Elbadawi

    (Epidemic Intelligence Service, Centers for Disease Control and Prevention
    Division of Public Health, Wisconsin Department of Health Services)

  • Maroya Spalding Walters

    (Centers for Disease Control and Prevention)

  • Matthew B. Crist

    (Centers for Disease Control and Prevention)

  • Judith Noble-Wang

    (Centers for Disease Control and Prevention)

  • Gwen Borlaug

    (Division of Public Health, Wisconsin Department of Health Services)

  • Eduardo P. C. Rocha

    (Institut Pasteur, Microbial Evolutionary Genomics
    CNRS, UMR 3525)

  • Alexis Criscuolo

    (Institut Pasteur, Hub Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS)

  • Marie Touchon

    (Institut Pasteur, Microbial Evolutionary Genomics
    CNRS, UMR 3525)

  • Jeffrey P. Davis

    (Division of Public Health, Wisconsin Department of Health Services)

  • Kathryn E. Holt

    (Centre for Systems Genomics, University of Melbourne
    Bio21 Molecular Science and Biotechnology Institute, University of Melbourne)

  • John R. McQuiston

    (Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention)

  • Sylvain Brisse

    (Institut Pasteur, Microbial Evolutionary Genomics
    CNRS, UMR 3525
    Institut Pasteur, Molecular Prevention and Therapy of Human Diseases)

Abstract

An atypically large outbreak of Elizabethkingia anophelis infections occurred in Wisconsin. Here we show that it was caused by a single strain with thirteen characteristic genomic regions. Strikingly, the outbreak isolates show an accelerated evolutionary rate and an atypical mutational spectrum. Six phylogenetic sub-clusters with distinctive temporal and geographic dynamics are revealed, and their last common ancestor existed approximately one year before the first recognized human infection. Unlike other E. anophelis, the outbreak strain had a disrupted DNA repair mutY gene caused by insertion of an integrative and conjugative element. This genomic change probably contributed to the high evolutionary rate of the outbreak strain and may have increased its adaptability, as many mutations in protein-coding genes occurred during the outbreak. This unique discovery of an outbreak caused by a naturally occurring mutator bacterial pathogen provides a dramatic example of the potential impact of pathogen evolutionary dynamics on infectious disease epidemiology.

Suggested Citation

  • Amandine Perrin & Elise Larsonneur & Ainsley C. Nicholson & David J. Edwards & Kristin M. Gundlach & Anne M. Whitney & Christopher A. Gulvik & Melissa E. Bell & Olaya Rendueles & Jean Cury & Perrine H, 2017. "Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain," Nature Communications, Nature, vol. 8(1), pages 1-12, August.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms15483
    DOI: 10.1038/ncomms15483
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