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

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 Hugon, Dominique Clermont, Vincent Enouf, Vladimir Loparev, Phalasy Juieng, Timothy Monson, David Warshauer, Lina I. Elbadawi, Maroya Spalding Walters, Matthew B. Crist, Judith Noble-Wang, Gwen Borlaug, Eduardo P. C. Rocha, Alexis Criscuolo, Marie Touchon, Jeffrey P. Davis, Kathryn E. Holt, John R. McQuiston () and Sylvain Brisse ()
Additional contact information
Amandine Perrin: Institut Pasteur, Microbial Evolutionary Genomics
Elise Larsonneur: Institut Pasteur, Microbial Evolutionary Genomics
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
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
Jean Cury: Institut Pasteur, Microbial Evolutionary Genomics
Perrine Hugon: Institut Pasteur, Microbial Evolutionary Genomics
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
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
Alexis Criscuolo: Institut Pasteur, Hub Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS
Marie Touchon: Institut Pasteur, Microbial Evolutionary Genomics
Jeffrey P. Davis: Division of Public Health, Wisconsin Department of Health Services
Kathryn E. Holt: Centre for Systems Genomics, 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

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: 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.

Date: 2017
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DOI: 10.1038/ncomms15483

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