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

Amandine Perrin (1, 2) , Elise Larsonneur (1, 2) , Ainsley Nicholson (3) , David Edwards (4) , Kristin Gundlach (5) , Anne Whitney (3) , Christopher Gulvik (3) , Melissa Bell (3) , Olaya Rendueles (1) , Jean Cury (1) , Perrine Hugon (1) , Dominique Clermont (6) , Vincent Enouf (7, 8) , Vladimir Loparev (3) , Phalasy Juieng (3) , Timothy Monson (5) , David Warshauer (3) , Lina Elbadawi (3) , Maroya Spalding Walters (3) , Matthew Crist (3) , Judith Noble-Wang (3) , Gwen Borlaug (3) , Eduardo P C Rocha (1) , Alexis Criscuolo (2) , Marie Touchon (1) , Jeffrey Davis (3) , Kathryn Holt (4) , John Mcquiston (3) , Sylvain Brisse (1, 9)

1 Génomique évolutive des Microbes / Microbial Evolutionary Genomics
2 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
3 CDC - Centers for Disease Control and Prevention [Atlanta]
4 University of Melbourne
5 WSLH - Wisconsin State Laboratory of Hygiene [Madison]
6 CIP - Collection de l'Institut Pasteur
7 PIBNet - Pasteur International Bioresources network
8 P2M - Plateforme de Microbiologie Mutualisée (PIBnet) - Mutualized Platform for Microbiology
9 Prévention et Thérapie Moléculaires des Maladies humaines

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.

Mots clés: Pathogens; Bacterial infection; Bacterial genetics; Bacterial genes

Domaines: Biodiversité et Ecologie; Bactériologie

Amandine Perrin, Elise Larsonneur, Ainsley Nicholson, David Edwards, Kristin Gundlach, et al.. Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. Nature Communications, 2017, 8 (1), pp.15483. ⟨10.1038/ncomms15483⟩. ⟨hal-02613118⟩