GBE A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter Julie Jeukens1,LucaFreschi1, Antony T. Vincent1,2,3, Jean-Guillaume Emond-Rheault1, Irena Kukavica-Ibrulj1, Steve J. Charette1,2,3, and Roger C. Levesque1,* 1Institut de Biologie Inte´grative et des Syste`mes (IBIS), Universite´ Laval, Quebec City, Quebec, Canada 2Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Que´bec (CRIUCPQ), Quebec City, Quebec, Canada 3De´partement de Biochimie, de Microbiologie et de Bio-informatique, Universite´ Laval, Quebec City, Quebec, Canada *Corresponding author: E-mail:
[email protected]. Accepted: April 4, 2017 Data deposition: This project has been deposited at NCBI under the accession PRJNA343957. Abstract Over the past decade, there has been a rising interest in Achromobacter sp., an emerging opportunistic pathogen responsible for nosocomial and cystic fibrosis lung infections. Species of this genus are ubiquitous in the environment, can outcompete resident microbiota, and are resistant to commonly used disinfectants as well as antibiotics. Nevertheless, the Achromobacter genus suf- fers from difficulties in diagnosis, unresolved taxonomy and limited understanding of how it adapts to the cystic fibrosis lung, not to mention other host environments. The goals of this first genus-wide comparative genomics study were to clarify the taxonomy of this genus and identify genomic features associated with pathogenicity and host adaptation. This was done with a widely applicable approach based on pan-genome analysis. First, using all publicly available genomes, a combination of phylogenetic analysis based on 1,780 conserved genes with average nucleotide identity and accessory genome composition allowed the identi- fication of a largely clinical lineage composed of Achromobacter xylosoxidans, Achromobacter insuavis, Achromobacter dolens,and Achromobacter ruhlandii.