title: Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis.
abstract: Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology.
authors.affiliation: Unité Environnement et Santé, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, France, Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, France, Laboratoire de Microbiologie clinique et environnementale, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France.|Laboratoire de Microbiologie Clinique, Institut Pasteur de Bangui, Bangui, Central African Republic.
authors.forename: Sebastien
authors.initials: S
authors.lastname: Breurec
authors.affiliation: Institut Pasteur, Hub Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, Paris, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Criscuolo
authors.affiliation: Unité Environnement et Risques Infectieux, Institut Pasteur, Paris, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Diancourt
authors.affiliation: Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.|UMR 3525, CNRS, Paris, France.
authors.forename: Olaya
authors.initials: O
authors.lastname: Rendueles
authors.affiliation: Unité Environnement et Risques Infectieux, Institut Pasteur, Paris, France.
authors.forename: Mathias
authors.initials: M
authors.lastname: Vandenbogaert
authors.affiliation: Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.|UMR 3525, CNRS, Paris, France.
authors.forename: Virginie
authors.initials: V
authors.lastname: Passet
authors.affiliation: Unité Environnement et Risques Infectieux, Institut Pasteur, Paris, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Caro
authors.affiliation: Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.|UMR 3525, CNRS, Paris, France.
authors.forename: Eduardo P C
authors.initials: EP
authors.lastname: Rocha
authors.affiliation: Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.|UMR 3525, CNRS, Paris, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Touchon
authors.affiliation: Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.|UMR 3525, CNRS, Paris, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Brisse
mesh_terms: D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D041965:Flavobacteriaceae / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D016680:Genome, Bacterial; D010802:Phylogeny; D014774:Virulence / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements