title: Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups.
abstract: Multidrug-resistant and highly virulent Klebsiella pneumoniae isolates are emerging, but the clonal groups (CGs) corresponding to these high-risk strains have remained imprecisely defined. We aimed to identify K. pneumoniae CGs on the basis of genome-wide sequence variation and to provide a simple bioinformatics tool to extract virulence and resistance gene data from genomic data. We sequenced 48 K. pneumoniae isolates, mostly of serotypes K1 and K2, and compared the genomes with 119 publicly available genomes. A total of 694 highly conserved genes were included in a core-genome multilocus sequence typing scheme, and cluster analysis of the data enabled precise definition of globally distributed hypervirulent and multidrug-resistant CGs. In addition, we created a freely accessible database, BIGSdb-Kp, to enable rapid extraction of medically and epidemiologically relevant information from genomic sequences of K. pneumoniae. Although drug-resistant and virulent K. pneumoniae populations were largely nonoverlapping, isolates with combined virulence and resistance features were detected.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Bialek-Davenet
authors.forename: Alexis
authors.initials: A
authors.lastname: Criscuolo
authors.forename: Florent
authors.initials: F
authors.lastname: Ailloud
authors.forename: Virginie
authors.initials: V
authors.lastname: Passet
authors.forename: Louis
authors.initials: L
authors.lastname: Jones
authors.forename: Anne-Sophie
authors.initials: AS
authors.lastname: Delannoy-Vieillard
authors.forename: Benoit
authors.initials: B
authors.lastname: Garin
authors.forename: Simon
authors.initials: S
authors.lastname: Le Hello
authors.forename: Guillaume
authors.initials: G
authors.lastname: Arlet
authors.forename: Marie-Hélène
authors.initials: MH
authors.lastname: Nicolas-Chanoine
authors.forename: Dominique
authors.initials: D
authors.lastname: Decré
authors.forename: Sylvain
authors.initials: S
authors.lastname: Brisse
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D016000:Cluster Analysis; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D007710:Klebsiella Infections / Q000453:epidemiology / Q000382:microbiology*; D007711:Klebsiella pneumoniae / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000472:pathogenicity; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D012703:Serotyping; D014774:Virulence / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents