Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups.

Suzanne Bialek-Davenet (1, 2, 3) , Alexis Criscuolo (4, 1) , Florent Ailloud (2) , Virginie Passet (5, 1) , Louis Jones (6) , Anne-Sophie Delannoy-Vieillard (7) , Benoit Garin (8) , Simon Le Hello (9) , Guillaume Arlet (10, 11) , Marie-Hélène Nicolas-Chanoine (11, 3) , Dominique Decré (10, 11) , Sylvain Brisse (5, 1)

1 CNRS - Centre National de la Recherche Scientifique
2 Institut Pasteur [Paris]
3 Hôpital Beaujon
4 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
5 PF8 - Génotypage des Pathogènes et Santé Publique (Plate-forme)
6 Centre d'Informatique pour la Biologie
7 ERI - Environnement et Risques infectieux - Environment and Infectious Risks
8 Institut Pasteur de Madagascar
9 CNR-ESS - Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella
10 Hôpitaux de l'Est Parisien
11 INSERM - Institut National de la Santé et de la Recherche Médicale

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.

Domains: Life Sciences [q-bio]; Santé publique et épidémiologie

Suzanne Bialek-Davenet, Alexis Criscuolo, Florent Ailloud, Virginie Passet, Louis Jones, et al.. Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups.. Emerging Infectious Diseases, 2014, 20 (11), pp.1812-20. ⟨10.3201/eid2011.140206⟩. ⟨pasteur-01118613⟩