Luca Freschi 1 , Julie Jeukens 1 , Irena Kukavica-Ibrulj 1 , Brian Boyle 1 , Marie-Josée Dupont 1 , Jérôme Laroche 1 , Stéphane Larose 1 , Halim Maaroufi 1 , Joanne L. Fothergill 2 , Matthew Moore 2 , Geoffrey L. Winsor 3 , Shawn D. Aaron 4 , Jean Barbeau 5 , Scott C. Bell 6 , Jane L. Burns 7 , Miguel Camara 8 , André Cantin 9 , Steve J. Charette 1 , 10 , 11 , Ken Dewar 12 , Éric Déziel 13 , Keith Grimwood 14 , Robert E. W. Hancock 15 , Joe J. Harrison 16 , Stephan Heeb 8 , Lars Jelsbak 17 , Baofeng Jia 18 , Dervla T. Kenna 19 , Timothy J. Kidd 20 , 21 , Jens Klockgether 22 , Joseph S. Lam 23 , Iain L. Lamont 24 , Shawn Lewenza 16 , Nick Loman 25 , François Malouin 9 , Jim Manos 26 , Andrew G. McArthur 18 , Josie McKeown 8 , Julie Milot 27 , Hardeep Naghra 8 , Dao Nguyen 12 , 28 , Sheldon K. Pereira 18 , Gabriel G. Perron 29 , Jean-Paul Pirnay 30 , Paul B. Rainey 31 , 32 , Simon Rousseau 12 , Pedro M. Santos 33 , Anne Stephenson 34 , Véronique Taylor 23 , Jane F. Turton 19 , Nicholas Waglechner 18 , Paul Williams 8 , Sandra W. Thrane 17 , Gerard D. Wright 18 , Fiona S. L. Brinkman 3 , Nicholas P. Tucker 35 , Burkhard Tümmler 22 , Craig Winstanley 2 , Roger C. Levesque 1
29 September 2015
The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database ( http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care.