Frontiers in Microbiology (Sep 2015)

Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

  • Luca eFreschi,
  • Julie eJeukens,
  • Irena eKukavica-Ibrulj,
  • Brian eBoyle,
  • Marie-Josée eDupont,
  • Jérôme eLaroche,
  • Stéphane eLarose,
  • Halim eMaaroufi,
  • Joanne L. Fothergill,
  • Matthew eMoore,
  • Geoffrey L. Winsor,
  • Shawn D. Aaron,
  • Jean eBarbeau,
  • Scott C. Bell,
  • Jane L. Burns,
  • Miguel eCamara,
  • André eCantin,
  • Steve J Charette,
  • Steve J Charette,
  • Steve J Charette,
  • Ken eDewar,
  • Eric eDéziel,
  • Keith eGrimwood,
  • Robert E W Hancock,
  • Joe J. Harrison,
  • Stephan eHeeb,
  • Lars eJelsbak,
  • Baofeng eJia,
  • Dervla T. Kenna,
  • Timothy J. Kidd,
  • Timothy J. Kidd,
  • Jens eKlockgether,
  • Joseph S. Lam,
  • Iain L. Lamont,
  • Shawn eLewenza,
  • Nick eLoman,
  • Francois eMalouin,
  • Andrew G. McArthur,
  • Josie eMcKeown,
  • Julie eMilot,
  • Hardeep eNaghra,
  • Dao eNguyen,
  • Sheldon K. Pereira,
  • Gabriel G. Perron,
  • Jean-Paul ePirnay,
  • Paul. B. Rainey,
  • Simon eRousseau,
  • Pedro M. Santos,
  • Anne eStephenson,
  • Véronique eTaylor,
  • Jane F. Turton,
  • Nicholas eWaglechner,
  • Paul eWilliams,
  • Sandra eWingaard Thrane,
  • Gerard D. Wright,
  • Fiona S.L. Brinkman,
  • Nicholas P. Tucker,
  • Burkhard eTümmler,
  • Craig eWinstanley,
  • Roger C. Leveque

DOI
https://doi.org/10.3389/fmicb.2015.01036
Journal volume & issue
Vol. 6

Abstract

Read online

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.

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