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

Freschi, Luca and Jeukens, Julie and Kukavica-Ibrulj, Irena and Boyle, Brian and Dupont, Marie-Josée and Laroche, Jérôme and Larose, Stéphane and Maaroufi, Halim and Fothergill, Joanne L. and Moores, Matthew and Winsor, Geoffrey L. and Aaron, Shawn D. and Barbeau, Jean and Bell, Scott C. and Burns, Jane L. and Camara, Miguel and Cantin, André and Charette, Steve J. and Dewar, Ken and Déziel, Éric and Grimwood, Keith and Hancock, Robert E. W. and Harrison, Joe J. and Heeb, Stephan and Jelsbak, Lars and Jia, Baofeng and Kenna, Dervla T. and Kidd, Timothy J. and Klockgether, Jens and Lam, Joseph S. and Lamont, Iain L. and Lewenza, Shawn and Loman, Nick and Malouin, François and Manos, Jim and McArthur, Andrew G. and McKeown, Josie and Milot, Julie and Naghra, Hardeep and Nguyen, Dao and Pereira, Sheldon K. and Perron, Gabriel G. and Pirnay, Jean-Paul and Rainey, Paul B. and Rousseau, Simon and Santos, Pedro M. and Stephenson, Anne and Taylor, Véronique and Turton, Jane F. and Waglechner, Nicholas and Williams, Paul and Thrane, Sandra W. and Wright, Gerard D. and Brinkman, Fiona S. L. and Tucker, Nicholas P. and Tümmler, Burkhard and Winstanley, Craig and Levesque, Roger C. (2015) Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Frontiers in Microbiology, 6. 1036. ISSN 1664-302X (https://doi.org/10.3389/fmicb.2015.01036)

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Abstract

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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