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

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 Ken Dewar 11 Éric Déziel 12 Keith Grimwood 13 Robert E W Hancock 14 Joe J Harrison 15 Stephan Heeb 8 Lars Jelsbak 16 Baofeng Jia 17 Dervla T Kenna 18 Timothy J Kidd 19, 20 Jens Klockgether 21 Joseph S Lam 22 Iain L Lamont 23 Shawn Lewenza 15 Nick Loman 24 François Malouin 9 Jim Manos 25 Andrew G Mcarthur 17 Josie Mckeown 8 Julie Milot 26 Hardeep Naghra 8 Dao Nguyen 11 Sheldon K Pereira 17 Gabriel G Perron 27 Jean-Paul Pirnay 28 Paul B Rainey 29, 30 Simon Rousseau 11 Pedro M Santos 31 Anne Stephenson 32 Véronique Taylor 22 Jane F Turton 18 Nicholas Waglechner 17 Paul Williams 8 Sandra W Thrane 16 Gerard D Wright 17 Fiona S L Brinkman 3 Nicholas P Tucker 33 Burkhard Tümmler 21 Craig Winstanley 2 Roger C Levesque 1, *
* Corresponding author
1 ULaval - Université Laval [Québec]
2 University of Liverpool
3 SFU.ca - Simon Fraser University
4 OHRI - Ottawa Hospital Research Institute [Ottawa]
5 UdeM - Université de Montréal
6 QIMR Berghofer Medical Research Institute
7 University of Washington School of Medicine
8 UON - University of Nottingham, UK
9 UdeS - Université de Sherbrooke
10 Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie
11 McGill University = Université McGill [Montréal, Canada]
12 INRS-IAF - Institut Armand Frappier
13 Griffith University [Brisbane]
14 UBC - University of British Columbia
15 University of Calgary
16 DTU - Technical University of Denmark [Lyngby]
17 McMaster University [Hamilton, Ontario]
18 Public Health England [London]
19 University of Queensland [Brisbane]
20 QUB - Queen's University [Belfast]
21 Klinische Forschergruppe
22 University of Guelph
23 University of Otago [Dunedin, Nouvelle-Zélande]
24 University of Birmingham [Birmingham]
25 The University of Sydney
26 IUCPQ - Institut Universitaire de Cardiologie et de Pneumologie de Québec
27 Bard College Annandale
28 Queen Astrid Military Hospital [Brussels]
29 Max Planck Institute for Evolutionary Biology
30 Massey University
31 University of Minho [Braga]
32 St. Michael's Hospital
33 University of Strathclyde [Glasgow]
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.
Keywords : phylogeny next-generation sequencing database cystic fibrosis clinical microbiology bacterial genome antibiotic resistance Pseudomonas aeruginosa
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Submitted on : Friday, August 5, 2016 - 4:21:35 PM
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Luca Freschi, Julie Jeukens, Irena Kukavica-Ibrulj, Brian Boyle, Marie-Josée Dupont, et al.. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium.. Frontiers in Microbiology, Frontiers Media, 2015, 6, pp.1036. ⟨10.3389/fmicb.2015.01036⟩. ⟨pasteur-01352145⟩

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