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

Freschi, Luca; Jeukens, Julie; Kukavica-Ibrulj, Irena; Boyle, Brian; Dupont, Marie-Josée; Laroche, Jérôme; Larose, Stéphane; Maaroufi, Halim; Fothergill, Joanne L.; Moore, Matthew; Winsor, Geoffrey L.; Aaron, Shawn D.; Barbeau, Jean; Bell, Scott C.; Burns, Jane L.; Cámara, Miguel; Cantin, André; Charette, Steve J.; Dewar, Ken; Déziel, Éric; Grimwood, Keith; Hancock, Robert E.W.; Harrison, Joe J.; Heeb, Stephan; Jelsbak, Lars; Jia, Baofeng; Kenna, Dervla T.; Kidd, Timothy J.; Klockgether, Jens; Lam, Joseph S.; Lamont, Iain L.; Lewenza, Shawn; Loman, Nick; Malouin, François; Manos, Jim; McArthur, Andrew G.; McKeown, Josie; Milot, Julie; Naghra, Hardeep; Nguyen, Dao; Pereira, Sheldon K.; Perron, Gabriel G.; Pirnay, Jean-Paul; Rainey, Paul B.; Rousseau, Simon; Santos, Pedro M.; Stephenson, Anne; Taylor, Véronique; Turton, Jane F.; Waglechner, Nicholas; Williams, Paul; Thrane, Sandra W.; Wright, Gerard D.; Brinkman, Fiona S.L.; Tucker, Nicholas P.; Tümmler, Burkhard; Winstanley, Craig; Levesque, Roger C.

Authors

Luca Freschi

Julie Jeukens

Irena Kukavica-Ibrulj

Brian Boyle

Marie-Josée Dupont

Jérôme Laroche

Stéphane Larose

Halim Maaroufi

Joanne L. Fothergill

Matthew Moore

Geoffrey L. Winsor

Shawn D. Aaron

Jean Barbeau

Scott C. Bell

Jane L. Burns

Miguel Cámara

André Cantin

Steve J. Charette

Ken Dewar

Éric Déziel

Keith Grimwood

Robert E.W. Hancock

Joe J. Harrison

Lars Jelsbak

Baofeng Jia

Dervla T. Kenna

Timothy J. Kidd

Jens Klockgether

Joseph S. Lam

Iain L. Lamont

Shawn Lewenza

Nick Loman

François Malouin

Jim Manos

Andrew G. McArthur

Josie McKeown

Julie Milot

Hardeep Naghra

Dao Nguyen

Sheldon K. Pereira

Gabriel G. Perron

Jean-Paul Pirnay

Paul B. Rainey

Simon Rousseau

Pedro M. Santos

Anne Stephenson

Véronique Taylor

Jane F. Turton

Nicholas Waglechner

PAUL WILLIAMS paul.williams@nottingham.ac.uk
Professor of Molecular Microbiology

Sandra W. Thrane

Gerard D. Wright

Fiona S.L. Brinkman

Nicholas P. Tucker

Burkhard Tümmler

Craig Winstanley

Roger C. Levesque



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.

Journal Article Type Article
Journal Frontiers in Microbiology
Electronic ISSN 1664-302X
Publisher Frontiers Media
Peer Reviewed Peer Reviewed
Volume 6
Issue 1036
APA6 Citation Freschi, L., Jeukens, J., Kukavica-Ibrulj, I., Boyle, B., Dupont, M., Laroche, J., …Levesque, R. C. (in press). Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Frontiers in Microbiology, 6(1036), https://doi.org/10.3389/fmicb.2015.01036
DOI https://doi.org/10.3389/fmicb.2015.01036
Keywords Pseudomonas aeruginosa, next-generation sequencing, bacterial genome, phylogeny, database,
cystic fibrosis, antibiotic resistance, clinical microbiology
Publisher URL http://journal.frontiersin.org/article/10.3389/fmicb.2015.01036/full
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0





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