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

Freschi, Luca; Jeukens, Julie; Kukavica-Ibrulj, Irena; Boyle, Brian; Dupont, Marie-Jos�e; Laroche, J�r�me; Larose, St�phane; Maaroufi, Halim; Fothergill, Joanne L.; Moore, Matthew; Winsor, Geoffrey L.; Aaron, Shawn D.; Barbeau, Jean; Bell, Scott C.; Burns, Jane L.; C�mara, Miguel; Cantin, Andr�; Charette, Steve J.; Dewar, Ken; D�ziel, �ric; 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, Fran�ois; 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, V�ronique; Turton, Jane F.; Waglechner, Nicholas; Williams, Paul; Thrane, Sandra W.; Wright, Gerard D.; Brinkman, Fiona S.L.; Tucker, Nicholas P.; T�mmler, Burkhard; Winstanley, Craig; Levesque, Roger C.

doi:10.3389/fmicb.2015.01036

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

Freschi, Luca; Jeukens, Julie; Kukavica-Ibrulj, Irena; Boyle, Brian; Dupont, Marie-Jos?e; Laroche, J?r?me; Larose, St?phane; Maaroufi, Halim; Fothergill, Joanne L.; Moore, Matthew; Winsor, Geoffrey L.; Aaron, Shawn D.; Barbeau, Jean; Bell, Scott C.; Burns, Jane L.; C?mara, Miguel; Cantin, Andr?; Charette, Steve J.; Dewar, Ken; D?ziel, ?ric; 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, Fran?ois; 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, V?ronique; Turton, Jane F.; Waglechner, Nicholas; Williams, Paul; Thrane, Sandra W.; Wright, Gerard D.; Brinkman, Fiona S.L.; Tucker, Nicholas P.; T?mmler, Burkhard; Winstanley, Craig; Leve...

Authors

Luca Freschi

Julie Jeukens

Irena Kukavica-Ibrulj

Brian Boyle

Marie-Jos�e Dupont

J�r�me Laroche

St�phane Larose

Halim Maaroufi

Joanne L. Fothergill

Matthew Moore

Geoffrey L. Winsor

Shawn D. Aaron

Jean Barbeau

Scott C. Bell

Jane L. Burns

Professor MIGUEL CAMARA MIGUEL.CAMARA@NOTTINGHAM.AC.UK
PROFESSOR OF MOLECULAR MICROBIOLOGY

Andr� Cantin

Steve J. Charette

Ken Dewar

�ric D�ziel

Keith Grimwood

Robert E.W. Hancock

Joe J. Harrison

Dr STEPHAN HEEB stephan.heeb@nottingham.ac.uk
ASSISTANT PROFESSOR

Lars Jelsbak

Baofeng Jia

Dervla T. Kenna

Timothy J. Kidd

Jens Klockgether

Joseph S. Lam

Iain L. Lamont

Shawn Lewenza

Nick Loman

Fran�ois 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

V�ronique Taylor

Jane F. Turton

Nicholas Waglechner

Professor 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 T�mmler

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.

Citation

Freschi, L., Jeukens, J., Kukavica-Ibrulj, I., Boyle, B., Dupont, M.-J., Laroche, J., Larose, S., Maaroufi, H., Fothergill, J. L., Moore, M., Winsor, G. L., Aaron, S. D., Barbeau, J., Bell, S. C., Burns, J. L., Cámara, M., Cantin, A., Charette, S. J., Dewar, K., Déziel, É., …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

Journal Article Type	Article
Acceptance Date	Sep 11, 2015
Online Publication Date	Sep 29, 2015
Deposit Date	Jan 26, 2017
Publicly Available Date	Jan 26, 2017
Journal	Frontiers in Microbiology
Electronic ISSN	1664-302X
Publisher	Frontiers Media
Peer Reviewed	Peer Reviewed
Volume	6
Issue	1036
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
Public URL	https://nottingham-repository.worktribe.com/output/760382
Publisher URL	http://journal.frontiersin.org/article/10.3389/fmicb.2015.01036/full
Contract Date	Jan 26, 2017