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

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 Camara; André Cantin; Steve J. Charette; Ken Dewar; Éric Déziel; Keith Grimwood; Robert E.W. Hancock; Joe J. Harrison; Stephan Heeb; 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; Sandra W. Thrane; Gerard D. Wright; Fiona S.L. Brinkman; Nicholas P. Tucker; Burkhard Tümmler; Craig Winstanley; Roger C. Levesque

doi:10.3389/fmicb.2015.01036

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

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 Camara, André Cantin, Steve J. Charette, Ken Dewar, Éric DézielKeith Grimwood, Robert E.W. Hancock, Joe J. Harrison, Stephan Heeb, 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, Sandra W. Thrane, Gerard D. Wright, Fiona S.L. Brinkman, Nicholas P. Tucker, Burkhard Tümmler, Craig Winstanley, Roger C. Levesque

Research output: Contribution to journal › Article › peer-review

119 Citations (Scopus)

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.

Original language	English
Article number	01036
Journal	Frontiers in Microbiology
Volume	6
Issue number	SEP
DOIs	https://doi.org/10.3389/fmicb.2015.01036
Publication status	Published or Issued - 2015
Externally published	Yes

Keywords

Antibiotic resistance
Bacterial genome
Clinical microbiology
Cystic fibrosis
Database
Next-generation sequencing
Phylogeny
Pseudomonas aeruginosa

ASJC Scopus subject areas

Microbiology
Microbiology (medical)

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10.3389/fmicb.2015.01036

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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., Camara, M., Cantin, A., Charette, S. J., Dewar, K., ... Levesque, R. C. (2015). Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Frontiers in Microbiology, 6(SEP), Article 01036. https://doi.org/10.3389/fmicb.2015.01036

@article{bdbdf802d11b4f02a940495991d6b0bd,

title = "Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium",

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 = "Antibiotic resistance, Bacterial genome, Clinical microbiology, Cystic fibrosis, Database, Next-generation sequencing, Phylogeny, Pseudomonas aeruginosa",

author = "Luca Freschi and Julie Jeukens and Irena Kukavica-Ibrulj and Brian Boyle and Dupont, {Marie Jos{\'e}e} and J{\'e}r{\^o}me Laroche and St{\'e}phane Larose and Halim Maaroufi and Fothergill, {Joanne L.} and Matthew Moore and Winsor, {Geoffrey L.} and Aaron, {Shawn D.} and Jean Barbeau and Bell, {Scott C.} and Burns, {Jane L.} and Miguel Camara and Andr{\'e} Cantin and Charette, {Steve J.} and Ken Dewar and {\'E}ric D{\'e}ziel and Keith Grimwood and Hancock, {Robert E.W.} and Harrison, {Joe J.} and Stephan Heeb and Lars Jelsbak and Baofeng Jia and Kenna, {Dervla T.} and Kidd, {Timothy J.} and Jens Klockgether and Lam, {Joseph S.} and Lamont, {Iain L.} and Shawn Lewenza and Nick Loman and Fran{\c c}ois Malouin and Jim Manos and McArthur, {Andrew G.} and Josie McKeown and Julie Milot and Hardeep Naghra and Dao Nguyen and Pereira, {Sheldon K.} and Perron, {Gabriel G.} and Pirnay, {Jean Paul} and Rainey, {Paul B.} and Simon Rousseau and Santos, {Pedro M.} and Anne Stephenson and V{\'e}ronique Taylor and Turton, {Jane F.} and Nicholas Waglechner and Paul Williams and Thrane, {Sandra W.} and Wright, {Gerard D.} and Brinkman, {Fiona S.L.} and Tucker, {Nicholas P.} and Burkhard T{\"u}mmler and Craig Winstanley and Levesque, {Roger C.}",

note = "Publisher Copyright: {\textcopyright} 2015 Freschi, Jeukens, Kukavica-Ibrulj, Boyle, Dupont, Laroche, Larose, Maaroufi, Fothergill, Moore, Winsor.",

year = "2015",

doi = "10.3389/fmicb.2015.01036",

language = "English",

volume = "6",

journal = "Frontiers in Microbiology",

issn = "1664-302X",

publisher = "Frontiers Media S.A.",

number = "SEP",

}

Freschi, L, Jeukens, J, Kukavica-Ibrulj, I, Boyle, B, Dupont, MJ, Laroche, J, Larose, S, Maaroufi, H, Fothergill, JL, Moore, M, Winsor, GL, Aaron, SD, Barbeau, J, Bell, SC, Burns, JL, Camara, M, Cantin, A, Charette, SJ, Dewar, K, Déziel, É, Grimwood, K, Hancock, REW, Harrison, JJ, Heeb, S, Jelsbak, L, Jia, B, Kenna, DT, Kidd, TJ, Klockgether, J, Lam, JS, Lamont, IL, Lewenza, S, Loman, N, Malouin, F, Manos, J, McArthur, AG, McKeown, J, Milot, J, Naghra, H, Nguyen, D, Pereira, SK, Perron, GG, Pirnay, JP, Rainey, PB, Rousseau, S, Santos, PM, Stephenson, A, Taylor, V, Turton, JF, Waglechner, N, Williams, P, Thrane, SW, Wright, GD, Brinkman, FSL, Tucker, NP, Tümmler, B, Winstanley, C & Levesque, RC 2015, 'Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium', Frontiers in Microbiology, vol. 6, no. SEP, 01036. https://doi.org/10.3389/fmicb.2015.01036

TY - JOUR

T1 - Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

AU - Freschi, Luca

AU - Jeukens, Julie

AU - Kukavica-Ibrulj, Irena

AU - Boyle, Brian

AU - Dupont, Marie Josée

AU - Laroche, Jérôme

AU - Larose, Stéphane

AU - Maaroufi, Halim

AU - Fothergill, Joanne L.

AU - Moore, Matthew

AU - Winsor, Geoffrey L.

AU - Aaron, Shawn D.

AU - Barbeau, Jean

AU - Bell, Scott C.

AU - Burns, Jane L.

AU - Camara, Miguel

AU - Cantin, André

AU - Charette, Steve J.

AU - Dewar, Ken

AU - Déziel, Éric

AU - Grimwood, Keith

AU - Hancock, Robert E.W.

AU - Harrison, Joe J.

AU - Heeb, Stephan

AU - Jelsbak, Lars

AU - Jia, Baofeng

AU - Kenna, Dervla T.

AU - Kidd, Timothy J.

AU - Klockgether, Jens

AU - Lam, Joseph S.

AU - Lamont, Iain L.

AU - Lewenza, Shawn

AU - Loman, Nick

AU - Malouin, François

AU - Manos, Jim

AU - McArthur, Andrew G.

AU - McKeown, Josie

AU - Milot, Julie

AU - Naghra, Hardeep

AU - Nguyen, Dao

AU - Pereira, Sheldon K.

AU - Perron, Gabriel G.

AU - Pirnay, Jean Paul

AU - Rainey, Paul B.

AU - Rousseau, Simon

AU - Santos, Pedro M.

AU - Stephenson, Anne

AU - Taylor, Véronique

AU - Turton, Jane F.

AU - Waglechner, Nicholas

AU - Williams, Paul

AU - Thrane, Sandra W.

AU - Wright, Gerard D.

AU - Brinkman, Fiona S.L.

AU - Tucker, Nicholas P.

AU - Tümmler, Burkhard

AU - Winstanley, Craig

AU - Levesque, Roger C.

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

KW - Antibiotic resistance

KW - Bacterial genome

KW - Clinical microbiology

KW - Cystic fibrosis

KW - Database

KW - Next-generation sequencing

KW - Phylogeny

KW - Pseudomonas aeruginosa

UR - http://www.scopus.com/inward/record.url?scp=84946833974&partnerID=8YFLogxK

U2 - 10.3389/fmicb.2015.01036

DO - 10.3389/fmicb.2015.01036

M3 - Article

AN - SCOPUS:84946833974

SN - 1664-302X

VL - 6

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

IS - SEP

M1 - 01036

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

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