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

Freschi, Luca; Jeukens, Julie; Kukavica-Ibrulj, Irene; Boyle, Brian; Dupont, Marie-Josee; Laroche, Jerome; Larose, Stephane; Maaroufi, Halim; Fothergill, Joanne L.; Moore, Matthew; Winsor, Geoffrey L.; Aaron, Shawn D.; Barbeau, Jean; Bell, Scott C.; Burns, Jane L.; Camara, Miguel; Cantin, Andre; Charette, Steve J.; Dewar, Ken; Deziel, Eric; Grimwood, Keith; Hancock, Robert E. W.; Harrison, Joe J.; Heebs, Stephan; Jelsbak, Lars; Jia, Baofeng; Kenna, Dervla T.; Kidd, Timothy J.; Klockgether, Jens; Lam, Joseph S.; Lamont, Iain L.; Lewenza, Shawn; Loman, Nick; Malouin, Francois; 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, P. M.; Stephenson, Anne; Taylor, Veronique; Turton, Jane F.; Waglechner, Nicholas; Williams, Paul

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

Detalhes bibliográficos
Autor(a) principal:	Freschi, Luca
Data de Publicação:	2015
Outros Autores:	Jeukens, Julie, Kukavica-Ibrulj, Irene, Boyle, Brian, Dupont, Marie-Josee, Laroche, Jerome, Larose, Stephane, Maaroufi, Halim, Fothergill, Joanne L., Moore, Matthew, Winsor, Geoffrey L., Aaron, Shawn D., Barbeau, Jean, Bell, Scott C., Burns, Jane L., Camara, Miguel, Cantin, Andre, Charette, Steve J., Dewar, Ken, Deziel, Eric, Grimwood, Keith, Hancock, Robert E. W., Harrison, Joe J., Heebs, Stephan, Jelsbak, Lars, Jia, Baofeng, Kenna, Dervla T., Kidd, Timothy J., Klockgether, Jens, Lam, Joseph S., Lamont, Iain L., Lewenza, Shawn, Loman, Nick, Malouin, Francois, 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, P. M., Stephenson, Anne, Taylor, Veronique, Turton, Jane F., Waglechner, Nicholas, Williams, Paul
Tipo de documento:	Artigo
Idioma:	eng
Título da fonte:	Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo:	http://hdl.handle.net/1822/51981
Resumo:	The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2015.01036

Metadados do item

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repository_id_str	7160
spelling	Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortiumPseudomonas aeruginosanext-generation sequencingbacterial genomephylogenydatabasecystic fibrosisantibiotic resistanceclinical microbiologyScience & TechnologyThe Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2015.01036The 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. aerugihosa 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.We express our gratitude to members of the Plateforme d’analyses génomiques and bioinformatics platform at IBIS. We also thank Tariq Elsayegh (Royal College of Surgeons in Ireland) for his assistance with annotation of polymyxin resistance genes. JJ is supported by a Cystic Fibrosis Canada postdoctoral fellowship. RL is funded by Cystic Fibrosis Canada and by a CIHR-UK team grant. CW, JF, and MM are supported by the UK Cystic Fibrosis Trust. CW and NL would like to acknowledge funding from Fight for Sight. JB was supported by NIH grant P30 DK089507. SB is supported by a Queensland Health Fellowship. SB, TK, PR, and KG were supported by grants by NHMRC (#455919) and the TPCH Foundation. TK is the recipient of an ERS-EU RESPIRE2 Marie Skłodowska-Curie Postdoctoral Research Fellowship— MC RESPIRE2 1st round 4571-2013. IL is supported by grants from CureKids, Cystic Fibrosis New Zealand, and the New Zealand Lotteries Board (Health). AM holds a Cisco Research Chair in Bioinformatics, supported by Cisco Systems Canada, Inc. GD Wright’s laboratory is funded by the Canadian Institutes of Health Research (CIHR), the Natural Sciences and Engineering Research Council (NSERC), and a Canada Research Chair. NW is supported by a CIHR Doctoral research award. GW and FB acknowledge Cystic Fibrosis Foundation Therapeutics and Genome Canada for support. ED’s laboratory is supported by Canadian Institutes of Health Research (CIHR) operating grant MOP-142466 and a Canada Research Chair.info:eu-repo/semantics/publishedVersionFrontiers MediaUniversidade do MinhoFreschi, LucaJeukens, JulieKukavica-Ibrulj, IreneBoyle, BrianDupont, Marie-JoseeLaroche, JeromeLarose, StephaneMaaroufi, HalimFothergill, Joanne L.Moore, MatthewWinsor, Geoffrey L.Aaron, Shawn D.Barbeau, JeanBell, Scott C.Burns, Jane L.Camara, MiguelCantin, AndreCharette, Steve J.Dewar, KenDeziel, EricGrimwood, KeithHancock, Robert E. W.Harrison, Joe J.Heebs, StephanJelsbak, LarsJia, BaofengKenna, Dervla T.Kidd, Timothy J.Klockgether, JensLam, Joseph S.Lamont, Iain L.Lewenza, ShawnLoman, NickMalouin, FrancoisManos, JimMcArthur, Andrew G.McKeown, JosieMilot, JulieNaghra, HardeepNguyen, DaoPereira, Sheldon K.Perron, Gabriel G.Pirnay, Jean-PaulRainey, Paul B.Rousseau, SimonSantos, P. M.Stephenson, AnneTaylor, VeroniqueTurton, Jane F.Waglechner, NicholasWilliams, Paul2015-09-292015-09-29T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/51981eng1664-302X10.3389/fmicb.2015.01036info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-05-11T05:36:09Zoai:repositorium.sdum.uminho.pt:1822/51981Portal AgregadorONGhttps://www.rcaap.pt/oai/openairemluisa.alvim@gmail.comopendoar:71602024-05-11T05:36:09Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv	Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium
title	Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium
spellingShingle	Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium Freschi, Luca Pseudomonas aeruginosa next-generation sequencing bacterial genome phylogeny database cystic fibrosis antibiotic resistance clinical microbiology Science & Technology
title_short	Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium
title_full	Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium
title_fullStr	Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium
title_full_unstemmed	Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium
title_sort	Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium
author	Freschi, Luca
author_facet	Freschi, Luca Jeukens, Julie Kukavica-Ibrulj, Irene Boyle, Brian Dupont, Marie-Josee Laroche, Jerome Larose, Stephane Maaroufi, Halim Fothergill, Joanne L. Moore, Matthew Winsor, Geoffrey L. Aaron, Shawn D. Barbeau, Jean Bell, Scott C. Burns, Jane L. Camara, Miguel Cantin, Andre Charette, Steve J. Dewar, Ken Deziel, Eric Grimwood, Keith Hancock, Robert E. W. Harrison, Joe J. Heebs, Stephan Jelsbak, Lars Jia, Baofeng Kenna, Dervla T. Kidd, Timothy J. Klockgether, Jens Lam, Joseph S. Lamont, Iain L. Lewenza, Shawn Loman, Nick Malouin, Francois 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, P. M. Stephenson, Anne Taylor, Veronique Turton, Jane F. Waglechner, Nicholas Williams, Paul
author_role	author
author2	Jeukens, Julie Kukavica-Ibrulj, Irene Boyle, Brian Dupont, Marie-Josee Laroche, Jerome Larose, Stephane Maaroufi, Halim Fothergill, Joanne L. Moore, Matthew Winsor, Geoffrey L. Aaron, Shawn D. Barbeau, Jean Bell, Scott C. Burns, Jane L. Camara, Miguel Cantin, Andre Charette, Steve J. Dewar, Ken Deziel, Eric Grimwood, Keith Hancock, Robert E. W. Harrison, Joe J. Heebs, Stephan Jelsbak, Lars Jia, Baofeng Kenna, Dervla T. Kidd, Timothy J. Klockgether, Jens Lam, Joseph S. Lamont, Iain L. Lewenza, Shawn Loman, Nick Malouin, Francois 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, P. M. Stephenson, Anne Taylor, Veronique Turton, Jane F. Waglechner, Nicholas Williams, Paul
author2_role	author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author
dc.contributor.none.fl_str_mv	Universidade do Minho
dc.contributor.author.fl_str_mv	Freschi, Luca Jeukens, Julie Kukavica-Ibrulj, Irene Boyle, Brian Dupont, Marie-Josee Laroche, Jerome Larose, Stephane Maaroufi, Halim Fothergill, Joanne L. Moore, Matthew Winsor, Geoffrey L. Aaron, Shawn D. Barbeau, Jean Bell, Scott C. Burns, Jane L. Camara, Miguel Cantin, Andre Charette, Steve J. Dewar, Ken Deziel, Eric Grimwood, Keith Hancock, Robert E. W. Harrison, Joe J. Heebs, Stephan Jelsbak, Lars Jia, Baofeng Kenna, Dervla T. Kidd, Timothy J. Klockgether, Jens Lam, Joseph S. Lamont, Iain L. Lewenza, Shawn Loman, Nick Malouin, Francois 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, P. M. Stephenson, Anne Taylor, Veronique Turton, Jane F. Waglechner, Nicholas Williams, Paul
dc.subject.por.fl_str_mv	Pseudomonas aeruginosa next-generation sequencing bacterial genome phylogeny database cystic fibrosis antibiotic resistance clinical microbiology Science & Technology
topic	Pseudomonas aeruginosa next-generation sequencing bacterial genome phylogeny database cystic fibrosis antibiotic resistance clinical microbiology Science & Technology
description	The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2015.01036
publishDate	2015
dc.date.none.fl_str_mv	2015-09-29 2015-09-29T00:00:00Z
dc.type.status.fl_str_mv	info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv	info:eu-repo/semantics/article
format	article
status_str	publishedVersion
dc.identifier.uri.fl_str_mv	http://hdl.handle.net/1822/51981
url	http://hdl.handle.net/1822/51981
dc.language.iso.fl_str_mv	eng
language	eng
dc.relation.none.fl_str_mv	1664-302X 10.3389/fmicb.2015.01036
dc.rights.driver.fl_str_mv	info:eu-repo/semantics/openAccess
eu_rights_str_mv	openAccess
dc.format.none.fl_str_mv	application/pdf
dc.publisher.none.fl_str_mv	Frontiers Media
publisher.none.fl_str_mv	Frontiers Media
dc.source.none.fl_str_mv	reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP
instname_str	Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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collection	Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv	Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv	mluisa.alvim@gmail.com
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Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

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