Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium
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 avai...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
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Frontiers
2015
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| Online Access: | https://eprints.nottingham.ac.uk/40064/ |
| _version_ | 1848795977159278592 |
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| author | 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. |
| author_facet | 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. |
| author_sort | Freschi, Luca |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T19:40:39Z |
| format | Article |
| id | nottingham-40064 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:40:39Z |
| publishDate | 2015 |
| publisher | Frontiers |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-400642020-05-04T17:16:17Z https://eprints.nottingham.ac.uk/40064/ 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. 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. Frontiers 2015-09-29 Article PeerReviewed 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 and Levesque, Roger C. (2015) Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Frontiers in Microbiology, 6 (1036). pp. 1-8. ISSN 1664-302X Pseudomonas aeruginosa next-generation sequencing bacterial genome phylogeny database cystic fibrosis antibiotic resistance clinical microbiology http://journal.frontiersin.org/article/10.3389/fmicb.2015.01036/full doi:10.3389/fmicb.2015.01036 doi:10.3389/fmicb.2015.01036 |
| spellingShingle | Pseudomonas aeruginosa next-generation sequencing bacterial genome phylogeny database cystic fibrosis antibiotic resistance clinical microbiology 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. 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 |
| 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_short | 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 |
| topic | Pseudomonas aeruginosa next-generation sequencing bacterial genome phylogeny database cystic fibrosis antibiotic resistance clinical microbiology |
| url | https://eprints.nottingham.ac.uk/40064/ https://eprints.nottingham.ac.uk/40064/ https://eprints.nottingham.ac.uk/40064/ |