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

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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. ... view all 52 authors (2015)
  • Publisher: Frontiers Media SA
  • Journal: volume 6 (issn: 1664-302X, eissn: 1664-302X)
  • Related identifiers: pmc: PMC4586430, doi: 10.3389/fmicb.2015.01036, doi: 10.3389/fmicb.2015.01036, doi: 10.3389/fmicb.2015.01036/full
  • Subject: Pseudomonas aeruginosa | [ SDV ] Life Sciences [q-bio] | bacterial genome | next-generation sequencing | Microbiology | [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] | [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology | RC | database | Science & Technology | antibiotic resistance | cystic fibrosis | phylogeny | Perspective | clinical microbiology
    mesheuropmc: education

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. 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 genomiques 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 Sklodowska-Curie Postdoctoral Research Fellowship-MC RESPIRE2 1st round 4571-2013. IL is supported by grants from Cure Kids, 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/publishedVersion