Genomic analysis of Pseudomonas aeruginosa PA96, the host of carbapenem resistance plasmid pOZ176

Authors

  • Maxime Déraspe,

    1. Centre de Recherche en Infectiologie, CHU de Québec, Québec, QC, Canada
    2. Département de Biochimie, de microbiologie, et de bio-informatique, Université Laval, Québec, QC, Canada
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  • David C. Alexander,

    1. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
    2. Public Health Ontario Laboratories, Toronto, ON, Canada
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  • Jianhui Xiong,

    1. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
    Current affiliation:
    1. Microbiology, St. Joseph's Health Centre, Toronto, ON, Canada
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  • Jennifer H. Ma,

    1. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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  • Donald E. Low,

    1. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
    2. Public Health Ontario Laboratories, Toronto, ON, Canada
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    • Deceased.

  • Frances B. Jamieson,

    1. Public Health Ontario Laboratories, Toronto, ON, Canada
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  • Paul H. Roy

    Corresponding author
    1. Centre de Recherche en Infectiologie, CHU de Québec, Québec, QC, Canada
    2. Département de Biochimie, de microbiologie, et de bio-informatique, Université Laval, Québec, QC, Canada
    • Correspondence: Paul H. Roy, Centre de Recherche en Infectiologie, 2705 Boul. Laurier, Suite RC-709, Québec, QC G1V 4G2, Canada. Tel.: +1 418 654 2705; fax: +1 418 654 2715; e-mail: paul.roy@crchul.ulaval.ca

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Abstract

Pseudomonas aeruginosa PA96 is a clinical isolate from Guangzhou, China, that is multiresistant to antibiotics. We previously described the 500-kb IncP-2 plasmid, pOZ176 that encodes many resistance genes including the IMP-9 carbapenemase. Whole-genome sequencing of PA96 enabled characterization of its genomic islands, virulence factors, and chromosomal resistance genes. We filled gaps using PCR and used optical mapping to confirm the correct contig order. We automatically annotated the core genome and manually annotated the genomic islands. The genome is 6 444 091 bp and encodes 5853 ORFs. From the whole-genome sequence, we constructed a physical map and constructed a phylogenetic tree for comparison with sequenced P. aeruginosa strains. Analysis of known core genome virulence factors and resistance genes revealed few differences with other strains, but the major virulence island is closer to that of DK2 than to PA14. PA96 most closely resembles the environmental strain M18, and notably shares a common serotype, pyoverdin type, flagellar operon, type IV pilin, and several genomic islands with M18.

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