title: Genomic analysis of Pseudomonas aeruginosa PA96, the host of carbapenem resistance plasmid pOZ176.
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.
authors.affiliation: Centre de Recherche en Infectiologie, CHU de Québec, Québec, QC, Canada; Département de Biochimie, de microbiologie, et de bio-informatique, Université Laval, Québec, QC, Canada.
authors.forename: Maxime
authors.initials: M
authors.lastname: Déraspe
authors.forename: David C
authors.initials: DC
authors.lastname: Alexander
authors.forename: Jianhui
authors.initials: J
authors.lastname: Xiong
authors.forename: Jennifer H
authors.initials: JH
authors.lastname: Ma
authors.forename: Donald E
authors.initials: DE
authors.lastname: Low
authors.forename: Frances B
authors.initials: FB
authors.lastname: Jamieson
authors.forename: Paul H
authors.initials: PH
authors.lastname: Roy
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D015780:Carbapenems / Q000494:pharmacology*; D002681:China; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D016680:Genome, Bacterial; D044404:Genomic Islands; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D020161:Physical Chromosome Mapping; D010957:Plasmids; D011552:Pseudomonas Infections / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D037521:Virulence Factors / Q000235:genetics; D018440:beta-Lactam Resistance
chemical_list: D000900:Anti-Bacterial Agents; D015780:Carbapenems; D004269:DNA, Bacterial; D037521:Virulence Factors
keywords: bioinformatics; genomic islands; genomics; resistance; virulence