Poster Presentation BACPATH 2019

Detailed genomic analysis of Pseudomonas aeruginosa piliated reference strain PAK (#220)

Geraldine J Sullivan 1 , Laura M Nolan 2 , Cynthia Whitchurch 3 , Alain A. M. Filloux 2 , Julian Parkhill 4 , Amy K Cain 1
  1. Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
  2. MRC Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington, London, England
  3. ithree Institute, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
  4. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, England

Pseudomonas aeruginosa is a deadly opportunistic pathogen that has been flagged by the World Health Organisation and classed as one of the highly drug-resistant nosocomial "ESKAPE" pathogens. First described in 1971, P. aeruginosa strain PAK is a piliated laboratory reference strain, globally used to study P. aeruginosa virulence and pathogenesis. Despite this, a closed, high quality whole genome sequence (WGS) does not yet exist. Here, we report the WGS of P. aeruginosa PAK. A Pacific Biosciences (PacBio) RS II sequencing platform was used for WGS, generating 6,395,872 base pairs in one single chromosomal contig with over 65x coverage. The PAK genome contains 5763 CDS and 97 RNA, with an average GC content of 66.44%. De novo annotation was performed using PROKKA[1] followed by a secondary annotation transfer from reference strain PAO1 with RATT[2]. Further manual annotation was performed by searching for resistance genes using ResFinder 2.0[3], and 5 acquired resistance genes were identified, all of which are also in PAO1. PHAST[4] was used to identify 2 potential bacteriophages and IslandViewer 4[5] identified 8 genomic islands. The type IV pilus genes pilA-F, pilG-K and chA-C, pilM-Q, pilR-Z, and fimL, S-V were identified. The 3 Type VI secretion system (T6SS) clusters H1, H2 and H3 were also identified. Comparisons of PAK with reference strain PAO1 revealed 44,127 SNPs between the strains and 5421 orthologous genes, as defined by OrthoFinder[6] using default settings. We identified a large inversion of 4.19 Mbp between the strains and the possible insertion site: two sets of rRNA genes of 5847 bp with >99% sequence identity flank the inversion in a complementary orientation. The complete genome sequence of P. aeruginosa PAK will advance future understanding of this pathogen, whilst also allowing decades of research on this strain to be placed into genomic context.

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