Abstract
The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.
Highlights
The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes
KRP1 belongs to the P. aeruginosa species
We employed a combination of a short and long read assembler, followed by a manual curation to ensure fulfillment of the suggested 3 C criteria[22]. Synteny comparisons between this initial in silico assembly and closely related P. aeruginosa strains showed multiple rearrangements of the open reading frames (ORFs) encoded on the putative mega plasmid
Summary
The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For the frequently researched P. aeruginosa PA14 strain this increased virulence, as compared to the type strain PAO1, is mainly due to the presence of additional virulence factors Their genes are predominantly clustered on two genomic islands (GIs) termed P. aeruginosa pathogenicity islands (PAPI)[5]. By assigning different functional modules, it can be sorted into (i) integrative and conjugative elements (ICEs), (ii) replacement islands, (iii) prophages and phage-like elements, and (iv) transposons, insertion sequences (ISs) and integrons[7] These genes are only shared by certain, but not all strains of the species and are mainly located in GIs and genomic islets (GIts).
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