Dynamics of Pseudomonas aeruginosa genome evolution

Abstract

One of the hallmarks of the Gram-negative bacterium Pseudomonas aeruginosa is its ability to thrive in diverse environments that includes humans with a variety of debilitating diseases or immune deficiencies. Here we report the complete sequence and comparative analysis of the genomes of two representative P. aeruginosa strains isolated from cystic fibrosis (CF) patients whose genetic disorder predisposes them to infections by this pathogen. The comparison of the genomes of the two CF strains with those of other P. aeruginosa presents a picture of a mosaic genome, consisting of a conserved core component, interrupted in each strain by combinations of specific blocks of genes. These strain-specific segments of the genome are found in limited chromosomal locations, referred to as regions of genomic plasticity. The ability of P. aeruginosa to shape its genomic composition to favor survival in the widest range of environmental reservoirs, with corresponding enhancement of its metabolic capacity is supported by the identification of a genomic island in one of the sequenced CF isolates, encoding enzymes capable of degrading terpenoids produced by trees. This work suggests that niche adaptation is a major evolutionary force influencing the composition of bacterial genomes. Unlike genome reduction seen in host-adapted bacterial pathogens, the genetic capacity of P. aeruginosa is determined by the ability of individual strains to acquire or discard genomic segments, giving rise to strains with customized genomic repertoires. Consequently, this organism can survive in a wide range of environmental reservoirs that can serve as sources of the infecting organisms.

Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens

“…GIs found by IslandViewer did not contain flanking direct sequences compared with our results [20]. Mathee et al [21] identified more GI regions in P. aeruginosa PAO1 and PA14 than the current study, but did not accurately localize these GIs. Mavrodi et al [22] obtained GIs with incomplete flanking DRs in P. fluorescens Pf-5, in particular, Pf0-1GI-1 was divided into 2 parts [23].…”

“…The genomic location of six GIs in P. aeruginosa was identical to those in our previous report [18], but their mobility was not determined. A number of studies have also described the regions of GIs in these four strains [14,[19][20][21][22][23]. These data have been presented in comparison with the 11 GIs of the present study ( Table 4).…”

“…This result was similar to our study, however, we selected a more precise crossing-combining approach of primers [11], and also determined that PAO1GI-1 (prophage Pf4) not only exists in the chromosome, but also can be excised from the chromosome to form a circular intermediate. Mathee et al [21] also found a similar region (RGP5) with PAO1GI-1 ( Table 4) that only determined the excision of RGP5 from the genome. Further, the circular intermediate was not detected by Mathee et al [21] because GIs with unclear boundaries were identified and crossing-combining primers were nonspecific resulting in the inability to produce all four amplification products, including the circular intermediates.…”

“…Mathee et al [21] also found a similar region (RGP5) with PAO1GI-1 ( Table 4) that only determined the excision of RGP5 from the genome. Further, the circular intermediate was not detected by Mathee et al [21] because GIs with unclear boundaries were identified and crossing-combining primers were nonspecific resulting in the inability to produce all four amplification products, including the circular intermediates. PA14GI-4, namely PAPI-1, was also determined similarly [11].…”

Divergence of a strain of Pseudomonas aeruginosa during an outbreak of ovine mastitis

“…Insertions and deletions in the genome of strain PSE305 in comparison to the genome of strain PAO1 are summarised in Supplementary Tables 3 and 4. Many of these were located in previously reported regions of genome plasticity (Mathee et al, 2008). Most of the larger insertions corresponded to known genomic islands or prophages.…”