Abstract:
BACKGROUND: Adaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution
resulting in genomic diversity between strains of the same clonal lineage. In order to detect the impact of colonized
habitats on P. aeruginosa microevolution we determined the genomic diversity between the highly virulent cystic fibrosis
(CF) isolate CHA and two temporally and geographically unrelated clonal variants. The outcome was compared with the
intraclonal genome diversity between three more closely related isolates of another clonal complex.
RESULTS: The three clone CHA isolates differed in their core genome in several dozen strain specific nucleotide exchanges
and small deletions from each other. Loss of function mutations and non-conservative amino acid replacements affected
several habitat- and lifestyle-associated traits, for example, the key regulator GacS of the switch between acute and
chronic disease phenotypes was disrupted in strain CHA. Intraclonal genome diversity manifested in an individual
composition of the respective accessory genome whereby the highest number of accessory DNA elements was observed
for isolate PT22 from a polluted aquatic habitat. Little intraclonal diversity was observed between three spatiotemporally
related outbreak isolates of clone TB. Although phenotypically different, only a few individual SNPs and deletions were
detected in the clone TB isolates. Their accessory genome mainly differed in prophage-like DNA elements taken up by
one of the strains.
CONCLUSIONS: The higher geographical and temporal distance of the clone CHA isolates was associated with an increased
intraclonal genome diversity compared to the more closely related clone TB isolates derived from a common source
demonstrating the impact of habitat adaptation on the microevolution of P. aeruginosa. However, even short-term habitat
differentiation can cause major phenotypic diversification driven by single genomic variation events and uptake of phage
DNA.
