Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB

Oliver Ki Bezuidt,Ina Attree,Jens Klockgether,Burkhard Tümmler,Sylvie Elsen,Colin F Davenport

doi:10.1186/1471-2164-14-416

Abstract

BackgroundAdaptation 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.ResultsThe 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.ConclusionsThe 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.

Highlights

Adaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage
Intraclonal whole-genome variation in P. aeruginosa has mainly been studied in isolates from cystic fibrosis (CF) lungs that had been collected from the same patient longitudinally or at one time point [8,9,10,11,12]
Intraclonal genome diversity in the two investigated strain triplets presented in a low number of strain-specific de novo mutations in the core genome and a variable composition of the accessory genome

Summary

Introduction

Adaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage. Pseudomonas aeruginosa is a metabolically versatile gamma-proteobacterium that preferentially thrives in aquatic habitats and the rhizosphere [1]. This opportunistic pathogen is the most dominant bacterium causing chronic airway infections in cystic fibrosis (CF) [2] and has become one of the most important causative agents of nosocomial infections, in intensive care units [3]. The paired isolates from one patient typically differed due to a few dozens of single nucleotide substitutions (SNPs) and small insertions/deletions (indels) in the core genome, a few RGPs in the accessory genome and occasionally one large deletion or inversion. Close to 1,000 de novo SNPs and indels, were gained in hypermutable strains defective in DNA repair [10,12]

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Conclusion