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Open Access Research article

Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB

Oliver KI Bezuidt12, Jens Klockgether1*, Sylvie Elsen3456, Ina Attree3456, Colin F Davenport1 and Burkhard Tümmler17

Author Affiliations

1 Klinische Forschergruppe, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover D-30625, Germany

2 Bioinformatics and Computational Biology Unit; Department of Biochemistry, University of Pretoria, Pretoria, South Africa

3 INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble, France

4 CNRS, ERL 5261, Bacterial Pathogenesis and Cellular Responses, Grenoble, France

5 UJF-Grenoble 1, Grenoble F-38041, France

6 6CEA, DSV/iRTSV, Grenoble F-38054, France

7 Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research, Hannover, Germany

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BMC Genomics 2013, 14:416  doi:10.1186/1471-2164-14-416

Published: 22 June 2013

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.

Keywords:
Pseudomonas aeruginosa; Microevolution; Habitat adaptation; Genome diversity