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Open Access Research article

Burkholderia pseudomallei genome plasticity associated with genomic island variation

Sarinna Tumapa1, Matthew TG Holden2, Mongkol Vesaratchavest1, Vanaporn Wuthiekanun1, Direk Limmathurotsakul1, Wirongrong Chierakul1, Edward J Feil3, Bart J Currie4, Nicholas PJ Day15, William C Nierman67 and Sharon J Peacock15*

Author Affiliations

1 Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand

2 The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

3 Department of Biology and Biochemistry, University of Bath, UK

4 Menzies School of Health Research, Charles Darwin University, Darwin, Australia

5 Center for Clinical Vaccinology and Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, UK

6 J. Craig Venter Institute, Rockville, Maryland 20850, USA

7 The George Washington University School of Medicine, Department of Biochemistry and Molecular Biology, Washington DC 20037, USA

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BMC Genomics 2008, 9:190  doi:10.1186/1471-2164-9-190

Published: 25 April 2008

Abstract

Background

Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI) regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival.

Results

Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates) was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9), to 76% for a metabolic island (GI 16). The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands). The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3). The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27). The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing); these were ST 70 (n = 15 isolates), ST 54 (n = 11), and ST 167 (n = 9). The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained from the environment and from patients with melioidosis in order to examine the role of genomic islands in virulence and clinical associations. There was no reproducible association between the individual or cumulative presence of five GIs and a range of clinical features in 103 patients with melioidosis.

Conclusion

Horizontal gene transfer of mobile genetic elements can rapidly alter the gene repertoire of B. pseudomallei. This study confirms the utility of a range of approaches in defining the presence and significance of genomic variation in natural populations of B. pseudomallei.