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Open Access Research article

Genomic islands from five strains of Burkholderia pseudomallei

Apichai Tuanyok1, Benjamin R Leadem1, Raymond K Auerbach1, Stephen M Beckstrom-Sternberg12, James S Beckstrom-Sternberg1, Mark Mayo3, Vanaporn Wuthiekanun4, Thomas S Brettin5, William C Nierman67, Sharon J Peacock4, Bart J Currie3, David M Wagner1 and Paul Keim12*

Author Affiliations

1 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011-5640, USA

2 The Translational Genomics Research Institute, 445 N. Fifth St. Phoenix, AZ, 85004, USA

3 Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia

4 Mahidol-Oxford Research Unit, Mahidol University, Bangkok, Thailand

5 Los Alamos National Laboratory, Los Alamos, NM, 87545, USA

6 J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

7 George Washington University, 2300 Eye Street, NW, Washington DC, 20037, USA

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BMC Genomics 2008, 9:566  doi:10.1186/1471-2164-9-566

Published: 27 November 2008

Abstract

Background

Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species.

Results

We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3' end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described.

Conclusion

Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species.