Research article

Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

Jana M U'Ren^1* , James M Schupp^1* , Talima Pearson¹ , Heidie Hornstra¹ , Christine L Clark Friedman¹ , Kimothy L Smith¹ , Rebecca R Leadem Daugherty¹ , Shane D Rhoton¹ , Ben Leadem¹ , Shalamar Georgia¹ , Michelle Cardon¹ , Lynn Y Huynh¹ , David DeShazer² , Steven P Harvey³ , Richard Robison⁴ , Daniel Gal⁵ , Mark J Mayo⁵ , David Wagner¹ , Bart J Currie⁵ and Paul Keim¹

¹  Northern Arizona University, Center for Microbial Genetics and Genomics, Box 5640, Flagstaff Arizona, 86011 USA

²  U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, Maryland 21702-5011 USA

³  U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5454 USA

⁴  Brigham Young University, Provo, Utah 84602 USA

⁵  Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia

author email corresponding author email* Contributed equally

BMC Microbiology 2007, 7:23doi:10.1186/1471-2180-7-23

Published:	30 March 2007

Abstract

Background

The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations.

Results

B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10^-5 per locus per generation) to that of the most diverse tandemly repeated regions found in other less diverse bacteria.

Conclusion

The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were identical using previous typing methods. Given the health threat to humans and livestock and the potential for B. pseudomallei to be released intentionally, MLVA could prove to be an important tool for fine-scale epidemiological or forensic tracking of this increasingly important environmental pathogen.