Tandem Repeat Regions within the Burkholderia pseudomallei Genome and their Application for High-Resolution Genotyping

BackgroundThe facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized large 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 isolates including B. pseudomallei, B. mallei and B. thailandensis. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to analyze 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. ResultsB. pseudomallei contains a preponderance of large 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 were predominately found in intergenic regions of the genome. Across the geographically diverse isolates, the 32 VNTR loci displayed between 7 and 28 alleles, and Neis diversity values between 0.47 and 0.94 across all B. pseudomallei and B. mallei isolates. Mutation rates for these loci were comparable 10-5 per locus per generation to that of the most diverse tandemly repeated regions found in other less diverse bacteria. ConclusionsThe frequency, location and duplicate nature of large 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 genotyp