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

摘要

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 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. Results:B. 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 Nei's 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. Conclusions:The 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.