U'Ren Jana M, Schupp James M, Pearson Talima, Hornstra Heidie, Friedman Christine L Clark, Smith Kimothy L, Daugherty Rebecca R Leadem, Rhoton Shane D, Leadem Ben, Georgia Shalamar, Cardon Michelle, Huynh Lynn Y, DeShazer David, Harvey Steven P, Robison Richard, Gal Daniel, Mayo Mark J, Wagner David, Currie Bart J, Keim Paul
Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, Arizona 86011, USA.
BMC Microbiol. 2007 Mar 30;7:23. doi: 10.1186/1471-2180-7-23.
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.
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.
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.
兼性胞内菌类鼻疽伯克霍尔德菌是类鼻疽病的病原体，类鼻疽病是一种人和动物的严重传染病。我们鉴定并分类了类鼻疽伯克霍尔德菌K96243菌株基因组中的串联重复序列阵列及其分布情况，以便开发一种类鼻疽伯克霍尔德菌的基因分型方法。然后，我们在包括类鼻疽伯克霍尔德菌、鼻疽伯克霍尔德菌和泰国伯克霍尔德菌在内的31个不同菌株组成的样本中筛选了104个潜在的多态性位点，以鉴定具有不同程度多态性的位点。随后，这些串联重复序列阵列中的一部分被开发成多位点可变数目串联重复序列分析，用于检测来自世界各地的66种类鼻疽伯克霍尔德菌和21种鼻疽伯克霍尔德菌菌株，以及来自一个包含约18000代的连续传代实验的95个谱系。
类鼻疽伯克霍尔德菌在其整个基因组中含有大量串联重复位点，其中许多在基因组的其他地方也有重复。这些位点中的大多数由长度为6至9个碱基对、具有4至10个重复单元的重复基序组成，并且主要位于基因组的基因间区域。在地理分布广泛的类鼻疽伯克霍尔德菌和鼻疽伯克霍尔德菌菌株中，32个可变数目串联重复序列位点显示出7至28个等位基因，内氏多样性值在0.47至0.94之间。这些位点的突变率与在其他多样性较低的细菌中发现的最多样化的串联重复区域的突变率相当（每个位点每代>10-5）。
类鼻疽伯克霍尔德菌基因组中串联重复区域的频率、位置和重复性质表明，这些串联重复区域可能在产生和维持适应性基因组变异中发挥作用。多位点可变数目串联重复序列分析揭示了包含类鼻疽伯克霍尔德菌和鼻疽伯克霍尔德菌的全球菌株样本中的广泛多样性，并且检测到了这两个物种的克隆谱系中使用先前分型方法无法区分的基因型差异。鉴于对人类和家畜的健康威胁以及类鼻疽伯克霍尔德菌可能被故意释放的可能性，多位点可变数目串联重复序列分析可能被证明是对这种日益重要的环境病原体进行精细流行病学或法医追踪的重要工具。
