Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis
Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis
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DOI：
10.1038/s41598-018-21562-z
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发表时间：
2018-03-13
影响因子：
4.6
通讯作者：
Jagielski, Tomasz
中科院分区：
文献类型：
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作者：
Bakula, Zofia;Brzostek, Anna;Jagielski, Tomasz
由于缺乏高度歧视性的基因分型模式，堪萨斯分枝杆菌的分子流行病学研究受到阻碍。本研究的目的是设计一种新的、高分辨率的堪萨斯分枝杆菌指纹图谱方法。搜索堪萨斯分枝杆菌ATCC 12478参考菌株的完整基因组序列，寻找包含串联重复序列的卫星状重复DNA元件。共鉴定出24个具有潜在区分性的可变数目串联重复序列(VNTR)基因座。其中17个用于研究代表6个亚型(I-VI)的67株堪萨斯分枝杆菌的多态性。并与脉冲场凝胶电泳法(PFGE)结合ASNI消化的结果进行比较。6个VNTR1、2、8、14、20和23个VNTR1、2、8、14、20和23允许以与使用17位点板相同的区分能力来区分被分析的菌株。VNTR分型和PFGE结合显示了45种不同的模式，包括11个聚类群，33个分离物和34个独特的模式。Hunter-Gaston判别指数分别为0.95和0.66，对两种方法联合应用的判别指数为0.97。总之，这项研究提出了一种新的基于VNTR多态性的分型方案，并建议将其作为甘肃分枝杆菌两步分型策略中PFGE分析之前的一线检测。
Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M. kansasii strains representing six subtypes (I-VI). The results of VNTR typing were compared with those of pulsed-field gel electrophoresis (PFGE) with AsnI digestion. Six VNTRs i.e. (VNTR 1, 2, 8, 14, 20 and 23) allow to differentiate analyzed strains with the same discriminatory capacities as use of a 17-loci panel. VNTR typing and PFGE in conjunction revealed 45 distinct patterns, including 11 clusters with 33 isolates and 34 unique patterns. The Hunter-Gaston's discriminatory index was 0.95 and 0.66 for PFGE and VNTR typing respectively, and 0.97 for the two methods combined. In conclusion, this study delivers a new typing scheme, based on VNTR polymorphism, and recommends it as a first-line test prior to PFGE analysis in a two-step typing strategy for M. kansasii.