DETECTION OF INDEL-MARKERS IN GENOMES OF BURKHOLDERIA PSEUDOMALLEI STRAINS FOR INTRA-SPECIES GENOTYPING

Q3 Medicine Zhurnal mikrobiologii, epidemiologii, i immunobiologii Pub Date : 2017-08-28 DOI:10.36233/0372-9311-2017-4-35-41

M. L. Ledeneva, A. Vodopianov, G. A. Tkachenko, S. Vodopianov, S. Savchenko, I. Shpak

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Abstract

Aim. Search for potential INDEL-markers in genomes of Burkholderia pseudomallei strains, as well as evaluation of the possibility of their use for intra-species genotyping. Materials and methods. Full-genome sequences of 25 В. pseudomallei strains with known geographic regions of isolation from GenBank database were studied. INDEL-marker search was carried out using authors’ program Gene Expert. Cluster analysis was carried out using genetic distance by R. Sokal and C. Michener and neighbor joining method. Results. 11 INDEL-markers were detected that allowed to split the studied strains into 13 genotypes. Spectrum of INDEL-patterns characteristic for Australian strains was determined. A possibility of existence of certain phylogeographic patterns of Thailand isolates is shown. Conclusion. A possibility of INDEL-markers to differentiate isolates of B. pseudomallei into 2 geographic populations (Australian and South-eastern Asia origin) that allows to determine the source of melioidosis outbreak and transmission routes of the pathogen is detected.

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假麦氏伯克氏菌基因组中indel标记的检测及其种内基因分型研究

的目标。寻找假马氏伯克霍尔德菌基因组中潜在的indel标记，并评估其用于种内基因分型的可能性。材料和方法。25个全基因组序列В。对GenBank数据库中已知地理区域分离的假麦氏菌进行了研究。使用作者程序Gene Expert进行indel标记搜索。利用R. Sokal和C. Michener的遗传距离和邻居连接法进行聚类分析。结果:检测到11个indel标记，可将菌株分为13个基因型。测定了澳大利亚菌株的indel型特征谱。显示了泰国分离株存在某些系统地理模式的可能性。结论。检测到利用indel标记将假假芽孢杆菌分离物区分为2个地理种群(澳大利亚和东南亚起源)的可能性，从而可以确定类鼻疽病暴发的来源和病原体的传播途径。

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