Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme |
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| Authors: | Yanjun Li Yujun Cui Baizhong Cui Yanfeng Yan Xianwei Yang Haidong Wang Zhizhen Qi Qingwen Zhang Xiao Xiao Zhaobiao Guo Cong Ma Jing Wang Yajun Song Ruifu Yang |
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| Institution: | 1. State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.; 2. Laboratory Department, Navy General Hospital, Beijing, China.; 3. Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China.; 4. Institute of Health Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China.; Institut National de la Recherche Agronomique, France, |
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| Abstract: | BackgroundVariable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.Methodology/Principal FindingsCapillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a “14+12” loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.Conclusions/SignificanceAppropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized “14+12” loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis. |
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