目的 通过全基因组单核苷酸多态性（SNP）分析,了解青海省三江源地区鼠疫自然疫源地鼠疫耶尔森菌（鼠疫菌）种群结构特点,为该地区鼠疫科学防控提供理论依据。方法 选取三江源地区81株代表性鼠疫菌,通过比对全基因组测序数据中的2 298个SNPs位点的变异情况,用MEGA 6.0软件完成系统发育树,分析该地区鼠疫菌种群结构及分布特征。结果 81株鼠疫菌分布在3个SNPs分支中,分别为1.IN、2.ANT和0.PE。在整个三江源地区鼠疫自然疫源地中1.IN支群为该地区优势种群,均为喜马拉雅旱獭自然疫源地鼠疫菌,2.ANT和0.PE支群散在分布于玉树藏族自治州的称多县、囊谦县、曲麻莱县,青海田鼠鼠疫自然疫源地鼠疫菌仅存在0.PE4C支群。结论 三江源地区鼠疫菌全基因组SNP呈现明显的地区分布特征,可为该地区鼠疫疫情流行病学调查提供科学提示。
Objective To investigate the characteristics of Yersinia pestis population structure in natural plague foci in the Sanjiangyuan region of Qinghai Province using genomic single nucleotide polymorphisms (SNPs) analysis, so as to provide a theoretical basis for plague prevention and control in this region. Methods A total of 81 representative strains of Y. pestis collected in the Sanjiangyuan region were selected for analysis of variations across 2 298 SNP sites based on whole genome sequencing data. MEGA 6.0 software was used to construct a phylogenetic tree. The structure and distribution characteristics of Y. pestis population in this region were analyzed. Results The 81 strains of were classified into three SNP genotypes, designated as 1.IN, 2.ANT, and 0.PE. The strains in the 1.IN subpopulation were dominant in the natural plague foci of the Sanjiangyuan region, and all of them were isolated from the natural plague focus of Marmotahimalayana. The strains in the 2.ANT and 0.PE subpopulations were distributed across Chengduo County, Nangqian County, and Qumalai County in Yushu Tibetan Autonomous Prefecture. The strains of Y. pestis isolated from the natural plague focus of Neodon fuscus in Qinghai belonged exclusively to the 0.PE4C subpopulation. Conclusion Genomic SNP analysis of Y. pestis subpopulations showed obvious regional distribution characteristics in the Sanjiangyuan region, which provides scientific tips for the epidemiological investigation of plague epidemic in this region.
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