青海省三江源地区鼠疫耶尔森菌基因组单核苷酸多态性分析研究

doi:10.11853/j.issn.1003.8280.2024.06.002

摘要/Abstract

摘要： 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。

关键词: 鼠疫菌, 全基因组, 单核苷酸多态性, 基因分型, 三江源地区

Abstract: 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.

Key words: Yersinia pestis, Genomics, Single nucleotide polymorphism, Genotyping, Sanjiangyuan region

中图分类号:

R378.6⁺1

柏吉祥, 靳娟, 李胜, 辛有全, 杨晓艳, 张丽, 金泳, 李翔, 应凯业, 何建. 青海省三江源地区鼠疫耶尔森菌基因组单核苷酸多态性分析研究[J]. 中国媒介生物学及控制杂志, 2024, 35(6): 639-643.

BAI Ji-xiang, JIN Juan, LI Sheng, XIN You-quan, YANG Xiao-yan, ZHANG Li, JIN Yong, LI Xiang, YING Kai-ye, HE Jian. Analysis of genomic single nucleotide polymorphisms of Yersinia pestis in the Sanjiangyuan region of Qinghai Province, China[J]. Chinese Journal of Vector Biology and Control, 2024, 35(6): 639-643.

参考文献

[1] Hu GZ, Zeng WH, Ma BR. Roadmap for coordinated development of economic construction and ecological protection in protected areas:Take Sanjiangyuan area as an example[J]. Biodiversity Sci, 2022, 30（2）:169-179. DOI:10.17520/biods.2021225.（in Chinese）胡官正, 曾维华, 马冰然. 保护地区域经济建设与生态保护协同发展路线图:以三江源地区为例[J]. 生物多样性, 2022, 30（2）:169-179. DOI:10.17520/biods.2021225.
[2] Liu CH, Wang WY. Dynamic analysis and monitoring ecological environment quality in the Sanjiang source region based on RSEI considering NDSI[J]. J Beijing Univ Civil Eng Archit, 2022, 38（6）:68-76. DOI:10.19740/J.2096-9872.2022.06.08.（in Chinese）刘程辉, 王文宇. 顾及NDSI的三江源地区生态环境质量监测及动态分析[J]. 北京建筑大学学报, 2022, 38（6）:68-76. DOI:10.19740/j.2096-9872.2022.06.08.
[3] Wang X, Li Q, Wei YW, et al. Plague epidemiology in the Three Rivers Source Region, Qinghai Province, China, 1996 to 2015[J]. Chin J Zoonoses, 2017, 33（2）:178-183. DOI:10.3969/j.issn.1002-2694.2017.02.016.（in Chinese）王雪, 李千, 魏有文, 等. 1996－2015年青海省三江源地区鼠疫流行病学分析[J]. 中国人兽共患病学报, 2017, 33（2）:178-183. DOI:10.3969/j.issn.1002-2694.2017.02.016.
[4] Wu KM, Li C, Wang YZ, et al. A review on bacterium isolation from animals and vectors infected naturally by Yersinia pestis in Sanjiangyuan district[J]. Chin J Vector Biol Control, 2009, 20（4）:365-368. （in Chinese）吴克梅, 李超, 汪元忠, 等. 三江源地区自然感染鼠疫的动物及媒介昆虫细菌分离简述[J]. 中国媒介生物学及控制杂志, 2009, 20（4）:365-368.
[5] Jiang K, Xiong HM, Tian FZ, et al. Epidemiological characteristics of human plague in the Sanjiangyuan region, Qinghai Province, China, 1958-2021[J]. Chin J Vector Biol Control, 2022, 33（6）:838-842. DOI:10.11853/j.issn.1003.8280.2022.06.014.（in Chinese）蒋可, 熊浩明, 田富彰, 等. 青海省三江源地区1958－2021年人间鼠疫流行特征分析[J]. 中国媒介生物学及控制杂志, 2022, 33（6）:838-842. DOI:10.11853/j.issn.1003.8280.2022.06.014.
[6] Qi ZZ, Li C, Wang L, et al. Study on the pathogen of plague in Sanjiangyuan area in Qinghai Province[J]. Chin J Epidemiol, 2009, 30（1）:55-57. DOI:10.3760/cma.j.issn.0254-6450.2009.01.016.（in Chinese）祁芝珍, 李超, 王丽, 等. 青海省三江源地区鼠疫病原学分析[J]. 中华流行病学杂志, 2009, 30（1）:55-57. DOI:10.3760/cma.j.issn.0254-6450.2009.01.016.
[7] Cui YJ, Yu C, Yan YF, et al. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis[J]. Proc Natl Acad Sci USA, 2013, 110（2）:577-582. DOI:10.1073/pnas.1205750110.
[8] Xiong HM, Jin J, Xin YQ, et al. Study on the phylogenetic relationship and epidemic characteristics of Tibetan sheep Yersinia pestis in Qinghai Plateau[J]. Chin J Dis Control Prev, 2022, 26（12）:1473-1478. DOI:10.16462/j.cnki.zhjbkz.2022.12.019.（in Chinese）熊浩明, 靳娟, 辛有全, 等. 青海高原藏系绵羊鼠疫菌系统发育关系和流行特征的研究[J]. 中华疾病控制杂志, 2022, 26（12）:1473-1478. DOI:10.16462/j.cnki.zhjbkz.2022.12.019.
[9] Gou DC. Study on SNP population relationship of Yersinia pestis genome sequence in the natural foci of gerbil plague in Inner Mongolia Autonomous Region in 2019[D]. Hohhot:Inner Mongolia Medical University, 2021. DOI:10.27231/d.cnki.gnmyc.2021.000033.（in Chinese）勾德才. 2019年内蒙古自治区长爪沙鼠鼠疫自然疫源地鼠疫耶尔森菌基因组SNP种群关系研究[D]. 呼和浩特:内蒙古医科大学, 2021. DOI:10.27231/d.cnki.gnmyc.2021.000033.
[10] Achtman M, Morelli G, Zhu PX, et al. Microevolution and history of the plague bacillus, Yersinia pestis[J]. Proc Natl Acad Sci USA, 2004, 101（51）:17837-17942. DOI:10.1073/pnas.0408026101.
[11] Morelli G, Song YJ, Mazzoni CJ, et al. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity[J]. Nat Genet, 2010, 42（12）:1140-1143. DOI:10.1038/ng.705.
[12] Cui YJ. Development of genomic polymorphism database source-tracking system for Yersinia pestis[D]. Beijing:Academy of Military Medical Sciences, PLA, China, 2008. （in Chinese）崔玉军. 鼠疫耶尔森氏菌基因组多态性数据库及鉴定溯源系统的研究[D]. 北京:中国人民解放军军事医学科学院, 2008.
[13] Li YJ. Study of genomic polymorphism in Yersinia pestis and construction of the rapid source-tracking pipeline[D]. Beijing:Academy of Military Medical Sciences, PLA, China, 2009. （in Chinese）李艳君. 鼠疫耶尔森氏菌基因组多态性研究及快速鉴定溯源系统的建立[D]. 北京:中国人民解放军军事医学科学院, 2009.
[14] Wang N. The study on single nucleotide polymorphism of Yersinia pestis in China[D]. Beijing:Chinese Center for Disease Control and Prevention, 2011. （in Chinese）王娜. 中国鼠疫菌单核苷酸多态性研究[D]. 北京:中国疾病预防控制中心, 2011.
[15] Zhu P. Luminex-based SNP typing of Yersinia pestis[D]. Changsha:Hunan Agricultural University, 2012. （in Chinese）朱鹏. 基于液态悬浮芯片的鼠疫耶尔森氏菌SNP分型[D]. 长沙:湖南农业大学, 2012.
[16] Riehm JM, Vergnaud G, Kiefer D, et al. Yersinia pestis lineages in Mongolia[J]. PLoS One, 2012, 7（2）:e30624. DOI:10.1371/journal.pone.0030624.
[17] Li YJ, Dai EH, Cui YJ, et al. Different region analysis for genotyping Yersinia pestis isolates from China[J]. PLoS One, 2008, 3（5）:e2166. DOI:10.1371/journal.pone.0002166.
[18] Bai JX, Jin J, Li S, et al. Research on the CRISPR genotyping and epidemic characteristics of Yersinia pestis in the Sanjiangyuan region[J]. Chin J Hyg Insect Equip, 2019, 30（2）:161-165. DOI:10.19821/j.1671-2781.2024.02.015.（in Chinese）柏吉祥, 靳娟, 李胜, 等. 三江源地区鼠疫耶尔森菌CRISPR基因分型及流行特征研究[J]. 中华卫生杀虫药械, 2024, 30（2）:161-165. DOI:10.19821/j.1671-2781.2024.02.015.
[19] Wang H, Jiao BT, Wang GJ, et al. Study on an epidemic of human lung plague in Nangqian County, Qinghai Province[J]. Chin J Epidemiol, 2005, 26（9）:684-686. DOI:10.3760/j.issn:0254-6450.2005.09.015.（in Chinese）王虎, 焦巴太, 王国钧, 等. 青海省囊谦县人间肺鼠疫爆发的调查[J]. 中华流行病学杂志, 2005, 26（9）:684-686. DOI:10.3760/j.issn:0254-6450.2005.09.015.