云南省家鼠疫源地鼠疫耶尔森氏菌分子流行病学特征研究

Molecular epidemiological characteristics of Yersinia pestis strains in Rattus flavipectus plague foci in Yunnan Province

目的探讨云南家鼠疫源地鼠疫菌在云南鼠疫菌遗传进化上所处的位置,及其种群流行演化规律。方法按照不同地点、时间及分离源随机选取186株家鼠疫源地鼠疫菌,采用差异区段(DFR)、规律成簇的间隔短回文重复序列(CRISPRs)及多位点可变数目串联重复序列分析(MLVA)3种方法进行分子分型分析;以DFR+CRISPRs双重方法聚类分析划分基因簇,以MLVA26对基因簇再次聚类分析划分亚簇。结果 186株家鼠疫源地鼠疫菌中的184株聚为一个簇(家鼠鼠疫簇),其余2株为独立株;近史流行期、复燃流行期和2016年疫情分离株分别处于不同的亚簇,它们之间的位点差异至少有5个;复燃流行期菌株共有5个亚簇和6个独立株,其中2个亚簇为主要的基因亚簇,即滇西亚簇和滇西南-滇东-广西-贵州亚簇,它们之间有4个位点差异。结论家鼠鼠疫菌是云南鼠疫菌中最晚出现的菌株,近史流行期菌株与复燃流行期菌株菌株存在较大差异,而复燃流行期的鼠疫流行是复燃和扩散并存的结果。

Objectives To explore the position of Yersinia pestis strains in Rattus flavipectus plague foci in the phylogenesis of Y. pestis strains in Yunnan and the evolutionary rules governing Y. pestis strains in Rattus flavipectus plague foci. Methods One hundred and eighty-six strains isolated from Rattus flavipectus(buff-breasted rat) plague foci were randomly selected based on isolation at different sites, at different times, and from different sources. In addition, 36 strains isolated from wild rodent plague foci were selected as controls. Three genotyping methods including different region(DFR) analysis, clustered regularly interspaced short palindromic repeats(CRISPRs), and multiple-locus variable-number tandem repeat analysis(MLVA) were used in this study. Clusters were formed based on both the DFR and CRISPR methods, and then the cluster was divided into subclusters based on MLVA26. Results One hundred and eighty-four of the 186 Y. pestis strains in buff-breasted rats were clustered into one cluster, which was designated the Buff-breasted Rat Plague Cluster, and the remaining 2 strains constituted single branches. Strains isolated during recent outbreaks, strains isolated during a resurgence, and strains prevalent in 2016 were in different subclusters, and at least 5 different loci differed among them. Isolates from the resurgence were divided into 5 subclusters and 6 single branches, and 2 of the subclusters were the main gene subclusters, designated the West-Yunnan Subcluster and the Southwest-east-Yunnan-Guangxi-Guizhou Subcluster. Four loci differed between them. Conclusion Y. pestis strains in Rattus flavipectus plague foci are the most recent Yunnan Y. pestis strains to appear. Strains from recent outbreaks and strains from a resurgence differed considerably. Strains from the resurgence are the result of both a resurgence and spread of Y. pestis.