摘要
目的比较四川省肠炎沙门菌暴发菌株的分子分型方法,为暴发溯源提供快速可靠的依据。方法采用脉冲场凝胶电泳(PFGE)、多位点可变数目重复序列分析(MLVA)、规律间隔成簇短回文重复序列(CRISPR)、多位点序列分型(MLST)和基于全基因组测序的单核苷酸多态性(WGS-SNP)对2008—2018年四川省肠炎沙门菌暴发分离株进行分型。以辛普森多样性指数(DI)为指征,比较单一方法及方法联用的分型能力差异。结果PFGE、MLVA、CRISPR和MLST单独使用时,其DI值均<0.9,PFGE_XbaⅠ和MLVA联合使用DI值能提高到0.9以上,WGS-SNP的DI值最高,可达0.971。结论对四川省肠炎沙门菌暴发菌株进行分子分型的最适方法为WGS-SNP,在缺乏基因组分析能力的情况下,推荐使用PFGE_XbaⅠ与MLVA联合的方法。
Objective To compare the molecular typing methods for the Salmonella Enteritidis strains isolated from the outbreaks in Sichuan province and provide evidence for the rapid and reliable source tracing of the outbreaks.Methods Pulse-field gel electrophoresis(PFGE),multilocus variable-number of tanden-repeat analysis(MLVA),clustered regularly interspaced short palindromic repeats(CRISPR),multilocus sequence typing(MLST)and whole genome sequencingbased Single Nucleotide Polymorphism(WGS-SNP)were used for the subtyping of S.Enteritidis strains isolated from the outbreaks in Sichuan from 2008 to 2018.Simpson Diversity Index(DI)was used as an indicator to compare the subtyping power of a single method and a combination of methods.Results When PFGE,MLVA,CRISPR,and MLST were used alone,the DI values were all lower than 0.9.The DI value of PFGE_XbaⅠand MLVA increased to above 0.9 when PFGE_XbaⅠand MLVA were used together.WGS-SNP had the highest DI value(0.971).Conclusion The most suitable method for the molecular subtyping of S.Enteritidis strains isolated from the outbreaks in Sichuan was WGS-SNP.In the absence of genome analysis capability,the PFGE_XbaⅠ+MLVA method is recommended.
作者
肖桃
雷高鹏
黄伟峰
吕虹
刘丽
杨小蓉
何树森
Xiao Tao;Lei Gaopeng;Huang Weifeng;Lyu Hong;Liu Li;Yang Xiaorong;He Shusen(Sichuan Provincial Center for Disease Control and Prevention,Chengdu 610041,Sichuan,China)
出处
《疾病监测》
CAS
CSCD
北大核心
2021年第11期1172-1178,共7页
Disease Surveillance
基金
四川省卫生和计划生育委员会科研课题(No.16PJ395)
四川省科技项目(No.2020YFS0581)。
关键词
肠炎沙门菌
脉冲场凝胶电泳
多位点可变数目重复序列分析
全基因组测序
分子分型
Salmonella Enteritidis
Pulsed-field gel electrophoresis
Multilocus variable-number of tanden-repeat analysis
Whole genome sequencing
Molecular subtyping
