2008-2018年四川省肠炎沙门菌暴发的分子分型比较

肖桃 雷高鹏 黄伟峰 吕虹 刘丽 杨小蓉 何树森

肖桃, 雷高鹏, 黄伟峰, 吕虹, 刘丽, 杨小蓉, 何树森. 2008-2018年四川省肠炎沙门菌暴发的分子分型比较[J]. 疾病监测. doi: 10.3784/jbjc.202104260227
引用本文: 肖桃, 雷高鹏, 黄伟峰, 吕虹, 刘丽, 杨小蓉, 何树森. 2008-2018年四川省肠炎沙门菌暴发的分子分型比较[J]. 疾病监测. doi: 10.3784/jbjc.202104260227
Xiao Tao, Lei Gaopeng, Huang Weifeng, Lyu Hong, Liu Li, Yang Xiaorong, He Shusen. Comparison of subtyping methods for Salmonella enterica serotype Enteritidis strains isolated from outbreaks in Sichuan, 2008–2018[J]. Disease Surveillance. doi: 10.3784/jbjc.202104260227
Citation: Xiao Tao, Lei Gaopeng, Huang Weifeng, Lyu Hong, Liu Li, Yang Xiaorong, He Shusen. Comparison of subtyping methods for Salmonella enterica serotype Enteritidis strains isolated from outbreaks in Sichuan, 2008–2018[J]. Disease Surveillance. doi: 10.3784/jbjc.202104260227

2008-2018年四川省肠炎沙门菌暴发的分子分型比较

doi: 10.3784/jbjc.202104260227
基金项目: 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)
详细信息
    作者简介:

    肖桃,女,四川省成都市人,硕士研究生,检验师,主要从事病原微生物学相关工作,Email:793438338@qq.com

    通讯作者:

    雷高鹏,Tel:028–85989023,Email:lionleonleo@126.com

Comparison of subtyping methods for Salmonella enterica serotype Enteritidis strains isolated from outbreaks in Sichuan, 2008–2018

Funds: This study was supported by grants of Application of Genome Analysis in the Surveillance of Foodborne Salmonella Enteritidis in Sichuan, China (No. 16PJ395) and Science and technology project of Sichuan Province (No. 2020YFS0581)
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  • 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_Xba与MLVA联合的方法。
  • 图  1  PFGE_Xba和MLVA方法联合使用的聚类分析

    注:PFGE. 脉冲场凝胶电泳;MLVA. 多位点可变数目串联重复序列分析

    Figure  1.  Cluster analysis of combination of PFGE_Xba and MLVA

    图  2  PFGE_Xba_Bln+MLVA和PFGE_Xba+MLVA的聚类比对

    注: PFGE. 脉冲场凝胶电泳;MLVA. 多位点可变数目串联重复序列分析

    Figure  2.  Comparison of cluster analysis between PFGE_Xba_Bln+MLVA and PFGE_Xba+MLVA

    图  3  WGS-SNP的聚类分析

    注:Outbreaks代表菌株分离自不同暴发事件,括号中的数字代表同一起事件菌株的WGS-SNP差异数;P125109(accession no. NC_011294.1)是参考菌株;WGS-SNP. 全基因组测序的单核苷酸多态性

    Figure  3.  Cluster analysis of WGS-SNP

    表  1  2008-2018年四川省肠炎沙门菌暴发选取菌株信息

    Table  1.   Information about selected S. Enteritidis strains isolated from outbreaks in Sichuan, 2008–2018

     菌株号暴发事件分离地市分离时间
    (年–月)
    样本
    ZD2008038A攀枝花市2008–06粪便
    ZD2008039A攀枝花市2008–06粪便
    ZD2008042B广元市 2008–07粪便
    ZD2008045B广元市 2008–07粪便
    ZD2008072C达州市 2008–07粪便
    ZD2008074C达州市 2008–07粪便
    ZD2008078D广元市 2008–07粪便
    ZD2008087D广元市 2008–07粪便
    ZD2009030E达州市 2009–07粪便
    ZD2009033E达州市 2009–07粪便
    ZD2009037F乐山市 2009–08粪便
    ZD2009039F乐山市 2009–08粪便
    ZD2009058G达州市 2009–08粪便
    ZD2009060G达州市 2009–08粪便
    ZD2011029H攀枝花市2011–09食品
    ZD2011032H攀枝花市2011–09粪便
    ZD2011039I南充市 2011–08食品
    ZD2011041I南充市 2011–08粪便
    ZD2011048J攀枝花市2011–09环境
    ZD2011065J攀枝花市2011–09粪便
    ZD2011081K攀枝花市2011–10粪便
    ZD2011082K攀枝花市2011–10粪便
    ZD2012032L攀枝花市2012–10粪便
    ZD2012034L攀枝花市2012–10粪便
    ZD2014028M绵阳市 2014–07粪便
    ZD2014030M绵阳市 2014–07粪便
    ZD2014031N雅安市 2014–07粪便
    ZD2014032N雅安市 2014–07粪便
    ZD2014043O绵阳市 2014–11粪便
    ZD2014044O绵阳市 2014–11粪便
    ZD2015006P广元市 2015–06粪便
    ZD2015010P广元市 2015–06粪便
    ZD2016047Q绵阳市 2016–07粪便
    ZD2016048Q绵阳市 2016–07粪便
    ZD2016135R泸州市 2016–11粪便
    ZD2016139R泸州市 2016–11粪便
    ZD2017004S绵阳市 2017–01粪便
    ZD2017013S绵阳市 2017–01环境
    ZD2017032T雅安市 2017–06粪便
    ZD2017035T雅安市 2017–06食品
    ZD2017037U绵阳市 2017–07粪便
    ZD2017040U绵阳市 2017–07粪便
    ZD2017140V雅安市 2017–11粪便
    ZD2017141V雅安市 2017–11粪便
    ZD2017149W成都市 2017–12粪便
    ZD2017151W成都市 2017–12粪便
    ZD2018016X成都市 2018–03粪便
    ZD2018018X成都市 2018–03粪便
    ZD2018037Y绵阳市 2018–04粪便
    ZD2018040Y绵阳市 2018–04粪便
    ZD2018131Z绵阳市 2018–06粪便
    ZD2018132Z绵阳市 2018–06粪便
    下载: 导出CSV

    表  2  各种方法分型能力概述

    Table  2.   Summary of subtyping power of methods

     试验方法分支数最大分支菌数辛普森指数CI(95%)CINA(95%)
    MLVA 4220.6610.599~0.7220.594~0.727
    PFGE_Xba13180.8450.772~0.9190.769~0.921
    PFGE_Bln 9320.6120.461~0.7640.460~0.765
    PFGE_XbaⅠ_Bln15180.8510.775~0.9280.773~0.930
    PFGE_BlnⅠ+MLVA12180.8360.762~0.9090.760~0.911
    PFGE_XbaⅠ+MLVA17140.9040.850~0.9590.848~0.961
    PFGE_XbaⅠ_BlnⅠ+MLVA18140.9060.851~0.9610.849~0.963
    WGS-SNP24 60.9710.958~0.9850.954~0.989
      注:PFGE. 脉冲场凝胶电泳;MLVA. 多位点可变数目串联重复序列分析;MLST. 多位点序列分型;CRISPR. 规律间隔成簇短回文重复序列;WGS-SNP. 全基因组测序的单核苷酸多态性
    下载: 导出CSV
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  • 收稿日期:  2021-04-26
  • 网络出版日期:  2021-07-30

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