山东省聊城市2020-2021年小肠结肠炎耶尔森菌食品分离株分子特征分析

Molecular characterization of foodborne Yersinia enterocolitica strains in Liaocheng City,Shandong Province,from 2020 to 2021

目的了解2020-2021年山东省聊城市小肠结肠炎耶尔森菌(Y.e)食品分离株分子特征。方法对聊城市市售生肉与肉制品中Y.e开展分离培养、药敏试验、毒力基因检测、PFGE和全基因组测序(WGS)。利用微生物基因组注释系统对全基因组数据进行拼接组装,对组装基因组开展多位点序列分型(MLST)和核心基因组多位点序列分型(cgMLST),并应用基于WGS的单核苷酸多态性(wg-SNPs)分型方法与美国生物技术信息中心上获取的14株国内外Y.e的基因组进行遗传进化分析。结果165份样品中共检出21株Y.e,检出率为12.73%,20株Y.e测序成功。Y.e携带多种耐药基因和毒力基因,出现多重耐药现象,毒力基因PCR检测显示21株Y.e呈现2种毒力基因特征;PFGE、MLST和cgMLST聚类分析显示,21株Y.e呈高度多样性;wg-SNPs遗传进化分析显示20株Y.e可分为2个进化主分支。结论聊城市生肉与肉制品中分离的Y.e携带多种耐药基因和毒力基因,且分子分型呈现高度多样性,应加强生肉与肉制品中Y.e分子生物学监测,开展基因组测序及分子分型检测工作,为预防由Y.e引起的食源性疾病提供理论依据。

Objective To understand the genome analysis and molecular typing of foodborne Yersinia enterocolitica(Y.e)strains in Liaocheng City of Shandong Province from 2020 to 2021.Methods The Y.e strains were isolated from raw meat and meat products.Then we made the strain identification,drug sensitivity test,virulence gene test,pulsed-field gel electrophoresis(PFGE),and whole genome sequencing(WGS).The genome sequencing data were assembled with the microbial genome annotation package.We performed the multilocus sequence typing(MLST)and core genome multilocus sequence typing(cgMLST)and used WGS-based single nucleotide polymorphism typing(wg-SNPs)method to carry out genetic evolution analysis with 14 domestic and Y.e genomes obtained from the NCBI.Results A total of 21 strains of Y.e were detected from 165 samples,with a detection rate of 12.73%.The 20 strains of Y.e were sequenced successfully.The 20 strains of Y.e carries a variety of drug resistance genes and virulence genes,showing multiple drug resistance.The virulence gene PCR test showed that 21 strains of Y.e having two virulence genes.Cluster analysis of PFGE,MLST,and cgMLST showed that the genomics of 21 strains was highly diverse.The genetic evolution analysis of wg-SNPs showed that 20 Y.e strains could be divided into two main evolutionary branches.Conclusions Y.e strains isolated from raw meat in Liaocheng City carry a variety of drug resistance genes and virulence genes,and the molecular typing is highly diverse,which may cause infection risk.The molecular biological monitoring of Y.e in raw meat should be strengthened,and genome sequencing and molecular typing detection be carried out to provide the theoretical basis for foodborne illness caused by Y.e.