苏州市食源性单核细胞增生李斯特菌的全基因组测序分析

Whole genome sequencing analysis of foodborne Listeria monocytogenes in Suzhou

目的 应用高通量测序技术分析苏州市食源性单核细胞增生李斯特菌(Listeria monocytogenes, Lm)的毒力基因携带情况、分子分型、遗传进化谱系及遗传进化关系等分子特征。方法 对2016—2020年分离自食品的42株Lm进行全基因组测序,运用CLC Genomics Workbench 21.0.4软件进行组装及毒力基因和耐药基因分析;通过与BIGSdb-Lm数据库比对获得谱系、克隆群(clone complexes,CC)、血清群、多位点序列分型(multilocus sequence typing,MLST)、核心基因组多位点序列分型(core genome multilocus sequence typing,cgMLST);利用柏熠微生物分析平台v4.0构建最大似然树。结果 42株Lm共包含两个谱系,谱系Ⅰ和谱系Ⅱ,以谱系Ⅱ为主(83.3%)。血清群分为Ⅱa、Ⅱb和Ⅱc,以Ⅱa为主(57.1%)。42株Lm分为11个CC型, 11个序列型(sequence type, ST型),优势型别是CC9、CC8和CC121,占比61.9%。菌株携带毒力基因数量均在30个以上,涉及LIPI-1、LIPI-2、LIPI-3 3个毒力岛。LIPI-1中actA检出率为76.2%, prfA、plcA、hly、mpl、plcB检出率均为100.0%。LIPI-2中inlF的检出率为81.0%, inlB检出率为97.6%, inlA、inlC、inlJ、inlK、inlP等5种基因检出率均为100.0%。只有1株菌携带LIPI-3。菌株携带耐药基因有FosX、mprF、lin、norB、tetM、dfrG等6个基因,携带3种以上毒力基因的菌株数量达到78.6%。结论 苏州市食源性Lm的分子型别较为多样且具有优势型别,普遍携带较多毒力基因和多个耐药基因,应加强监测。

Objective To analyze the molecular characteristics of foodborne Listeria monocytogenes(Lm)in Suzhou by high-throughput sequencing technology,including virulence gene carrying status,molecular typing,genetic evolutionary lineage and genetic evolutionary relationship.Methods The whole genomes of 42 strains of Lm isolated from food during 2016 to 2020 were sequenced.CLC Genomics Workbench 21.0.4 software was used to assemble the genomes,and analyze their drug-resistance genes and virulence genes.Lineage,clone complexes(CC),serogroup,multilocus sequence typing(MLST),core genome multilocus sequence typing(cgMLST)were obtained by aligning with the BIGSdb-Lm database.The maximum likelihood tree was constructed using the Baiyi microbial analysis platform v4.0.Results The 42 strains of Lm contained 2 lineages,lineage I and lineage II,and lineage II was the predominant(83.3%).The serogroups were divided into IIa,IIb and IIc,with IIa being the predominant(57.1%).The 42 strains of Lm were divided into 11 CC types(also 11 sequence types),and the dominant types were CC9,CC8 and CC121,accounting for 61.9%.Each strain carried more than 30 virulence genes,involving LIPI-1,LIPI-2 and LIPI-3.The detection rate of actA in LIPI-1 was 76.2%,and the detection rates of prfA,plcA,hly,mpl,and plcB were all 100.0%.In LIPI-2,the detection rate of inlF was 81.0%,that of inlB was 97.6%,and that of inlA,inlC,inlJ,inlK,and inlP were all 100.0%.Only one strain carried LIPI-3.The Lm strains carried 6 drug resistance genes,such as FosX、mprF、lin、norB、tetM、dfrG,and 78.6%of the strains carried more than 3 virulence genes.Conclusion The molecular types of foodborne Lm in Suzhou are diverse but have dominant types.The strains generally carried many virulence genes and multiple drug resistance genes,and monitoring should be strengthened.