食品来源粪肠球菌的全基因组分析

Complete genome analysis of food-derived Enterococcus faecalis

中文关键词:  粪肠球菌  全基因组测序  系统发育分析  比较基因组学

英文关键词:Enterococcus faecalis  whole genome sequencing  phylogenetic analysis  comparative genomics

中文摘要:

      目的 了解食品来源粪肠球菌的全基因组分子特征, 并与临床分离菌株进行比较基因组学分析。 方法 对收集的食品来源粪肠球菌进行全基因组测序和生物信息学分析, 比较分析3株食品来源粪肠球菌和7株已发表的临床分离粪肠球菌基因组, 对比粪肠球菌基因组中携带的耐药基因、毒力基因和移动元件, 筛选核心基因, 构建系统进化树。结果 3株食品来源粪肠球菌染色体全基因组序列全长分别为2816436、3005875和2818728 bp, 共含有2733、2853和2756个基因, 基因平均鸟嘌呤和胞嘧啶(guanine and cytosine, GC)含量为38.0%。在全基因组核酸水平上, 食品与临床分离的粪肠球菌线性关系良好, 基因组结构高度相似。3株食品来源菌株基因组中含有3~7种耐药基因、8~19种毒力基因和42~67个移动元件, 与临床分离菌株比较, 无显著性差异(P>0.05)。系统进化树分析发现食品来源和临床分离粪肠球菌分布在一个进化分枝, 分子遗传关系距离较近。结论 本研究获得了食品来源粪肠球菌全基因组基本特征的背景材料, 证实了食品来源和临床分离粪肠球菌进化溯源关系相近, 基因组无显著差异(P>0.05), 为后续食品工业界实际应用粪肠球菌的安全性评价奠定了基础。

英文摘要:

      Objective To understand molecular characteristics of the whole genome of food-derived Enterococcus faecalis, and conduct comparative genomic analysis with clinical isolates. Methods The whole genome sequencing and bioinformatics analysis were performed on the collected food-derived E. faecalis, drug resistance genes, virulence genes and mobile genetic elements were compared and analyzed between 3 strains of food-derived E. faecalis and 7 strains of clinical isolates of E. faecalis, the core genes were screened and phylogenetic tree was constructed. Results The full length of 3 strains of food-derived E. faecalis genomes were 2816436, 3005875 and 2818728 bp, containing 2733, 2853 and 2756 genes with an average guanine and cytosine content of 38.0%. Good linearity and high similarity were found between the genomic structure of food-derived and clinical isolates. The genomes of 3 strains of food-derived strains contained 3-7 drug-resistance genes, 8-19 virulence genes and 42-67 mobile genetic element, and no significant difference were showed when compared with the clinical isolates (P>0.05). Phylogenetic tree analysis revealed that food-derived and clinically isolated E. faecalis were distributed in an evolutionary branch with a relatively close molecular genetic relationship distance. Conclusion The background materials for the whole genomic features of food-derived E. faecalis is obtained, which confirmed that the evolutionary relationship between the food-derived and clinical isolates of E. faecalis is similar, and there is no significant difference between the bacterial genomes from 2 sources (P>0.05), this study laies a foundation for the safety evaluation of the practical application of E. faecalis in the practical application in the food industry.