不同来源屎肠球菌的全基因组序列分析

Whole genome sequence analysis of Enterococcus faecium from different sources

目的 了解不同分离来源的屎肠球菌(Enterococcus faecium)标准菌株的全基因组特征。方法 采用高通量测序技术对中国医学细菌保藏管理中心保藏的分离于食品和临床患者的6株屎肠球菌标准菌株进行全基因组测序,采用velvet 1.2.03和glimmer 3.02等生物信息学软件对测序数据进行基因组装、基因预测及功能注释,分析基因组中所含耐药基因和毒力基因;并与已发表的6株临床分离的代表性屎肠球菌进行核心基因组和泛基因组比较分析,构建系统发育分子进化树。结果 6株屎肠球菌标准菌株的基因组序列大小约为2.9Mbp,不同菌株基因组中共鉴定出2669~3085个基因,平均G+C含量为38.0%;基因组耐药基因注释分析发现,每株屎肠球菌含有21~37种数量不等的耐药基因,食品来源菌株所携带耐药基因明显少于临床分离株(P=0.009)。而不同来源菌株之间所含毒力基因数量无显著性差异,含有5~8种数量不等的毒力基因,其中参与生物膜形成的基因BopD和胆盐水解酶基因bsh存在于所有菌株中。比较基因组学分析结果显示,随着屎肠球菌基因组测序数量的增加,泛基因组所含基因数量随之增加,而核心基因组则趋于稳定。全基因组的系统发育树进化分析结果显示, 12株屎肠球菌被分成3个进化分支,其中5株食品来源的菌株均分布在同一个进化分支。结论 本研究获得6株屎肠球菌标准菌株的全基因组序列,证实食品来源菌株均携带一定数量的耐药基因和毒力基因,提示应加强食源性菌株的安全监测。本研究结果可为后续屎肠球菌耐药机制、致病性等研究提供数据支持。

Objective To understand the whole genomic characteristics of standard strains of Enterococcus faecium from different sources.Methods High-throughput sequencing technology was used to sequence the whole genome of 6 standard strains of E.faecium isolated from food and clinical patients preserved by China Medical Bacteria Collection Center,bioinformatics software such as velvet 1.2.03 and glimmer 3.02 were used for gene assembly,gene prediction and functional annotation,the resistance genes and virulence genes contained in the genomes were analyzed;the core genome and pan-genome were compared with 6 strains of clinically isolated representative E.faeciums and a phylogenetic molecular evolutionary tree was constructed.Results The genome size of 6 strains of E.faecium standard strains was about 2.9 Mbp,and 2669-3085 genes were identified in the genomes of different strains,with an average G+C content of 38.0%.Annotation analysis showed that each E.faecium contained 21-37 resistance genes,and the drug resistance genes carried by food-derived strains were significantly less than that of clinical isolates(P=0.009).However,there was no significant difference in the number of virulence genes between strains from different sources,and there were 5 to 8 virulence genes,among them,the gene BopD involved in biofilm formation and the bile salt hydrolase gene bsh existed in all strains.The comparative genomics analysis showed that with the increase of the number of E.faecium genomes,the number of genes contained in the pan-genome increased,while the core genome tended to be stable.The phylogenetic tree evolution analysis showed that the 12 strains of E.faecium were divided into 3 evolutionary clades,of which 5 food-derived strains were all distributed in the same evolutionary clade.Conclusion The whole genome sequences of 6 strains of E.faecium standard strains were obtained in this study,confirming that the food-derived strains all carried a certain number of drug resistance genes and virulence genes,suggesting that the safety monitoring of food-derived strains should be strengthened.These findings can provide data supports for subsequent studies on the resistance mechanism and pathogenicity of E.faecium.