肠致病性大肠埃希菌EPEC Deng致病岛基因进化特点

Genomic evolution characteristics of pathogenicity islands of enteropathogenic Escherichia coli Deng strain

目的分析肠致病性大肠埃希菌(EPEC)致病岛(PAIs)基因进化特点。方法 EPEC Deng分离自我国婴幼儿腹泻患者粪便标本,鉴定该菌株血清型并进行药敏试验;采用Illumina 2000仪器对菌株进行全基因序列测序,PHAST软件定位菌株原噬菌体(prophages,PPs)在染色体中的位置,MUMmer软件进行共线性分析,构建系统发育树,了解同源基因进化规律。应用PAI_finder软件对基因组进行PAIs预测,了解PAIs核心区域(LEE)和核心基因同源进化规律,并进行遗传多态性分析。结果 EPEC Deng菌株归属O119∶H6,药敏结果显示该菌株对环丙沙星、左氧氟沙星及氨苄西林耐药,对其余的抗菌药物均敏感。基因组(染色体)序列大小为5 025 482 bp(GC含量为50.52%),质粒序列大小为207 564 bp(GC含量为49.50%)。共找到17个PPs,系统发育树分析发现,EPEC Deng株基因组与O26∶H11、O111∶H同源性较高;EPEC Deng株PAIs和核心基因均与RDEC-1和O26∶H413/89-1株具有高同源性;遗传多样性分析结果显示,紧密素(eae)及其受体(tir)多态性丰富,π值均>0.10,Ⅲ型分泌系统(TTSS)分泌蛋白相对稳定。结论此研究明确了EPEC Deng株基因组及PAIs的进化特点,有助于了解了本土分离的EPEC基因特点。

Objective To analyze the genomic evolution characteristics of pathogenicity islands（PAIs）in Deng strain of enteropathogenic Escherichia coli（E.coli,EPEC Deng）.Methods EPEC Deng was isolated from infant stool specimen,serotypes were identified and antimicrobial susceptibility testing was performed;whole-genome sequencing was performed by Illumina 2000 system,the locations of prophages（PPs）in the chromosome were detected using PHAST software,collinearity analysis was performed by MUMmer software,phylogenetic trees of homologous gene were constructed in order to understand the evolutional rule of homology gene.PAIs prediction was performed using PAI_finder software,the homologous evolutionary rule of PAIs core region（LEE）and core genes were clarified,genetic polymorphism was analyzed.Results The serotype of EPEC Deng strain was O119：H6,the strain was resistant to ciprofloxacin,levofloxacin,and ampicillin,but sensitive to other antimicrobial agents.The complete circular chromosome contained 5 025 482 bp with a GC content of 50.52 %,and the plasmid contained207 564 bp with a GC content of 49.50%.A total of 17 PPs in the chromosomal genome were discovered,phylogenetic trees analysis suggested that EPEC Deng strain was highly homologous with O26：H11 and O111：H strains;PAIs and core genes were highly homologous with RDEC-1 and O26：H413/89-1 strains;genetic diversity analysis showed that the intimin（eae）and its receptor tir had high polymorphism,with the pi（π）value〉0.10,the genes in type III secretion system was relatively stable.Conclusion The study clarified the genomic evolution characteristics of EPEC Deng genome and it’s PAIs,and is helpful for understanding genetic characteristics of native EPEC.