Genomic evolution characteristics of pathogenicity islands of enteropatho-genic Escherichia coli Deng strain
10.3969/j.issn.1671-9638.2016.01.001
- VernacularTitle:肠致病性大肠埃希菌EPECDeng致病岛基因进化特点
- Author:
Zhong CHEN
;
Jinxin ZHENG
;
Weizhi YANG
;
Hongyan WANG
;
Weiming YAO
;
Xiangbin DENG
;
Duoyun LI
;
Xiaojun LIU
;
Zhijian YU
;
Qiwen DENG
- Publication Type:Journal Article
- Keywords:
enteropathogenic Escherichia coli;
high-throughput sequencing;
complete genome sequence;
patho-genicity island;
core gene;
homology
- From:
Chinese Journal of Infection Control
2016;(1):1-9
- CountryChina
- Language:Chinese
-
Abstract:
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 se-quencing 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 homolo-gous gene were constructed in order to understand the evolutional rule of homology gene.PAIs prediction was per-formed 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 contained 207 564 bp with a GC content of 49.50%.A total of 17 PPs in the chromosomal genome were discovered,phyloge-netic 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 characteris-tics of EPEC Deng genome and it’s PAIs,and is helpful for understanding genetic characteristics of native EPEC.
