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

Abstract:

ObjectiveTo analyze the genomic evolution characteristics of pathogenicity islands (PAIs) in Deng strain of enteropathogenic Escherichia coli (E. coli,EPEC Deng).MethodsEPEC 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.ResultsThe 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, 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.ConclusionThe study clarified the genomic evolution characteristics of EPEC Deng genome and it’s PAIs, and is helpful for understanding genetic characteristics of native EPEC.