Comparative genome and evolution analysis of the locus of enterocyte effacement from enteropathogenic Escherichia coli Deng and its transcriptional response to ciprofloxacin.

ABSTRACT

PURPOSE: In this study, we aimed to investigate the genomic characteristics and evolution of pathogenicity islands of an enteropathogenic Escherichia coli (EPEC) strain, and to obtain a transcriptional profile of EPEC under different concentrations of ciprofloxacin using microarray analysis. METHODOLOGY: The complete EPEC Deng genome was sequenced and compared to genomes of 12 previously sequenced E. coli strains. A 180 min time course experiment was performed in which the effect of ciprofloxacin on EPEC Deng growth was evaluated. Microarray profiling was used to study the effect of varying ciprofloxacin pressure on genome-wide transcriptional expression. Differential expression of the genes identified using microarray data was confirmed using real-time quantitative reverse transcriptase PCR (RTQ). Target gene-defective recombineering strains were created to investigate the influence of the grlA gene on ciprofloxacin susceptibility. RESULTS: Genomic comparisons revealed a close phylogenic relationship between EPEC Deng and E. coli strains O111_H_11128 and O26_H11_11368, with low genetic diversity among their type III secretion system genes and typically genetic variation in the map, tir, eae and espA genes of EPEC. It is noteworthy that 21 genes were down-regulated at all time points examined in the group exposed to 2 µg ml-1 of ciprofloxacin. A grlA-mutant derivative with increased susceptibility to ciprofloxacin was discovered. CONCLUSIONS: The present findings provide an overview of the phylogenetic characteristics of EPEC Deng and its transcriptional response to ciprofloxacin, further suggesting that GrlA may play a clinically important role in EPEC responses to ciprofloxacin.