COMPARATIVE GENOMICS FOR IDENTIFICATION OF UROPATHOGENIC Escherichia coli SPECIFIC GENES SERVING AS TARGETS FOR MOLECULAR DIAGNOSIS OF URINARY TRACT INFECTIONS
NOURELHOUDA CHALAL *
School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham NG11 8NS, UK
*Author to whom correspondence should be addressed.
Abstract
Introduction: Uropathogenic E. coli strains (UPEC) are considered as the main etiological agents of urinary tract infections (UTIs) and account for more than 80% of all UTIs. The aim of this work was to identify UPEC specific genes which could serve as targets for molecular diagnosis of urinary tract infections.
Materials and Methods: In this study, comparative genome analysis of three different strains of E. coli was performed, using several bioinformatics tools. Additionally, primers regarding the selected gene “HlyA” were designed. Agarose gel electrophoresis was then applied to analyze PCR products.
Results: The findings from our study revealed that hlyA, hlyB, hlyC, hlyD, pap E, pap F, pap G, sat, mchC, mchD genes were found to be specific to CFT073 E. coli and therefore, are UPEC specific genes. PCR results revealed several bands with different sizes (< 500 bp). HlyA primers were successfully designed and were found to be specific to UPEC.
Conclusions: UPEC specific genes identified from bioinformatics analysis could be considered as attractive diagnostic markers for urinary tract infections. Fast pathogen detection is essential in order to save time as well as to prevent serious complications. PCR method represents a powerful genotypic, informative as well as specific assay for the detection of a variety of virulence factors that contribute to the development and occurrence of UTIs.
Keywords: Urinary tract infections, uropathogenic E. coli, genes, PCR