Molecular characterization and virulence gene markers of Escherichia coli strains isolated from different patients in Saudi Arabia

The main objectives of this study were molecular characterization of isolated strains of E. coli 
collected from diseased patients from Al-Taif, Saudi Arabia, and screening the existence of some 
virulence genes in these isolated strains. Molecular characterization was carried out through two 
approaches (16S rRNA and rep-PCR). The existence of Stx1, Stx2, eaeA, hly, KpsII, fimH, UidA and 
YaiO genes were examined using polymerase chain reaction. Most of the examined isolates were 
sensitive to amoxicillin/clavulanic acid, cefoxitin, gentamicin, and nitrofurantoin, whereas high 
resistance to ampicillin, ceftazidime, and cefepime was observed with isolates TU-1 to TU-18. All 
isolates were sensitive to meropenem and amikacin. BLAST results of the sequenced 16S rRNA gene 
revealed that 19 isolates belong to E. coli and four isolates belong to other species, clustered into 
three different clusters. The previous results were attained using fingerprinting based on 16 rep
PCR primers. The rep-PCR primers yielded 302 distinct bands, of which 222 (73.5%) were 
considered polymorphic and 80 (26.5%) were considered monomorphic. The virulence genes KpsII 
and YaiO were detected in all E. coli isolates, neither stx2 nor eaeA were detected in all the 
examined isolates. Stx1, fimH, hly, and UidA were detected in 16.7%, 33.3%, 37.5%, and 66.7% of 
isolates. In conclusion, the findings of the present work suggested that 16S rRNA is more efficient 
approach in molecular characterization of bacterial isolates while, PCR is more suitable and rapid 
method for detection of virulence genes in most bacteria.