Molecular Analysis of Shigella sonnei Strains Isolated from Hospitals of Tehran and Ilam Cities Using Repetitive Extragenic Palindromic Polymerase Chain Reaction (REP-PCR)

Background and Objective: Shigella species belong to the family Enterobacteriaceae, which cause dysentery with abdominal pain and tenesmus in human. Our country is one of the endemic and occasional epidemic areas of the disease. In the present study, Repetitive Extragenic Palindromic Polymerase Chain Reaction (REP-PCR) technique that has high differentiation and specificity power compared to phenotypic markers, was used to investigate diversity and geographical distribution of colones as well as typing of Shigella strains. Materials and Methods: In this study, a total of 40 Shigella sonnei samples were isolated from stool of patients with diarrhea and divided into 5 groups. After identification and confirmation of the isolates by biochemical and serotyping methods, one colony of each isolate was cultured on LB medium and after DNA extraction, PCR was performed. After electrophoresis of the PCR product, gel images were saved in the computer for further analysis and typing of the isolates.  Results: In this research, 40 isolates were examined using REP-PCR and a similarity matrix was constructed based on Dice's coefficient. According to this matrix, some isolates were completely similar (genetic similarity coefficient= 1) and some isolates showed the least similarity (genetic similarity coefficient= 0). The dendrogram was obtained using the UPGMA algorithm. The calculated Cophenetic correlation coefficient for this dendrogram was 0.91645. Conclusion: From the results of the present study, it was concluded that we can type the Shigella sonnei strains using palindromic repetitive sequences. The extent of polymorphism indicates that REP-PCR technique is a useful method for genetic variation analysis in molecular typing of shigella sonnei strains. Although, some strains were completely similar, a high genetic variation was found among the studied population of Shigella sonnei. This level of variation is probably due to wide geographic distribution of this species in Iran.