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MOLECULAR TYPING OF WATERBORNE E. COLI STRAINS USING REP-PCR

Reza Ranjbar, Maryam Makhmalzadeh, Naser Harzandi, Faham Khamesipour

Water borne bacteria, including E. coli as the top bacterial quality indicator, are over to be the vital concerns of some society. Typing of bacterial strains is used to confirm or reject epidemiologic evidence that a particular bacterium is the source of infection in a food type, water source or nosocomial infection. Molecular typing is a valued instrument for analysis of genetic relationship among the microbial strains. The purpose of the present study was to determine the molecular types of waterborne E. coli strains using REP-PCR. Present study comprised 100 waterborne E. coli strains isolated from different water sources in Karaj, Iran in 2013. Bacterial isolates were detected and identified via standard microbiological and biochemical exams. Genomic DNA was extracted via Genomic DNA Extraction Kit and genetic relationship among the strains was evaluated via REP-PCR using REP1 and REP2 primers. PCR amplicons were electrophoresed in 1.5% agarose gel and staining using ethidium bromide and visualized via a Gel DocTM XR+(BIORAD) and dendrogram was constructed based on Dice Comparison method and UPGMA Clustering. Using REP-PCR, all strains were typeable. Over 15 different bands ranging from 130 to 2300 bp were amplified in different profiles. Following digitizing (0 and 1) the positive genes and dendrogram construction by PAUP 4.0 software, dendrogram analysis showed the REP-PCR differentiated 100 environmental E. coli strains into 8 rep clusters however the r6 (28%) was the most prevalent cluster. Results of the present study indicated that E. coli strains isolated from different water sources in Karaj belong to diverse clones and different genotypes. Our finding also showed that REP-PCR is a powerful molecular tool with high performance and good discriminatory power for molecular typing of waterborne E. coli.