Genotyping of Escherichia coli by PFGE

In the present study, 75 Escherichia coli isolated from seven different fish farms located in Trabzon and Rize. Water and sediment samples were taken from water inlet and outlet. Isolates were screened in the presence of erythromycin (ereA and ereB) and florfenicol (floR) genes. Potential relationship between antibiotic resistance genes and Pulse Field Gel Electrophoresis (PFGE) profile was determined. For this purpose, genomic DNA of the strains was digested with XbaI and ApaI restriction enzymes separately and run on the PFGE. Based on 93% similarity ratio, strains were grouped in 4 clusters (X1-X4) after cutting with XbaI. The similarity ratios among all isolates were 79.1%, and when TASWG 0411, TASSC 0811, TASSC 0211, SURWG 1010 and AASG 0810 strains of were separated from the other groups, similarity ratio was increased to 85.1%. Similar to XbaI restriction enzyme profile, after digesting bacterial DNA with ApaI, strains separated in 4 clusters (A1-A4). Largest cluster was A1 and it contained 51% of the strains. It was determined that the most common antibiotic resistance gene was ereB followed by ereA and floR. There was relationship was found between presence of antibiotic resistance genes and PFGE profile.