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Abstract This study aims to determine the impact of five main drains as sources of pollution on the water quality of River Nile at Rosetta branch, concerning physicochemical and microbiological characteristics. Eco-diversity studies of bacterial isolates were carried out through: antibiotic sensitivity, virulence and genetic variability. Eco-diversity studies of viral isolates were throughout: plaque morphology, host range, particle size, shape and molecular weight of genome. The results of physicochemical, bacteriological and virological analyses revealed that, all drains selected in the study were suffering from varying levels of pollution. There was a gradual decrease in pollution levels along Rosetta branch (from downstream El-Rahawy to downstream Tala drain). The pollution impact caused by drains on Rosetta branch was remarkable from El-Rahawy drain which was considered the main point source of pollution. Results of water quality index was very bad in El-Rahawy and Sabal drains outlet and bad for all sites taken in this study except for upstream El-Rahawy drain, it was evaluated as being of medium quality. Identification of bacterial isolates was carried out according to Bergey‟ s Manual of Systematic Bacteriology and confirmed using the analytical profile index 20 E strip system. Results revealed that, out of 225 isolates, 212 were belonging to four main bacterial families. The results of antibiotics resistance patterns for different bacterial isolates showed that Ecoli isolates were resistant to about (75%), Citrobacter freundii isolates (45%), Salmonella sp. isolates (85%), Proteus vulgaris isolates (87.5%), Pseudomonas aeruginosa isolates (100%), Enterococcus faecalis isolates (82.5%) and Staphylococcus aureus isolates (77.5%) of the tested antibiotics. Most of isolates were multiple antibiotic resistant (MAR). Methicillin resistant Staphylococcus aureus (MRSA) was reported in four isolates from drains and thirteen isolates from Rosetta branch. While, vancomycin resistant isolates (VRSA) were recorded, three isolates from drains and four isolates from Rosetta branch. Results of virulence test for all isolated bacteria showed positive congo red test (100%) for C.freundii and Salmonella sp, followed by P.aeruginosa (98%), P.vulgaris (91%), E.coli (60%), E.faecalis (40%) and S.aureus (72.3%). The three P.aeruginosa isolates selected from different sites were successfully amplified and sequenced using 16s rDNA gene. Data showed that partial nucleotide sequences were 1274, 1280 and 1286bp, respectively |