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Abstract Pseudomonas fluorescens and Pseudomonas aeruginosa are widely distributed in the freshwater ecosystem and are recognized the primary causal agents of bacterial haemorrhagic septicaemia in fish. P.fluorescens was isolated from tilapia Oreochromis niloticus fish. Three concentrations 4x1011, 4x108 and 4x105 cells/ml and 4.8x1011, 4.8x108 and 4.8x105 were used to study the pathogenic of P. fluorescens and P. aeruginosa respectively. The percentage of cumulative mortality in the O. niloticua fingerlings after seven weeks from inoculation with P. fluorescens was 76.7, 60 and 36.6%, respectively and 90, 50 and 36.7% mortality, for P. aeruginosa after five weeks, respectively. The highest percentage of mortality of fish having 4x1011, 4x108 cells/ml of P. fluorescens was in the first week, whereas it had achieved in the third week with concentration of 4x105. The LD50 for the P. fluorescens was (4 X107cells/ml) while it was (4.8X107 cells/ml) for P. aeruginosa. Specific primers of 16S rRNA gene of the two pathogens in PCR, DNA probe and restriction enzymes digestion (EcoR1, Tru91, HI, HaeIII and HindIII) of PCR product (RFLP-PCR) were used as the most commonly applied molecular methods used in routine diagnosis of fish diseases. Different annealing temperatures and different samples (purified DNA, bacterial colonies and different concentrations of diseased fish tissue homogenates were used. The specific primers of P. fluorescens and P. |