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Microbiological and physicochemical profiles of water samples collected from three aquatic ecosystems in Akwa Ibom State were determined using standard microbiological and chemical techniques. The antibiotic susceptibility profiles of the isolates were determined using disc diffusion technique. Physicochemical parameters of the water samples were also carried out using standard chemical methods. The total heterotrophic bacterial counts and total coliform counts of the water samples ranged from 2.0x107±0.17 to 2.6x107±0.44 CFU/ml and 1.8x105±0.38 to 3.3x105±0.3 CFU/ml, respectively. The total fungal and total vibrio counts ranged from 1.2x105±0.07 to 1.7x105±0.49 CFU/ml and 5.2x104±2.31 to 1.8x105±0.19 CFU/ml, respectively. The faecal coliform and total salmonella-shigella counts of the water ranged from 6.8x104±0.3 to 2.3x105±0.38 CFU/ml and 1.2x105±2.58 to 3.8x105±0.24 CFU/ml, respectively. Nine bacterial genera comprising Bacillus, Salmonella, Escherichia, Pseudomonas, Shigella, Staphylococcus, Vibrio, Proteus and Streptococcus species were isolated from the samples, while the fungal isolates were Aspergillus, Mucor, Penicillum, Rhizopus and Candida species. The bacterial isolates were highly resistant to Amoxicillin/Clavulanates and Cefuroxime, while high sensitivities to Gentamicin were observed among E. coli, Staphylococcus spp. and Pseudomonas spp. Analysis of variance showed that there was a high significant difference (p<0.05) between total viable counts obtained in the three sample locations while the correlation coefficient showed positive relationship between the total viable counts and some of the physicochemical parameters studied. The aquatic ecosystem studied, based on the bacteriological and physicochemical parameters revealed that the human, animal and agricultural activities plays significant role in the contamination of the water source. Consequently, the water should be properly processed before use.
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