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Two hundred and twenty seven samples were collected from infected eyes producing 14(54%) from 26 the contact lens, 67(44%) from 152 conjunctivitis and 19(39%) from 49 keratitis. Bacteria in males (61.62%) was higher than females (38.37%) in conjunctivitis and keratitis, while, they isolated as 100% from conjunctivitis and keratitis together in females only. 16S rDNA sequencing of the 100 isolates showed 14 different bacterial species identified as Staphylococcus aureus (33%) and Staphylococcus epidermidis (28%) of most species followed by Pseudomonas aeruginosa and Enterococcus faecalis (7% for both), Bacillus subtilis (6%), Enterobacter hormaechei (4%). Streptococcus pyogenes, Staphylococcus hominis and Proteus mirabilis (3% for each). Staphylococcus lugdunensis (2%). Bacillus amyloliquefaciens, Staphylococcus haemolyticus, Enterobacter cloacae and Bacillus pumilus (1% for each). Nevertheless, 6 new global strains were isolated from contact lens cases (42.85%) comparing with 18 of non-contact lens cases (20.93%). OatA was detected in 22(91.6%) of S. aureus only using a new designed primer producing 2 novel OatA alleles from 15 different alleles groups. Generally, Moxifloxacin (96%), Gatifloxacin (95%) and Ofloxacin (95%) were the most effective antibiotics against all 100 isolated species. RAPD test for S. aureus strains showed only two strains from two different patients were identical, while all other S. aureus isolates were of different strains.