DNA sequence-based identification of pathogens from ocular samples of patients with clinically suspected eye infections was accomplished using 16S and internal transcribed spacer (ITS) ribosomal RNA gene sequence analysis. PCR was positive for 24 of 99 samples tested. Both culture and 16S rDNA sequence analysis identified Pseudomonas aeruginosa, streptococci and Enterobacteriaceae. Isolates misidentified as Burkholderia cepacia by biochemical tests were identified as Ralstonia mannitolilytica by 16S rDNA sequence analysis. Sequence analysis identified the following microorganisms from 19 culture-negative samples: Haemophilus influenzae, Sphingomonas sp., Klebsiella pneumoniae, Staphylococcus haemolyticus, Morganella morganii, Mycobacterium sp., Chryseobacterium sp., Pseudomonas saccharophila (Xanthomonas) and the fungus, Phaeoacremonium inflatipes.

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