The goal of this study was to determine whether sequence analysis of internal transcribed spacer/5.8S ribosomal DNA (rDNA) can be used to detect fungal pathogens in patients with ocular infections (endophthalmitis and keratitis). Internal transcribed spacer 1 (ITS1) and ITS2 and 5.8S rDNA were amplified by PCR and seminested PCR to detect fungal DNA. Fifty strains of 12 fungal species (yeasts and molds) were used to test the selected primers and conditions of the PCR. PCR and seminested PCR of this region were carried out to evaluate the sensitivity and specificity of the method. It proved possible to amplify the ITS2/5.8S region of all the fungal strains by this PCR method. All negative controls (human and bacterial DNA) were PCR negative. The sensitivity of the seminested PCR amplification reaction by DNA dilutions was 1 organism per PCR, and the sensitivity by cell dilutions was fewer than 10 organisms per PCR. Intraocular sampling or corneal scraping was undertaken for all patients with suspected infectious endophthalmitis or keratitis (nonherpetic), respectively, between November 1999 and February 2001. PCRs were subsequently performed with 11 ocular samples. The amplified DNA was sequenced, and aligned against sequences in GenBank at the National Institutes of Health. The results were PCR positive for fungal primers for three corneal scrapings, one aqueous sample, and one vitreous sample; one of them was negative by culture. Molecular fungal identification was successful in all cases. Bacterial detection by PCR was positive for three aqueous samples and one vitreous sample; one of these was negative by culture. Amplification of ITS2/5.8S rDNA and molecular typing shows potential as a rapid technique for identifying fungi in ocular samples.The microbiological spectrum of infectious endophthalmitis shows that the percentage of isolates that are fungi is 8 to 18.5% (2,7,12,22,23) and in keratitis the rate is 16 to 35.9% (8,42). Clinical diagnosis of these ocular infections is confirmed by obtaining intraocular (aqueous or vitreous) specimens or corneal scrapings. However, standard microbiological tests are positive in only 54 to 69% of endophthalmitis cases (13,22,23) (by culture) and 80% (8) of keratitis cases (by Gram and Giemsa stains and culture). In fungal infections, even when positive, results usually take longer than a week because these organisms are difficult to identify and/or are slow-growing. Early diagnosis and rapid intervention is a critical element for an effective treatment of ocular infections. This has led to the development of culture-independent diagnostic tests such as PCR. PCR-based detection methods with universal primers for bacterial DNA in ocular samples (5,16,20,21,26,27,34,36,40) have recently been developed. For detection of fungal pathogens, multicopy gene targets have been evaluated for increasing the sensitivity (33, 39) and universal fungal PCR primers have been developed for broadening the range of detectable fungi (9,14,18,31,37). Studies on fungal DNA detection in ocular ...