This study evaluated the utility of SYBR Green real-time PCR for simultaneous detection and differentiation of microsporidial infections in hundred stool samples of immunosuppressed patients in comparison to the modified trichrome stain, and in relation to the age, sex, and different causes of immunosuppression of the patients. DNA was extracted using ISOLATE Faecal DNA Kit and amplification was performed in a light cycler using a Sen-siFAST TM SYBRHi-ROX PCR kit using MsRTf1 and MsRTr1 primers. Of 100 stool samples routinely analysed for microsporidian spores, 49 were positive by microscopy. By measuring the spore size using micrometre, determination of the species of the positive cases was 17 Encephalitozoon intestinalis, 15 Enterocytozoon bieneusi, 11 Encephalitozoon hellem, and six Encephalitozoon cuniculi based on the reference spores' size of each species. By SYBR Green real-time PCR, 55 stool samples were positive for microspoidial DNA upon determination of their specific melting curves, comprising 16 Encephalitozoon cuniculi, 14 Encephalitozoon hellem, 13 Encephalitozoon intestinalis, 10 Enterocytozoon bieneusi, and two unspecified species with melting temperature of 84.2018 and 84.903˚C. There was a positive agreement reaching 84 % between both techniques as regard the number of positive cases. Moreover, real-time PCR was superior over microscopy in species identification with statistically significant difference between both methods. However, there was no statistically significant difference between patients' age, sex and causes of immunosuppression with different Microsporidia species detected by real-time PCR. Thus, SYBR Green real-time PCR can be considered a fast and reliable method for detection and identification of Microsporidia species.
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