Six genera of microsporidian organisms have been associated with human microsporidiosis (Enachiola, Enterocytozoon, Septata, Pleistophora, Trachipleistophora, and Vittaforma). Currently, diagnosis of microsporidiosis depends on direct visualization of the parasites by light and transmission electron microscopy (TEM). For exact species differentiation, ultrastructural analysis of spores and tissue stages has been necessary (Weber et al. 1992; Cali et al. 1993). Serology has not proved useful in the diagnosis of human microsporidial infections (Weber et al. 1994).

Using primers targeted to the small sub-unit (SSU) and internal transcribed spacers (ITS) of the rRNA gene of microsporidia, amplified DNA of Enterocytozoon bieneusi and Septata intestinalis in intestinal biopsies (Zhu et al. 1993; Franzen et al. 1995, 1996; Velasquez et al. 1996) and of E. bieneusi, E. cuniculi, and S. intestinalis in stool specimens, have been detected (Fedorko et al. 1995; Katzwinkel-Wladarsch et al. 1996; Velasquez et al. 1996; Ombrouck et al. 1997). Subsequently, species identification by Southern blot or endonuclease restriction digest is also reported (Fedorko et al. 1995; Franzen et al. 1996).

The resistant spores of microsporidia and the risk of co-extracting PCR inhibitors from stool specimens, have required laborious and time-consuming methods for extracting DNA from microsporidia, particularly from faecal samples (Fedorko and Hijazi 1996). However, Kock et al. (1997) presented recently two DNA preparation methods, facilitating a fast and simple DNA isolation from stool and tissue, not requiring toxic reagents. The potential for PCR to identify species of microsporidia, mainly from non-invasively acquired specimens, such as sputum and stool specimen, makes it an attractive diagnostic option. A recent comparison between microscopy, assuming to be the correct diagnostic tool, and PCR for detection of microsporidia, showed 88% sensitivity and 78% specificity for PCR. However, a previous study showed that sensitivity of microscopical detection of microsporidia was less than 100% (Beauvais et al. 1993).

Considering the pathognomonic clinical features of microsporidiosis, the true status of the PCR positive cases cannot yet be resolved (Katzwinkel-Wladarsch et al. 1997). Therefore, the paradigm for a laboratory diagnosis of microsporidiosis still involves screening for microsporidial organisms by morphological procedures, followed by confirmation and speciation with PCR (Federko et al. 1995; Ombrouck et al. 1997).

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