There are several methods for diagnosing microsporidia:

Microscopy

Light microscopic examination of the stained clinical smears, especially the fecal samples, is an inexpensive method of diagnosing microsporidial infections even though it does not allow identification of microsporidia to the species level. The most widely used staining technique is the Chromotrope 2R method or its modifications. This technique stains the spore and the spore wall a bright pinkish red. Often, a belt-like stripe, which also stains pinkish red, is seen in the middle of the spore. This technique, however, is lengthy and time consuming and requires about 90 min. A recently developed “Quick-Hot Gram Chromotrope technique” however, cuts down the staining time to less than 10 min and provides a good differentiation from the lightly stained background fecal materials so that the spores stand out for easy visualization.  The spores stain dark violet and the belt-like stripe is enhanced. In some cases dark staining Gram positive granules are also clearly seen.  Chemofluorescent agents such as Calcofluor white are also useful in the quick identification of spores in fecal smears. The spores measure from 0.8 to 1.4 µm in the case of Enterocytozoon bieneusi, and 1.5 to 4 µm in Anncaliia algerae, Encephalitozoon spp., Vittaforma corneae, and Nosema spp.

Transmission electron microscopy (TEM) is still the gold standard and is necessary for the identification of the microsporidian species. However, TEM is expensive, time consuming, and not feasible for routine diagnosis.

Immunofluorescence Assays (IFA)

IFAs are available for microsporidia using monoclonal and/or polyclonal antibodies.

Molecular Methods (PCR)

The CDC offers molecular identification of Enterocytozoon bieneusi, Encephalitozoon intestinalis, Encephalitozoon hellem and Encephalitozoon cuniculi using species-specific polymerase chain reaction (PCR) assays. Molecular identification of other microsporidia species can be attempted using genera-specific primers and sequencing analysis on a case-by-case basis.

References:

1. Visvesvara GS, Da Silva AJ, Croppo JP, Pieniazek NJ, Leitch GJ,  Ferguson D, De Moura H, Wallace S, Slemenda SB, Tyrrell I, Moore DF, Meador J. In Vitro Culture and Serologic and Molecular Identification of Septata intestinalis Isolated from Urine of a Patient with AIDS. Journal of Clinical Microbiology, Apr. 1995, p. 930–936 Vol. 33, No. 4
2. Da Silva AJ, Schwartz DA, Visvesvara GS, De Moura H, Slemenda SB, Pieniazek NJ. Sensitive PCR Diagnosis of Infections by Enterocytozoon bieneusi (Microsporidia) Using Primers Based on the Region Coding for Small-Subunit rRNA. Journal of Clinical Microbiology, Apr. 1996, p. 986–987 Vol. 34, No. 4
3. Del Aguila C, Croppo GP, Moura H, Da Silva AJ, Leitch GJ, Moss DM, Wallace S, Slemenda SB, Pieniazek NJ, Visvesvara GS. Ultrastructure, Immunofluorescence, Western Blot, and PCR Analysis of Eight Isolates of Encephalitozoon (Septata) intestinalis Established in Culture from Sputum and Urine Samples and Duodenal Aspirates of Five Patients with AIDS. Journal of Clinical Microbiology May 1998, p. 1201–1208 Vol. 36, No. 5
4. Meissner EG, Bennett JE, Qvarnstrom Y, da Silva A, Chu EY, Tsokos M and Gea-Banacloche J. Disseminated Microsporidiosis in an Immunosuppressed Patient. Emerging Infectious Diseases July 2012, Vol. 18, No. 7, p. 1155-1158.