The images from the kidney show small oval spores (approximately 1.5 x 0.5 micrometers) within the renal tubular cells. The fact that they are focally acid fast using Ziehl-Neelsen staining and nicely highlighted with Ryan's Trichrome Blue (a chromotrope 2R stain) is highly suggestive of microsporidiosis. The positively-stained spores in urine are also consistent with microsporidia, although as Jamal points out, this is not a specific stain and other organisms such as yeasts can stain (although not usually as darkly red-pink as microsporidia spores). Indeed, this can be a challenging stain to interpret, especially because many of the microsporidia (particularly those found in stool - Encephalitozoon intestinalis and Enterocytozoon bieneusi) are very tiny, measuring only 1 to 1.5 micrometers in length. Some of the other microsporidia (e.g. Nosema, Brachiola, Anncaliia) are significantly larger, measuring up to 5 micrometers in length and thus resemble small yeasts.
As many of the readers pointed out, it is the TEM image that provides confirmation of the diagnosis. As noted by Dr. Louis Weiss, this is most likely Encephalitozoon cuniculi based on the clinical presentation and EM appearance (although he notes that other Encephalitozoon spp. will have a similar appearance on EM.) We also performed PCR which was positive for E. cuniculi. Some of the characteristic EM features are demonstrated below: