Great comments for this case!
"The structures remind me of microsporidia. And because (a) trichrome staining of urine isn't typical, and (b) it's posted by a parisitologist, I'm guessing protist . . ."
Yes, good guess - although, as another anonymous commenter states: "this is another good 'parasite' that the mycologists stole." It's true - genomic evidence suggests that microsporidia are actually highly specialized fungi and NOT parasites. Alas.
Finally, Luke mentions "The use of the Ryan's blue modified Trichrome stain is usually specifically for detection of microsporidia spores. I think this is what this is. Given the increased serum creatinine levels, the patient evidently has renal dysfunction - the respiratory symptoms could be caused by the fungal microsporidia infecting mulitple organs - respiratory system has been involved in other cases but less frequently compared to small intestine, urinary tract and biliary tree, and most commonly seen in AIDS patients. The first documented case of an extra intestinal case of microsporidiosis in a renal transmplant patient was reported by Latib et al (2001) and can be found here".
So more on this case:
The modified or Ryan's trichrome blue stain is useful for staining the spores a bright red; while it's not specific (yeast can stain a fainter pink and other organisms may also be positive), it's helpful for identifying the spores of this small (2-5 micron) organism. The presence of a central bar (running perpendicular to the long axis of the spore) is a helpful feature for distinguishing microsporidia from various yeasts:
This patient ended up having renal involvement (diagnosed by renal biopsy) as well as lung involvement (diagnosed by BAL). By a lab-developed PCR assay, the BAL and urine were positive for Encephalitozoon cuniculi. This was also confirmed by electron microscopy of the the renal biopsy. This is consistent with infection with this species that commonly causes urinary and respiratory disease. So in the end, both this patients rising creatinine and respiratory symptoms could be attributed to a single infectious cause.
Thank you all for the great comments!