Answer: Visceral leishmaniasis involving the kidney
The diagnosis in this case is made by identifying Leishmania amastigotes within tissue macrophages (histiocytes) in the renal cortex. Although amastigotes resemble other small intracellular parasites (e.g. tachyzoites of Toxoplasma gondii), they can be differentiated by the presence of a rod-shaped kinetoplast (inset, arrow).
One of the readers raised the excellent question of how Leishmania amastigotes can be differentiated from those of Trypanosoma cruzi amastigotes. The short answer is that the amastigotes of these two related parasites are morphologically indistinguishable, and therefore it can be very difficult to differentiate them. Fortunately, there are some subtle clues which can help us: first, the organisms in this case are not forming pseudocysts in tissue (as is common for T. cruzi), but instead appear to be inside of macrophages (the cell of choice for Leishmania). The location (kidney) would also be extremely unusual for T. cruzi, which is predominantly seen in cardiac muscle, although it can less commonly be found in other tissues. Finally, the amastigotes in this case are extremely small, and it is difficult to make out the kinetoplast. In my experience, the amastigotes of T. cruzi appear to be slightly bigger in tissue than those of Leishmania, and it is much easier to make out the kinetoplast. Finally, the patient's history can be very useful supporting the morphologic diagnosis. In this case, the patient had a history of visceral leishmaniasis which had been inadequately treated.
One last interesting observation from this case is that the Jones silver stain was superior to the H&E for highlighting the kinetoplast . There is nothing in the literature about this stain being used this way, so I would love to hear feedback from anyone who has the chance to try it at their own institution!