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Identifying pathogens in tissue — special stains and morphology
In tissue, a pathogen is identified by combining the tissue reaction (pus, granuloma, necrosis) with a special stain that highlights it — Ziehl-Neelsen for acid-fast bacteria, GMS and PAS for fungi, mucicarmine for the Cryptococcus capsule, silver stains for spirochaetes and small bacteria — together with immunohistochemistry and PCR, and always alongside culture.
Why it matters in the exam
The bank shows an image and a stain and asks for the pathogen. Cryptococcus in the brain of an immunosuppressed patient appears as round yeasts with a thick capsule that stains red with mucicarmine. Pneumocystis jirovecii in the lung of a patient with HIV and low CD4 causes a foamy alveolar exudate, and its cysts appear on GMS as "cups" or crushed spheres; it does not grow in routine culture. Aspergillus shows septate hyphae with acute-angle branching and invades vessels; Mucorales show broad ribbon-like hyphae with few septa and right-angle branching. Candida shows yeasts and pseudohyphae.
Viral inclusions: CMV causes cell enlargement with a large nuclear inclusion ("owl's eye") and cytoplasmic inclusions; HSV causes multinucleated cells, nuclear "moulding", margination of chromatin and nuclear inclusions; measles produces multinucleated giant cells. Acid-fast bacteria stain with Ziehl-Neelsen, and with Fite for leprosy bacilli and Nocardia. Helicobacter pylori is seen with Giemsa or a silver stain. Legionella is highlighted by dedicated silver stains and not by a routine Gram stain in tissue.
A hydatid cyst (Echinococcus) in the liver or lung is made of a laminated outer membrane, a germinal layer and protoscolices; its rupture can cause an anaphylactic reaction and secondary spread, so it must not be punctured without preparation. An important rule: a negative stain does not exclude infection, and tissue morphology does not always separate similar fungi — so fresh tissue is sent for culture and molecular testing when infection is suspected.
Key points
- Ziehl-Neelsen for acid-fast bacteria; Fite for leprosy and Nocardia.
- GMS and PAS for fungi; Pneumocystis on GMS.
- Mucicarmine for the Cryptococcus capsule.
- CMV — owl's eye; HSV — multinucleation and moulding.
- Always combine culture and molecular tests.
Summary table
| Stain | What it highlights | Example | Note |
|---|---|---|---|
| Ziehl-Neelsen and Fite | Acid-fast bacteria | Tuberculosis; Fite for leprosy and Nocardia | Negative does not exclude |
| GMS (methenamine silver) | Fungal wall | Pneumocystis, Aspergillus | Pneumocystis cysts as "cups" |
| PAS | Fungi, glycogen | Candida; macrophages in Whipple disease | — |
| Mucicarmine | Cryptococcus capsule | Cryptococcus in the brain | Red capsule |
| Silver stains and Giemsa | Spirochaetes, H. pylori, Bartonella, Legionella | Cat-scratch disease, H. pylori | Warthin-Starry |
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Sources
- Procop GW, Pritt BS. Pathology of Infectious Diseases, 2nd edition (2024) — Histochemical stains and morphological identification
- Robbins and Cotran Pathologic Basis of Disease, 10th edition (2021) — Infectious diseases
- Bancroft's Theory and Practice of Histological Techniques, 8th edition (2019) — Microorganisms
Sources are given for further reading; the text is written afresh and not copied from them.
Reviewed by the Examqo AI Professor · 2026-11-06. The text may contain errors; when in doubt, check the source.