Microscopy can be done quickly, but accuracy depends on the experience of the microscopist and quality of equipment. Regulations often limit physicians' use of microscopy for diagnostic purposes outside a certified laboratory. Microscopic examination of tissue may be required to distinguish invasive disease from surface colonization—a distinction not easily achieved by culture methods.

Most specimens are treated with stains that color pathogens, causing them to stand out from the background, although wet mounts of unstained samples can be used to detect fungi, parasites (including helminth eggs and larvae), vaginal clue cells, motile organisms (eg, Trichomonas), and syphilis (via darkfield microscopy). Visibility of fungi can be increased by applying 10% potassium hydroxide (KOH) to dissolve surrounding tissues and nonfungal organisms.

The clinician orders a stain based on the likely pathogens, but no stain is 100% specific. Most samples are treated with Gram stain and, if mycobacteria are suspected, with an acid-fast stain. However, some pathogens are not easily visible using these stains; if these pathogens are suspected, different stains or other identification methods are required. Because microscopic detection usually requires a microbe concentration of at least about 1 × 10^4-5/mL, most body fluid specimens (eg, CSF) are concentrated (eg, by centrifugation) before examination.

Gram stain: The Gram stain classifies bacteria according to whether they retain crystal violet stain (gram-positive—blue) or not (gram-negative—red) and highlights cell morphology (eg, bacilli, cocci) and cell arrangement (eg, clumps, chains, diploids). Such characteristics can direct antibiotic therapy pending definitive identification. Finding a mixture of microorganisms with multiple morphologies and staining characteristics on Gram stain suggests a polymicrobial bacterial infection. To do a Gram stain, technicians heat-fix specimen material to a slide and stain it by sequential exposure to Gram crystal violet, iodine, decolorizer, and counterstain (typically safranin).

Acid-fast and moderate (modified) acid-fast stains: These stains are used to identify acid-fast organisms (Mycobacterium sp) and moderately acid-fast organisms (primarily Nocardia sp). These stains are also useful for staining Rhodococcus and related genera, as well as oocysts of some parasites (eg, Cryptosporidium).

Although detection of mycobacteria in sputum requires at least 10,000 organisms/mL, mycobacteria are often present in lower levels, so sensitivity is limited. Usually, several mL of sputum are decontaminated with Na hydroxide and concentrated by centrifugation for acid-fast staining. Specificity is better, although some moderately acid-fast organisms are difficult to distinguish from mycobacteria.

Fluorescent stains: These stains allow detection at lower concentrations (< 1 × 10⁴ cells/mL). Examples are acridine orange (bacteria and fungi), auramine-rhodamine and auramine O (mycobacteria), and calcofluor white (fungi, especially dermatophytes).

Coupling a fluorescent dye to an antibody directed at a pathogen (direct or indirect immunofluorescence) should theoretically increase sensitivity and specificity. However, these tests are difficult to read and interpret, and few (eg, Pneumocystis and Legionella direct fluorescent antibody tests) are commercially available and commonly used.

India ink (colloidal carbon) stain: This stain is used to detect mainly Cryptococcus neoformans and other encapsulated fungi in a cell suspension (eg, CSF sediment). The background field, rather than the organism itself, is stained, making any capsule around the organism visible as a halo. In CSF, the test is not as sensitive as cryptococcal antigen. Specificity is also limited; leukocytes may appear encapsulated.

Warthin-Starry stain and Dieterle stain: These stains are used to visualize bacteria such as spirochetes, Helicobacter pylori, microsporidia, and Bartonella henselae (the cause of cat-scratch disease).

Wright stain and Giemsa stain: These stains are used for detection of parasites in blood, Histoplasma capsulatum in phagocytes and tissue cells, intracellular inclusions formed by viruses and chlamydia, trophozoites of Pneumocystis jirovecii, and some intracellular bacteria.

Trichrome stain (Gomori-Wheatley stain) and iron hematoxylin stain: These stains are used to detect intestinal protozoa.

The Gomori-Wheatley stain is used to detect microsporidia. It may miss helminth eggs and larvae and does not reliably identify Cryptosporidium. Fungi and human cells take up the stain.

The iron hematoxylin stain differentially stains cells, cell inclusions, and nuclei. Helminth eggs may stain too dark to permit identification.

Last full review/revision February 2013 by Kevin C. Hazen, PhD

Content last modified March 2013