All appropriate specimens should have a direct microscopic examination. The direct examination serves several purposes, first, the quality of the specimen can be assessed; for example, sputa can be rejected that represent saliva and not lower respiratory tract secretions by quantitation of white blood cells or squamous epithelial cells present in the specimen. Second, the microbiologist and clinician can be given an early indication of what may be wrong with the patient (e.g., 4+ gram-positive cocci in clusters in an exudate). Third, the workup of the specimen can be guided by comparing what grows in culture to what was seen on smear. A situation in which three different morphotypes (cellular types) are seen on direct Gram stain but only two grow out in culture, for example, alerts the microbiologist to the fact that the third organism may be an anaerobic bacterium.
Direct examinations are usually not performed on throat, nasopharyngeal, or stool specimens but are indicated from most other sources.
The most common stain in bacteriology is the Gram stain, which helps to visualize rods, cocci, white blood cells, red blood cells, or squamous epithelial cells present in the sample. The most common direct fungal stains are KOH (potassium hydroxide), PAS (periodic-acid Schiff), and calcofluor white. The most common direct add-fast stains are AR (auramine rhodamine), ZN (Ziehl-Neelsen), and Kinyoun. Chapter 6 describes the use of microscopy in clinical diagnosis in more detail.
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