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A basic stain stains the bacteria (the stain is a positively charged molecule that attaches to cells which are negatively charged or to negatively charged molecules in cells.) A negative stain does not stain cells (why its called a negative stain), it stains the background around the cells.
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 Ã 10 4-5 /mL, most body fluid specimens (eg, CSF) are concentrated (eg, by centrifugation) before examination.