Correct collection and handling of swab specimens helps laboratory staff members identify pathogens accurately with a minimum of contamination from normal bacterial flora.

Collection methods vary depending on the type of specimen being collected. For instance, collection of throat, nasopharyngeal, wound, external ear, and eye specimens usually involves sampling inflamed tissues and exudates, typically using sterile swabs of cotton or other absorbent material; wound exudate may also be aspirated into a syringe. Collection of fluid from the middle ear is performed by a doctor using a needle and syringe.

Because the normal bacterial flora in stool include several potentially pathogenic organisms, bacteriologic examinations are valuable for identifying pathogens that cause overt GI disease—such as typhoid and dysentery—and carrier states. A sensitivity test may follow isolation of the pathogen. Identifying the organism is vital to treat the patient, to prevent possible fatal complications (especially in a debilitated patient), and to prevent the spread of a severe infectious disease.