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Side effects describe the non-therapeutic consequences of the use of any pharmaceutical. All drugs have side effects in addition to their therapeutic effect, and doctors must consider both when deciding what medication to give a patient. For example, penicillin's therapeutic effect is killing bacteria in the bloodstream and digestive tract, but it also causes destruction of healthy digestive bacteria in all patients, diarrhea in some patients, and in some other patients it causes an allergic reaction. As such, it is clearly contraindicated for patients who are allergic to it, and may be contraindicated for patients with existing digestive tract problems.
A side effect should not be mistaken for an adverse effect. Often, the side effects may be neutral or even beneficial. In addition to aspirin's primary therapeutic effect - painkilling, some of its side effects are a reduction in inflammation (making it a good choice for those suffering from diseases such as arthritis which cause inflammation) and blood thinning (making it a good choice for patients who suffer from clotting). However, it's other side effect is gastritis (making it a poor choice for those suffering from any stomach ailment, particularly a gastric ulcer).
Poor pharmaceutical management often results in side effects of medication overwhelming the patient, resulting in additional medications to treat the side effect when instead the original drug should be reconsidered.