Antibiotics kill living bacteria but do nothing to the toxins leaching from calculus/tartar. Therefore, the inflammation persists and the infection returns shortly after the effect of the antibiotics wears off. Plus, when taken orally, all of the body's tissues are exposed to the antibiotics, which could lead to future allergies or the development of bacterial resistance. We use antibiotics for certain acute infections or after implant placement or when grafting with foreign materials.
Recently, time-released, localized antibiotic treatments have been developed and marketed. These treatments involve the dental therapist inserting or squirting an antimicrobial material under the gumline and leaving it there to slowly dissolve and release the medication into the pocket. The advantages of these treatments are that they deliver a very high, focused dose of medication to the periodontal pocket with little systemic or full body exposure. Scientific evidence shows that short-term improvements in pocket depth and health can be achieved. Unfortunately, the calculus/tartar that is the likely cause for the pocket's failure to heal, still remains on the root surface under the gumline. Unless these areas are carefully monitored and retreated when the infection returns, the risk of disease progression and bone loss is still high. This can be seen as a potential ticking time-bomb, where short-term improvements lull everyone into a false sense of security but danger persists. We rarely use these medications anymore.
In short, until the calculus/tartar is adequately cleaned out, the problems and risks of periodontal disease progression persist.