There are many reasons why root canal treatments fail, but all of them involve bacterial growth inside the tooth. If any spaces are left near the apices's (the opening at the end of the root), teeth can become contaminated with bacteria and become infected. Most dentists use gutta percha to obturate (fill)most of the root canal system and in addition use a thin coat of sealer to coat the gutta percha as it meets the walls of the root canal system. Although there are different types of sealers , most of the sealers,with the exception of one that is an epoxy type(AH26), will eventually wash out and leave a tiny gap. If the gutta percha doesn't adequately obturate the end of the root, then the remaining space is either filled by sealer or worse is empty. In either case, if the apice of the tooth is not obturated adequately with gutta percha,then endodontic failure can occur. (Sealer alone won't keep bacteria out of the rootcanal system, since, as mentioned earlier, sealers wash out over time).
Some roots have multiple canals with multiple exit points from the tooth and sometimes these extra canals can be difficult to predictably obturate and that too can lead to endodontic failures.
Cracks in the walls of the root can also be the cause failures, since these invariably become contaminated with bacteria and cause infections. Teeth that are cracked inside the bone are often hopeless and require extraction.
Another cause of endodontic failures are teeth that are not adequately restored. Perfectly adequately endodontically treated teeth can fail, if they loose a filling and get contaminated. Studies have shown that teeth left open, with out a proper restoration can require a re treatment of the root canal in as little as thirty days.
In addition, root canal therapies can fail for other reasons, including inadequate cleaning and shaping of the canal system, or a lack of aseptic techique. All failures involve a root canal system that becomes contaminated with bacteria.
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