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Antibiotics in endodontics: a desktop reference

CE Publish Date: April 2, 2024
CE Expiration Date: March 18, 2027
CEU (Continuing Education Unit):2 Credit(s)
AGD Code: 070

Educational aims and objectives

This self-instructional course for dentists aims to discuss the pros and cons of prescribing antibiotics for a range of endodontic procedures.

Expected outcomes

Endodontic Practice US subscribers can answer the CE questions by taking the quiz online to earn 2 hours of CE from reading this article. Correctly answering the questions will demonstrate the reader can:

  1. Recognize the statistics regarding antibiotic over-
  2. Realize how overprescribing may lead to antibiotic
  3. Identify types of endodontic infections, their causes, and detrimental effects.
  4. Realize some reasons that antibiotics may not be effective in certain endodontic situations.
  5. Identify guidelines for prescribing or not prescribing antibiotics in endodontic practice.
  6. Realize prophylaxis guidelines and possible antibiotic regimens, when

Knowing when to prescribe antibiotics in endodontics can be complex. Dr. Joseph C. Stern provides this reference of pros and cons.

Dr. Joseph C. Stern discusses the benefits and drawbacks of prescribing antibiotics in endodontics


Over the years, one of the biggest concerns with antibiotics has been their overuse. There have been many studies attesting to this. The Centers for Disease Control and Prevention (CDC) conservatively estimates that 47 million prescriptions for antibiotics (30% of all outpatient antibiotic prescriptions) are unnecessary.1-4 The result of this overuse is the development of microbial resistance. Antibiotics alter the natural balance of normal flora by attacking vulnerable organisms allowing resistant organisms to thrive and multiply. This overuse enables a greater quantity of our bacteria to become resistant to antibiotics over time.5 One of the ways to prevent this is with the very cautious use of antibiotics.

Regarding dental-related infections, antibiotics have limitations that should be understood before prescribing them.6-12 Without a blood supply in a necrotic and infected pulp, antibiotics have no access to the pulp space. They may only help to control the spread of the infection in the periapical area which is important in preventing the spread of infection beyond the fascial planes. Another point to be discussed is the importance of dental treatment as the primary way of combating dental infections rather than simply relying on antibiotic prescription. There are, however, times where antibiotics are indicated and should be prescribed.

Range of infection

Endodontic infections can range from being localized to life threatening. These infections are polymicrobial, characterized mostly by anaerobic bacteria and some facultative bacteria. Bacteria and their endotoxin by-products within the root canal produce a periradicular inflammatory response. With microbial invasion of periradicular tissues, an acute abscess and cellulitis may develop. The inflammatory response may give rise to a protective effect by isolating the infection to the periapical tissues and preventing it from spreading systemically. However, it can also be very destructive to surrounding tissue and may become systemic.

Severe and life-threatening infections can develop beyond the local environment depending on the pathogenicity of the microorganisms involved and the resistance of the host. Clinical signs and symptoms of an infection are the result of damage to the tissues caused by the microbe and the inflammatory response produced by the host. The spread of infection and the inflammatory response will continue until the source of the irritation is removed. Antibiotics (and incision for drainage) can only assist in controlling the infection, but only removal of the source of the infection will ultimately lead to healing. Effective treatment of endodontic infections includes removal of the reservoir of infection by either endodontic treatment or tooth extraction.13-19

Occasionally, a local infection may suddenly spread systemically, due to a breakdown in the patient’s immune response, and become a life-threatening situation. Unless the dentist is reachable 24/7, it might be wise to prescribe antibiotics up front, to be taken only if systemic symptoms (pain, swelling, fever, etc.) develop.


Patients often ask us, if I have an infection in my tooth, why do I need a root canal? Can’t I just take an antibiotic? We must be prepared to answer these questions in laymen’s terms, explaining the basics of root canal infections. Root canal infections are quite unique due to their isolated location. A root canal infection is a continuum of the carious process in which bacteria first invade the enamel and dentin and eventually make their way into the pulp. Bacteria inside the pulp create an inflammatory process which eventually leads to pulpal necrosis (destruction of the pulp tissue).

Unfortunately, the process doesn’t end there. As bacteria, and/or their endotoxins make their way through the apical foramen, they then trigger an inflammatory process (immune response) in the periapical tissues surrounding the root. This inflammatory response in the periapical tissues may give rise to a protective effect by walling off the infection in the periapical tissues and preventing it from spreading systemically. Eventually, with microbial invasion of periradicular tissues, an acute abscess and cellulitis may develop. This spread of infection can be very dangerous, even life threatening.

A common theme we speak of is: Location! Location! Location! A very unique component of root canal and periapical infections is their isolated nature and distance from an adequate blood supply. Herein lies the key as to why antibiotics don’t work to resolve root canal infections. Antibiotics travel via systemic circulation, while the root canal space and the body of a periapical lesion have very poor perfusion. Essentially, antibiotics have no circulatory pathway to enter the pulp. The “train” carrying antibiotics doesn’t “stop” at the root canal frequently enough, and thus, its inability to rid a root canal of its bacterial content. This begs the question of why we prescribe antibiotics at all? The answer is that it is the danger of a local root canal infection having the potential to spread systemically causing potentially life-threatening infections. In essence, antibiotics stand guard at the peripheral tissues to prevent the infection from spreading. Antibiotics are not prescribed to rid our body of a root canal infection but rather to aid our immune system in handling the infection in conjunction with root canal treatment.

Another reason antibiotics may be ineffective in removing root canal infections is because of the unique nature of these infections. The microbes in the canal are colonized in biofilm attached to the wall of the canal, and antibiotics don’t do well penetrating the powerful “fortresses” of the biofilm.20 Biofilm can be defined as a sessile multicellular microbial community characterized by cells that are firmly attached to a surface and enmeshed in a self-produced matrix of extracellular polymeric substance (EPS), usually a polysaccharide. This structure allows the biofilm to firmly adhere to the dentinal walls, essentially like “bacteria stuck in glue.” Bacteria form complex communities that are very resistant to removal by disinfecting agents including the most powerful antibiotics. Bacteria form biofilms on the dentin walls inside the main root canal as well as in lateral ramifications, isthmuses, and even within the dentinal tubules themselves. In advanced stages of endodontic disease, they can also be found attached to the outer surface of the root apex.

The microbes can be extremely difficult to remove due to the many virulent factors they contain:

  1. Biofilms can restrict the penetration of anti-microbial agents due to their sophisticated matrix and its neutralizing enzymes.
  2. Bacteria in biofilms can enter a special stage called the “stationary phase” which allows them to survive in even the harshest environments, such as when they are under attack by antimicrobials. It also allows them to survive extended periods without the nutrients that are usually needed for survival.
  3. Quorum sensing: bacteria living in biofilms have a very sophisticated form of communication. Think “iPhone for bacteria.” This form of communication is carried out by diffusible signal molecules or “auto-inducers,” which allow bacteria to communicate in a harmonious manner and survive and persist in harsh environments, such as the root canal.
  4. Lateral gene transfer (LTG): Microbes in a biofilm exchange DNA, some of which transfer antibiotic resistance and generally enhance survival.

Because of the above-mentioned factors, it is prudent to be very selective with the use of antibiotics and understand their limitations. The key to treatment of these infections is dental intervention whether through pulpal debridement, incision and drainage, or tooth extraction when indicated.

Antibiotic guidelines21-23

Generally antibiotics are not prescribed for the following:
  1. A patient with a diagnosis of pulpitis (irreversible or reversible) with or without apical periodontitis (pain to percussion caused by inflammation of the periapical tissues). Antibiotics are not indicated where the pulp is vital, even when severely inflamed. If the patient has signs and symptoms indicative of a vital but inflamed pulp, such as lingering pain to temperature or spontaneous pain caused by caries, a deep restoration, or a crack, the treatment of choice is root canal therapy, not antibiotics.
  2. A patient with a diagnosis of pulp necrosis with symptomatic or asymptomatic apical periodontitis (periapical radiolucency present). This also includes the category of patients who have had previous endodontic treatment and present with a periapical radiolucency, with or without symptoms. The key is pain management and endodontic treatment. If immediate treatment or thorough instrumentation of the root canal is not possible, then a “delayed prescription” can be implemented, where an antibiotic is prescribed to be taken only if the situation starts to deteriorate in terms of pain/swelling and systemic involvement. Many practitioners will prescribe antibiotics or a “delayed prescription” for an infected tooth whether immediate treatment is an option or not, as a precautionary measure.
  3. A diagnosis of chronic apical abscess (sinus tract/fistula/parulis). Endodontic intervention (or extraction if appropriate) is indicated.
Generally, antibiotics are indicated for the following:
  1. A patient with a diagnosis of pulp necrosis with acute apical abscess (a necrotic and infected pulp that causes a localized swelling) if immediate treatment is not a possibility. However, if immediate endodontic intervention is an option, then a delayed prescription can be employed rather than initially placing the patient on an antibiotic. Antibiotics are only an adjunct to treatments such as pulpal debridement, incision and drainage, or extraction if appropriate. Many practitioners will prescribe antibiotics to be taken in all cases of acute abscesses as a precautionary measure.
  2. A patient with a diagnosis of pulp necrosis with acute apical abscess and systemic involvement (swelling that is no longer localized). Systemic involvement includes one or more of these entities: evidence of lymph node involvement, facial space involvement, fever, or malaise. These are indicators that the infection is more widespread. Antibiotics are only an adjunct to treatments such as pulpal debridement, incision and drainage, or extraction if appropriate.
  3. Generally, if after initiating root canal therapy the patient’s symptoms rapidly worsen in terms of pain and swelling, antibiotics should be considered.
  4. Generally, if the patient is immunocompromised and being treated for an infected tooth, antibiotics should be considered to aid the patient’s immune system in resolving the infection.

Prophylaxis guidelines24-29

  1. The main indications for antibiotic prophylaxis have been to prevent infective endocarditis (IE) and prosthetic joint implant infection (PJI).
  2. Prophylaxis against IE is reasonable before dental procedures that involve manipulation of gingival tissue, manipulation of the periapical region of teeth, or perforation of the oral mucosa in patients with the following:
    1. Prosthetic cardiac valves, including transcatheter-implanted prostheses and homografts.
    2. Prosthetic material used for cardiac valve repair, such as annuloplasty rings and chords.
    3. Previous history of IE.
    4. Unrepaired cyanotic congenital heart disease or repaired congenital heart disease, with residual shunts or valvular regurgitation at the site of or adjacent to the site of a prosthetic patch or prosthetic device.
    5. Cardiac transplant with valve regurgitation due to a structurally abnormal valve.
  3. The risk of IE is highest in the first 6 months after a heart transplant because of endothelial disruption.
  4. The regiment includes 2g of amoxicillin 30-60 minutes before the procedure. If the patient is allergic to penicillin, then one can use 2g of cephalexin, 600 mg of clindamycin, or 500 mg of azithromycin. If the dosage of antibiotic was inadvertently not administered before the procedure, it may be administered for up to 2 hours after the procedure.
  5. For patients who require prophylaxis but are already taking antibiotics for another condition, select an antibiotic from a different class than the one the patient is already taking. For example, if the patient is taking amoxicillin, then select azithromycin or clarithromycin for prophylaxis.
  6. In general, for patients with prosthetic joint implants, prophylactic antibiotics are not recommended prior to dental procedures to prevent prosthetic joint infection (PJI). In cases where antibiotics are deemed necessary, it is most appropriate that the orthopedic surgeon recommend the appropriate antibiotic regimen, and when reasonable, write the prescription.
  7. If there is an increased medical risk, clinical recommendation should be integrated with the practitioner’s professional judgment and the patient’s needs and preferences. Consultation with the patient physician is prudent.

Table 1 Agent Instructions Dosage Penicillin Can be used as an alternative to amoxicillin. Loading dose of 1,000 mg followed by 500 mg every 4-6 hours for 3-7 days (4 times a day) Amoxicillin Stronger and more sustained serum levels than penicillin. Loading dose of 1,000 mg followed by 500 mg every 8 hours for 3-7 days (3 times a day) or 875 mg 2 times a day. Augmentin (amoxicillin with clavulanic acid) If the infection resists amoxicillin, then prescribe Augmentin. 500/125 mg every 8 hours for 3-7 days (3 times a day) Clindamycin Serious dental infections, but the patient is allergic to penicillin. (Clostridium difficile is a concern). Loading dose: 600 mg followed by 300 mg or 150 mg every 6 hours for 3-7 days (4 times a day) Azithromycin (Z-Pak) Serious dental infections, but the patient is allergic to penicillin. (Concern for causing cardiac arrhythmias). Loading dose of 500 mg on day 1 followed by 4 days of 250 mg. (1 time a day) Metronidazole (Flagyl) Add to penicillin or amoxicillin if needed. Only effective against anaerobes. Loading dose: 1,000 mg followed by 250 mg or 500 mg every 8 hours for 3-7 days. (3 times a day) Cephalexin (Keflex) Serious dental infections, but patient is allergic to penicillin (however if the patient has a history of anaphylaxis, angioedema, or hives with penicillin then azithromycin or clindamycin is indicated). 500 mg every 6 hours for 3-7 days (4 times a day)Recommended antibiotics (Table 1):

  1. If the patient is not allergic to penicillin, then the recommended antibiotic is amoxicillin 500 mg 3 times a day. Penicillin 500 mg. 4 times a day can also be used.
  2. If amoxicillin isn’t working, then either supplement with metronidazole 500 mg or switch patient to amoxicillin and clavulanate (Augmentin) 500/125 mg 3 times a day.
  3. If the patient has a reported penicillin allergy but no history of anaphylaxis, angioedema, or hives with penicillin, ampicillin, or amoxicillin, then prescribe cephalexin 500 mg. If they do have a history of anaphylaxis, angioedema, or hives, then prescribe azithromycin 250 mg or clindamycin 300 mg. If this fails, then add metronidazole 500 mg.
  4. The patient can stop the antibiotic after 3 days if the symptoms resolve instead of the usual 7-10 course.


Please note: The evidence based information in this article is not intended to substitute for a clinician’s expert judgment on a case-by-case basis.

After reading about cautions for providing antibiotics in endodontics, find out more about managing pain while reducing patients’ dependence on opioids in “Management of pre- and postoperative dental and surgical pain during the opioid crisis,” by Drs. Diana Bronstein and Rita Steiner here: Subscribers can take the CE quiz and receive 2 CE credits!

Author Info

Joseph C. Stern, DDS, is a Diplomate of the American Board of Endodontics. He is the Director of Endodontics at the Touro College of Dental Medicine and lectures frequently on the subject of clinical endodontics. He has lectured at many local county dental societies, the New Jersey Dental Association Annual Session in May 2019, and the Greater New York Dental Meeting in 2020. He maintains a private practice, Clifton Endodontics, in Clifton, New Jersey. He can be reached at

Disclosure: The author reports no conflicts of interest.


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Continuing Education (CE)

The continuing education article below is available to subscribers of Endodontic Practice US. In order to earn continuing education credits, you must be a Free or Paid subscriber and complete a short quiz about the content of the article. Our Free CE is limited to only 2 free credit hours per year.

Purchase a subscription now.

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