My patient needed a fecal transplant after a dental infection

Recently, a new patient walked into my practice angry, not at me, but at his previous dentist. Here's the irony: his general dentist did nothing wrong. The dentist correctly diagnosed a dental abscess and appropriately referred the patient to an endodontist. The endodontist, following what many consider standard protocol back in the day, prescribed clindamycin. What happened next transformed a dental infection into a medical nightmare that could have been avoided.

The patient developed severe watery diarrhea within days. He ended up hospitalized for IV fluids and received a diagnosis of Clostridioides difficile infection, commonly known as C. diff. Two rounds of antibiotics followed. Then came the recurrences—not one, but multiple episodes. Eventually, he faced a choice that no patient should have to make: continue suffering through endless cycles of infection or undergo fecal microbiota transplantation.

Understanding C. Diff: Beyond the textbook definition

We've all heard the term C. diff mentioned in dental school and continuing education courses. But do you truly understand the full cascade of suffering this infection unleashes, particularly the end-stage treatment? While I was familiar with fecal microbiota transplantation, or FMT, I had never met a patient who actually underwent the procedure.

Clostridioides difficile is an opportunistic pathogen lurking in approximately 0-15% of healthy adults' colons,¹ held in check by a diverse ecosystem of beneficial bacteria. When antibiotics decimate this protective flora, C. diff seizes the opportunity. The bacteria produce toxins: TcdA and TcdB, that attack the intestinal lining, causing inflammation and damage ranging from uncomfortable to life-threatening.²

The initial symptoms seem manageable enough: watery diarrhea, abdominal cramping, fever.³ But C. diff doesn't play by mild rules. The infection can progress to pseudomembranous colitis, where the colon develops inflammatory plaques visible on colonoscopy. In severe cases, patients develop toxic megacolon—a medical emergency where the colon dilates dangerously and can perforate.

C. difficile infection carries significant mortality. A large US surveillance study found that C. diff was responsible for approximately half a million infections and 29,000 deaths in a single year.⁴ Older adults are at particularly high risk for severe outcomes.

Here's what makes C. diff particularly insidious: recurrence.⁵ After treatment of an initial C. difficile infection, approximately 20%–30% of patients experience recurrence. With each subsequent episode, the risk of recurrence increases substantially, often reaching 40%–60%. Each recurrence becomes harder to treat, creating a vicious cycle that devastates patients' quality of life.

While any antibiotic can trigger C. diff by disrupting gut flora, certain classes pose dramatically higher risks. Clindamycin sits at the top of that dangerous list. Studies demonstrate that clindamycin use increases C. diff risk by 17-fold increased odds compared to nonuse.⁶ Read that again: 17 times higher risk. This isn't a marginal increase; it's an astronomical elevation that persists for months after even a short course of therapy.

The mechanism is straightforward but can be devastating. Clindamycin excels at killing anaerobic bacteria.⁷ Unfortunately, it can also substantially disrupt the beneficial anaerobic bacteria in the colon. This disruption reduces colonization resistance, creating conditions that allow C. difficile to proliferate. The drug's broad spectrum becomes its liability, creating exactly the conditions that allow this opportunistic pathogen to flourish.

The treatment that patients can't forget

My new patient's C. diff infections became recurrent and refractory to standard antibiotic therapy. This left one remaining option: fecal microbiota transplantation, or FMT. While cure rates exceed 90%,⁸ genuinely impressive in medicine, the psychological burden is substantial.

In 2023, the FDA approved Vowst, an oral version of FMT.⁹ Instead of receiving donor stool via colonoscopy or enema, patients now swallow oral capsules. But make no mistake: patients know exactly what they're ingesting. Those capsules contain fecal microbiota from rigorously screened donors, processed and freeze-dried, but unmistakably human stool. Despite extensive screening protocols, there remains a small chance that not all viruses can be completely removed. The capsules are designed to restore the diverse bacterial ecosystem that prevents C. diff colonization, a noble purpose that doesn't erase the psychological weight of the treatment.

My patient described the experience as humiliating and traumatic. He took four capsules daily for three consecutive days, each dose a stark reminder of how a routine dental antibiotic had derailed his health. The physical recovery took weeks. The psychological scars will likely last years, as they certainly would for me.

The alternatives we should have chosen first

Even for patients with documented penicillin allergies, safer alternatives exist.¹⁰ Azithromycin, a macrolide antibiotic, provides excellent coverage against gram-positive aerobes including Streptococcus species commonly implicated in dental infections.

While macrolides offer limited anaerobic coverage, combining azithromycin with metronidazole creates comprehensive antimicrobial coverage for odontogenic infections with dramatically lower C. diff risk. Metronidazole effectively targets gram-positive and gram-negative anaerobes including Prevotella and Porphyromonas species.

Recommended regimen for penicillin-allergic patients:

• Azithromycin: 500 mg on day 1, then 250 mg daily on days 2-4
• Metronidazole: 500 mg three times daily for 7 days

For patients without penicillin allergies, amoxicillin and amoxicillin-clavulanate remain safe, effective first-line options with significantly lower C. diff risk profiles.

What this means for your practice

The dental community must embrace antibiotic stewardship not as a bureaucratic burden but as fundamental patient care.

Before you write the next prescription, ask yourself: Is this truly the best choice, or simply the habitual one? Have I considered safer alternatives? Does this medication have drug interactions with the patient’s existing medications?

Most of us don't have sophisticated clinical decision support software that flags high-risk prescribing patterns. But tools exist: programs like MedAssent DDS offer real-time warnings about problematic antibiotic choices and suggest evidence-based alternatives with dosing guidance. The entire process takes less than one minute … one minute to potentially spare a patient months of suffering.

The bottom line

Our prescription pads and e-prescribing wield tremendous power over patients' lives. Every antibiotic we prescribe ripples through their microbiome, their immune system, and their overall health. We must wield this power with greater wisdom, always keeping in mind: First, do no harm.

The choice is yours. Choose wisely.

Also by the author:

• What physicians want dental providers to know
• Pause before your proceed: Why amiodarone should stop every dentist in their tracks

References

1. Furuya-Kanamori L, Marquess J, Yakob L, et al. Asymptomatic Clostridium difficile colonization: epidemiology and clinical implications. BMC Infect Dis. 2015;15:516. doi:1186/s12879-015-1258-4
2. Voth DE, Ballard JD. Clostridium difficile toxins: mechanism of action and role in disease. Clin Microbiol Rev. 2005;18(2):247-263. doi:10.1128/CMR.18.2.247-263.2005
3. Mada PK, Alam MU. Clostridioides difficile Infection. StatPearls [Internet]. StatPearls Publishing; 2026. https://www.ncbi.nlm.nih.gov/books/NBK431054/
4. Lessa FC, Mu Y, Bamberg WM, et al. Burden of Clostridium difficile infection in the United States. N Engl J Med. 2015;372(9):825-834. doi:1056/NEJMoa1408913
5. Management of recurrent Clostridioides difficile infection and use of fecal microbiota transplantation during the COVID-19 pandemic. Mayo Clinic. February 5, 2021. https://www.mayoclinic.org/medical-professionals/digestive-diseases/news/management-of-recurrent-clostridioides-difficile-infection-and-use-of-fecal-microbiota-transplantation-during-the-covid-19-pandemic/mac-20507272
6. Brown KA, Khanafer N, Daneman N, Fisman DN. Meta-analysis of antibiotics and the risk of community-associated Clostridium difficile infection. Antimicrob Agents Chemother. 2013;57(5):2326-2332. doi:10.1128/AAC.02176-12
7. Vincent C. Manges AR. Antimicrobial use, human gut microbiota and Clostridium difficile colonization and infection. Antiobiotics (Basel). 2015;4(3):230-253. doi:3390/antibiotics4030230
8. Baunwall SMD, Lee MM, Eriksen MK, et al. Faecal microbiota transplantation for recurrent Clostridioides difficile infection: an updated systematic review and meta-analysis. eClinicalMedicine. 2020;29-30:100642. doi:1016/j.eclinm.2020.100642
9. FDA approves first orally administered fecal microbiota product for the prevention of recurrence of Clostridioides difficile Press release. U.S. Food & Drug Administration. April 26, 2023. https://www.fda.gov/news-events/press-announcements/fda-approves-first-orally-administered-fecal-microbiota-product-prevention-recurrence-clostridioides
10. Safar J. Overview of dental emergencies. Merck Manual. Revised November 2024. https://www.merckmanuals.com/professional/dental-disorders/dental-emergencies/overview-of-dental-emergencies