Antibiotics and Crohn’s Disease: Help or Hurt?

Medically Reviewed by Minesh Khatri, MD on June 02, 2024
5 min read

Crohn’s disease is an inflammatory bowel disease (IBD). It’s characterized by chronic inflammation in the digestive tract. There’s no cure for Crohn’s, but medications including antibiotics may help manage the disease.

Antibiotics are medications used to treat or prevent infections caused by bacteria. They work by either killing bacteria or keeping the bacteria from growing and multiplying.

Medical experts speculate that an overgrowth of bacteria is one of the causes of Crohn’s disease. To get the bacteria under control, your provider might recommend antibiotics as part of your treatment plan.

Also, other medications for Crohn’s might weaken your immune system which may trigger infections. These infections may call for a round of antibiotics.

Antibiotics come in several forms, including:

  • Capsules or tablets
  • Liquids taken by mouth
  • Injections
  • Intravenous (IV) drip

If you have Crohn’s disease, antibiotics may help in many ways. Your provider may suggest you take antibiotics as a preventive plan, as a treatment for Crohn’s symptoms, or to see if you can go into remission. Antibiotics can:

Manage infections. Two common complications of Crohn’s are abscesses and fistulas.

Abscesses are infections with pockets of pus. You might develop an abscess in your abdomen, pelvis, or anal area. Fistulas are abnormal “tunnels” or connections from the intestines to other body parts like the bladder or vagina. They form to help drain infected areas or abscesses, but can cause symptoms such as passing undigested food or urinary tract infections.

Abscesses and fistulas can be treated with antibiotics, but your doctor may also recommend surgery to drain an abscess or heal a fistula.

Another way you might get an infection is after surgery, such as resection surgery. That’s an operation when a part of your intestine that Crohn’s has damaged is removed, and two healthy ends are joined together. With this type of surgery, there’s a risk of infection at the incision site. Antibiotics can lower that risk. Usually, your provider would prescribe antibiotics as a preventive measure.

Lower Inflammation. Research suggests that an abnormal immune response may trigger an excess of gut bacteria. This excess creates inflammation. Antibiotics may help reduce bacteria and control immune responses, which lowers inflammation.

Reduce post-surgery recurrence. Crohn’s disease symptoms often return after resection surgery. Your provider may recommend antibiotics for 3 months after surgery to prevent the symptoms from coming back.

Induce remission. Studies suggest that an antibiotic called rifaximin may help people with Crohn’s get to and then stay in remission. Rifaximin shows promise over other antibiotics because it’s not absorbed in your digestive tract. That causes fewer side effects and makes it a safer drug.

Antibiotics seem to work well in managing certain aspects of Crohn’s disease. Research suggests that antibiotics may help promote healthy gut bacteria. They might also wipe out harmful bacteria that are believed to play a role in Crohn’s disease and gut inflammation.

In fact, a review of several studies totaling more than 3,000 people with Crohn’s showed a huge improvement in disease activity with antibiotic treatment. The review gathered data on the antibiotics: ciprofloxacin , clarithromycin, metronidazole, and rifaximin . 

The most commonly prescribed antibiotics for Crohn’s disease are metronidazole and ciprofloxacin. These drugs are effective at treating three types of Crohn’s disease:

Ileal and ileocolonic Crohn’s disease. Ileal Crohn’s (or terminal ileal) affects the ileum, the last part of the small intestine. Ileocolonic Crohn’s affects the beginning of the large intestine.  

Research suggests that metronidazole may improve ileal and ileocolonic Crohn’s disease over time and may lower the chances of disease coming back after surgical resection.

Perianal Crohn’s disease. Inflammation of the area at or near the anus is called perianal Crohn’s disease. Research suggests that ciprofloxacin may successfully treat perianal Crohn’s.

Like many medications, antibiotics may cause side effects. These reactions range from mild to serious. It’s best to be aware of the following side effects and share any concerns with your doctor:

Ciprofloxacin. Tendonitis, tendon tears, light sensitivity, lack of cartilage growth in unborn babies and children, oral thrush, QT prolongation (a heart rhythm disorder)

Metronidazole. GI issues, permanent nerve damage, nausea, appetite loss, and a metallic taste

Rifaximin. Rare, but may include joint pain and muscle tightness

Vancomycin. Skin redness and itching on the face, neck, and upper body

Antibiotics may also cause other complications, such as:

  • A higher risk of getting an infection called Clostridioides difficile (C. diff) and having unfavorable outcomes
  • A rebound effect in the gut’s mucosa after stopping antibiotic treatment
  • Antibiotic resistance
  • Low tolerance due to side effects

Antibiotics can also trigger flares in your Crohn’s as they change the balance of gut bacteria. These changes may cause diarrhea or inflammation. But there are things you can do to manage flares, including:

  • Visit your health care provider regularly
  • Stay up to date with your screenings such a blood work and colonoscopies
  • Create a Crohn’s journal to track your symptoms and discuss changes with your doctor
  • Take your medications and vitamins or supplements as directed by your provider
  • Get exercise to boost your immune system and relieve stress
  • Give up smoking
  • Lower stress by practicing breathing exercises, doing yoga, or meditating
  • Avoid insoluble fiber foods such as fruit with skin and whole grains
  • Get rid of lactose sugars found in dairy products and nonabsorbable sugars (sorbitol, mannitol) found in sugar-free gum and pear juice
  • Ditch sweets like cookies and candy
  • Steer clear of high fat foods and spicy foods
  • Say no to beer, wine, alcohol, and caffeinated drinks

Studies show a connection between antibiotic use and getting an IBD diagnosis. One study found that children who took antibiotics by their first birthdays were three times more likely to develop IBD than children who didn’t take antibiotics in their first year.

Another study shows an increased connection between prior antibiotic use and an IBD diagnosis in adults. In fact, the greater the antibiotic use, the stronger the association to IBD.

Researchers have studied the tetracycline class of antibiotics in relation to IBD. Tetracyclines are considered broad-spectrum antibiotics that interfere with protein activity in certain bacteria. They are often used to treat acne, early Lyme’s disease, and traveler’s diarrhea.

Several tetracycline antibiotics, namely doxycycline and minocycline, have shown a link to IBD, particularly Crohn’s disease.