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Medications for IBD: Antibiotics

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Antibiotics kill bacteria, the word means “opposed to life.” Antibiotics are used in different scenarios in Crohn’s and colitis, such as when a fistula has developed, in pouchitis, or other infections. 



  • Metronidazole (Flagyl)
    • Destabilizes bacteria by reacting with its DNA, causing breaks and leading bacterial cell death. 
  • Ciprofloxacin (Cipro, Proquin) 
    • Blocks an enzyme in bacteria that unwinds their DNA, preventing the bacteria from dividing and causes the DNA to split apart and die. 
  • Vancomycin (Vancocin)
  • Rifaximin (Xifaxan)

How do they work? 

  • Antibiotics target specific parts of bacterial cells. Some work on parts of the bacterial cell that are absent and some target bacterial cells that are so different from human cells that they only affect the bacteria and not the human. 

When are they used?

  • Antibiotics should not be used as primary medications, but rather are typically used as an adjunct therapy. They are added to one or a combo of other drugs. They are important when bacteria gets outside of the bowels. 
  • Common scenarios when used: 
    • Active Crohn’s fistula
    • Abdominal abscess 
    • Intestinal infections such as c.Diff
    • Pouchitis 

Side effects: 

  • Metronidale (Flagyl)
    • Generally safe
    • Metallic taste in the mouth
    • Nausea
    • Vomiting
    • Indigestion
    • Diarrhea 
    • Long-term use, especially high doses  can cause nerve damage in the feet and legs (numbness, tingling, reversible)
    • Alcohol consumption with Flagyl can cause flushing of the face, shortness of breath, severe headache, rapid heartbeat, nausea, vomiting
  • Ciprofloxacin (Cipro)
    • Generally safe
    • Increases caffeine’s stimulant effect 
    • Can cause ruptured tendons, particularly in the Achilles tendon (especially in young kids)