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Pouchitis is the major long-term complication after ileal pouch-anal anastomosis for ulcerative colitis. Metronidazole and ciprofloxacin are commonly used for treatment; however, nothing is known about the effects on the pouch flora during and after pouchitis episodes. This study was designed to evaluate the effect of both antibiotics on eradication of pathogens and the restoration of normal pouch flora.The fecal flora obtained from 13 patients with ulcerative colitis was examined at the beginning of a pouchitis episode before treatment, during treatment with metronidazole or ciprofloxacin, and during pouchitis-free periods. Some patients experienced more than one pouchitis episode. Therefore, a total of 104 samples was obtained. Each sample was cultured under aerobic and anaerobic conditions and the isolated bacteria were identified. Furthermore, the clinical response to both antibiotics was compared using the Pouchitis Disease Activity Index score.During pouchitis-free periods, the patients had a flora characterized by high numbers of anaerobes and no or low numbers of pathogens. This flora resembles normal colon flora. During pouchitis episodes, we found a significant decrease of anaerobes (P= 0.01), a significant increase of aerobic bacteria (P= 0.01), and significantly more numbers of pathogens, such asClostridium perfringens(in 95 percent of the samples;P< 0.01) and hemolytic strains ofEscherichia coli(in 57 percent of the samples;P= 0.05). Treatment with metronidazole resulted in a complete eradication of the anaerobic flora, includingC. perfringens. However, no changes in the numbers ofE. coliwere found. In contrast, when the patient was treated with ciprofloxacin, not onlyC. perfringens, but also all coliforms including hemolytic strains ofE. colidisappeared. The larger part of the anaerobic flora was left undisturbed during the administration of ciprofloxacin. Patients treated with ciprofloxacin experienced significant larger reductions in Pouchitis Disease Activity Index score compared with patients treated with metronidazole (P= 0.04).This study strongly suggests a role of pathogenic bacteria (C. perfringensand/or hemolytic strains ofE. coli) in pouchitis. From a microbiologic and a clinical point of view, ciprofloxacin is preferable to metronidazole, because treatment with ciprofloxacin eradicates both pathogens and results in an optimal restoration of normal pouch flora.