Clostridium difficile bacteria with peritrichous flagella, computer illustration. C. difficile is a Gram-positive, anaerobic, spore forming, rod-shaped prokaryote with peritrichous flagella. It is a normal part of the intestinal flora, especially in young children. C. difficile is the major cause of pseudomembranous colitis and antibiotic-associated diarrhoea. It is now becoming resistant to most antibiotics. Treatment is by discontinuing antibiotics and starting specific anticlostridial antibiotics, such as metronidazole.