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Clostridium difficile is the causative agent of antibiotic associated colitis (AAC) and pseudomembranous colitis (PMC) mediated by the exotoxins A and B. Routine diagnosis of C. difficile is usually done by direct detection of both toxins A and B with enzyme immunoassays. Clostridium perfringens causes food-borne diseases and food infections. The Clostridium perfringens toxin epsilon (CPE), which is produced by type B and type D strains, is particularly relevant for diagnostic assays. Recombinantly expressed nontoxic fragments of clostridial toxins with similar or identical antigenic response are a good alternative to the expensive and difficult to purify native clostridial toxins.