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Background   Clostridium difficile  and  Clostridium perfringens  are commonly associated with colitis in equids, but healthy carriers exist.  S carce information is available on the prevalence of  Clostridium  spp. in gastrointestinal compartments other than faeces in healthy horses, and it is unknown whether faecal samples are representative of proximal compartments. The objectives were to investigate the prevalence of  C. difficile  and  C. perfringens  in different intestinal compartments of healthy adult horses and to determine whether faecal samples are representative of colonization in proximal sites and overall carrier status.    Results  Toxigenic  C. difficile  was isolated from 14/135 (10.3%) samples from 8/15 (53.3%) horses. Between zero and three sites were positive per horse, and multiple sites were positive in four horses. Isolates were recovered from duodenum, jejunum, ileum, right dorsal colon, small colon and rectum. When multiple compartments were positive in a single horse, two different  C. difficile  ribotypes were always present.  Clostridium perfringens  Type A (CPE, β 2  toxin gene negative) was recovered from the left ventral colon of one horse (0.74%, 1/135 samples). Agreement between faeces and overall  C. difficile  carrier status was good.    Conclusions   Clostridium difficile  can be found in different compartments of the gastrointestinal tract of healthy horses, and multiple strains can be present in an individual horse. The prevalence of  C. perfringens  in healthy adult hoses was low, consistent with previous reports. Faecal samples were representative for presence of  C. difficil e in proximal compartments in 5/8 horses (63%) but were not representative for the specific strain.

Presence and molecular characterization of Clostridium difficile and Clostridium perfringens in intestinal compartments of healthy horses