I would like to detect Clostridium difficile by real-time PCR collected in hospital environmental in order to compare it with bacterial strains isolated from patients.
A rapid real-time fluorescence-based multiplex PCR assay targeting the C. difficile toxin genes tcdA and tcdB, with the Smart Cycler. Two molecular beacons bearing different fluorophores are used as internal probes specific for each amplicon type. The analytical sensitivity of the assay is around 10 genome copies for all nine C. difficile strains tested, representing the 6 most common toxinotypes. The specificity could be demonstrated by the absence of amplification with DNA purified from bacterial species other than C. difficile (n = 14), including Clostridium sordellii for which the lethal toxin gene sequence is closely related to the toxin genes of C. difficile. Following a rapid (15 min) and simple fecal sample preparation protocol, both tcdA and tcdB can be efficiently amplified from 28 of 29 cytotoxin-positive feces samples. This is the first real-time PCR assay for the detection of C. difficile. It is rapid, sensitive, and specific and allows detection of C. difficile directly from feces samples.