We compared two multistep diagnostic algorithms based on C. Diff Quik Chek Complete and, as confirmatory tests, GenomEra C. difficile and Xpert C. difficile. The sensitivity, specificity, positive predictive value, and negative predictive value were 87.2%, 99.7%, 97.1%, and 98.3%, respectively, for the GenomEra-based algorithm and 89.7%, 99.4%, 95.5%, and 98.6%, respectively, for the Xpert-based algorithm. GenomEra represents an alternative to Xpert as a confirmatory test of a multistep algorithm for Clostridium difficile infection (CDI) diagnosis. R apid diagnosis of Clostridium difficile infection (CDI) is crucial for optimal disease control (1, 2). For this reason, many microbiology laboratories used sensitive algorithms based on enzyme immunoassay (EIA) for detection of glutamate dehydrogenase (GDH) with EIA detection of toxins A and B, followed by a confirmatory test based on toxin A or B gene amplification (3-6).C. Diff Quik Chek Complete (QC) (TechLab, Blacksburg, VA, USA) detects by immunochromatography both GDH and toxins A and B as a single procedure device (4). The real-time PCR assay Xpert C. difficile assay (Xpert) (GeneXpert; Cepheid, Sunnyvale, CA, USA) that detects the toxin B gene (tcdB), binary toxin genes, and tcdC 117-nucleotide (nt) deletion (epidemic 027 ribotype) is frequently used as a confirmatory test because of its speed and good internal validity values (7-11).The new assay, GenomEra C. difficile (GenomEra) (Abacus Diagnostica, Turku, Finland), is a promising amplification system that detects the tcdB gene in approximately 1 h using rapid thermal cycling by means of a multiblock thermal cycler and homogeneous time-resolved fluorescence detection technology using lanthanide chelates which has proved to be resistant to background effects (12). This molecular method has the CE mark but is not cleared at this moment by the FDA.The purpose of this study was to compare the diagnostic accuracy of two algorithms based on QC as the screening test and Xpert or GenomEra as confirmatory tests for the rapid diagnosis of CDI.From October 2012 to March 2013, all loose stool specimens sent to the laboratory of the Hospital General Universitario Gregorio Marañón (Madrid, Spain) for CDI diagnosis were tested in parallel with the direct cytotoxicity assay, toxigenic culture, and the two multistep algorithms evaluated. The gold standard was the combination of direct cytotoxicity assay with stool specimens and cytotoxicity assay with isolates as previously described (13). The multistep algorithm consisted of an initial test, QC, performed according to the manufacturer's recommendations. Specimens positive for both GDH and toxins were considered positive, while specimens negative for both antigens were considered negative. Specimens with uncertain (GDH-positive and toxin-negative) results were tested in parallel using Xpert and GenomEra for confirmation. Xpert was performed according to the manufacturer's recommendations. GenomEra was performed by diluting 1 l of sample in a tube with 1 ml of sample buffer...