Rapid identification of patients infected with clarithromycin-resistant Helicobacter pylori without the need for culture can help to avoid useless prescriptions of clarithromycin. We developed and tested a routine real-time quantitative PCR assay dedicated to that purpose. One hundred ninety-six consecutive gastric biopsy specimens were examined by culture, histology performed by a trained physician, and rapid PCR with the LightCycler apparatus. Infection was defined as (i) positivity of culture, (ii) positivity of histology, or (iii) positivity of PCR if confirmed by positivity of a concomitant indirect test (serology or urea breath test). Susceptibility to clarithromycin was tested by E-test and PCR. The prevalence of infection was 33.7% (66 of 196 samples). The sensitivities of culture, histology, and PCR were 90.9% (60 of 66 samples), 87.9% (58 of 66 samples), and 97.0% (64 of 66 samples), respectively. The specificity of PCR was 94.6% (123 of 130 samples). The linearity of the PCR results was achieved over a 6-log range of input DNA, and we were able to accurately quantify as few as 300 bacteria and to qualitatively detect as few as 30 bacteria per DNA sample. For clarithromycin susceptibility testing, there was 98.2% (55 of 56 samples) concordance between E-test and PCR. Forty-eight strains were clarithromycin susceptible, and 9 strains were clarithromycin resistant. The single discrepancy concerned a culture which was a mixture of mutant and wild type, with a susceptible-to-resistant ratio of 11.5: the resistant population was detected by E-test but not by PCR. Our PCR assay is accurate for fast detection of H. pylori as well as of clarithromycin resistance and is also able to objectively determine bacterial density.Many diagnostic assays have been developed for Helicobacter pylori: culture, histology, rapid urease test, urea breath test, serology, stool antigen test, and molecular-based tests (24). Culture has the great advantage of permitting subsequent determination of the antimicrobial susceptibility of the strain isolated, in particular to macrolides. Indeed, the macrolide drug clarithromycin is the key component of many combination therapies used to eradicate H. pylori, and macrolide resistance is the most important cause of treatment failure (13, 22). However, disadvantages of culture include special conditions for specimen transportation, the use of complicated media with special conditions for maintenance, the need for special incubation conditions, and the length of time necessary to obtain a result (20).Clarithromycin resistance in H. pylori is due to the lack of binding of the macrolides to the 23S rRNA components of the bacterial ribosome due to modification of the target site by occurrence of a single spontaneous point mutation in the peptidyltransferase region of the 23S rRNA gene (17,25). Mutations A2142G and A2143G are the most often observed, with the A2142C mutation being much rarer (25). Other mutations (A2115G, G2141A, and T2717C) have been described but appear to be exceptional (10,1...