infection is mainly diagnosed non-invasively, with susceptibility testing traditionally requiring endoscopy. Treatment is empiric, with clarithromycin triple therapy recommended where resistance rates are below 15%. Rising clarithromycin resistance resulting in high therapy failure rates is seen worldwide but United States data is limited. We developed a real-time PCR assay for simultaneous detection of and genotypic markers of clarithromycin resistance directly from stool specimens. The assay was validated by testing 524 stool samples using an stool antigen test as the reference method for detection accuracy and Sanger sequencing to confirm genotypic susceptibility results. A separate set of 223 antigen posi... More
infection is mainly diagnosed non-invasively, with susceptibility testing traditionally requiring endoscopy. Treatment is empiric, with clarithromycin triple therapy recommended where resistance rates are below 15%. Rising clarithromycin resistance resulting in high therapy failure rates is seen worldwide but United States data is limited. We developed a real-time PCR assay for simultaneous detection of and genotypic markers of clarithromycin resistance directly from stool specimens. The assay was validated by testing 524 stool samples using an stool antigen test as the reference method for detection accuracy and Sanger sequencing to confirm genotypic susceptibility results. A separate set of 223 antigen positive stool samples was tested and retrospective medical record review conducted to define clinical utility. PCR resulted in 88.6% and 92.8% sensitivity in the validation and clinical study sets, respectively. Sequencing confirmed correct detection of clarithromycin resistance-associated mutations in all positive validation samples. The PCR predicted clarithromycin resistance rate was 39% in the clinical data set overall and 28% in treatment naïve patients; the clarithromycin triple therapy eradication rate in treatment naïve patients was 62%. The clarithromycin triple therapy success was lower when resistance was predicted by PCR (41%) than when no resistance was predicted (70%, p=0.03). PCR was positive in 98% of antigen positive stools from patients tested for eradication. The described PCR assay can accurately and non-invasively diagnose , provide genotypic susceptibility, and test for eradication. Our findings support the need for susceptibility-guided therapy in our region if a clarithromycin-based regimen is considered.
