Despite Excellent Test Characteristics of the cobas 4800 CT/NG Assay, Detection of Oropharyngeal Chlamydia trachomatis and Neisseria gonorrhoeae Remains Challenging

Oropharyngeal Chlamydia trachomatis (CT) infections and, especially, Neisseria gonorrhoeae (NG) infections are common, but few commercial nucleic acid amplification tests (NAAT5) specify extragenital samples for intended use. The test characteristics of the cobas 4800 CT/NG assay were evaluated for oropharyngeal swabs. The technical validation included analysis of the specificity, sensitivity, dynamic range, linearity, efficiency, and precision. The probability of detection curve combined with historical data enabled the estimation of potentially missed diagnoses. A clinical evaluation was performed on a subset of 2,798 clinical samples available from routine diagnostics. Results of the cobas 4800 were compared with those from in-house C. trachomatis/N. gonorrhoeae PCR assays. Discrepant samples were tested with resolver assays, and these results were considered decisive. No cross- reactivity was seen in the analytical specificity analysis. High linearity (R-2 >= 0.983), efficiency (89% to 99%), and precision (cycle threshold [C-T] value of 0.1 to 0.9) were seen for both C. trachomatis and N. gonorrhoeae. The limit of detection in oropharyngeal samples was 3.2 x 10(2) inclusion-forming units (IFU)/ml for C. trachomatis and 6.7 x 10(2) CFU/ml for N. gonorrhoeae. Estimates on potentially missed diagnoses were up to 7.2% for C. trachomatis and up to 24.7% for N. gonorrhoeae. Clinical sensitivity and specificity were evaluated with 25 C. trachomatis-positive, 86 N. gonorrhoeae-positive, and 264 negative samples, resulting in 100% and 99.6% for C. trachomatis and 100% and 96.7% for N. gonorrhoeae, respectively. The findings in this study demonstrate the utility of the cobas 4800 CT/NG assay for oropharyngeal samples. Despite its being a highly accurate test, the range of reported C-T values, especially for N. gonorrhoeae, suggests relatively low oropharyngeal loads. Hence, consistent detection over the full range of oropharyngeal loads could be impaired