We evaluated self-sampling to detect pharyngeal Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infection among men who have sex with men attending a San Francisco STD clinic. The prevalence of pharyngeal NG and CT infection was 6.7% (32/480) and 1.3% (6/480), respectively. The percent agreement between self-collected and clinician-collected NG and CT specimens using nucleic acid amplification testing was 96.6% with a κ of 0.766 (95% confidence interval: 0.653-0.879) and 99.4% with a κ of 0.766 (95% confidence interval: 0.502-1.000), respectively. Acceptability was high among participants.
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