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Effect of Nucleic Acid Amplification Testing on Detection of Extragenital Gonorrhea and Chlamydial Infections in Men Who Have Sex With Men Sexually Transmitted Disease Clinic Patients

Background In 2010, the Centers for Disease and Control and Prevention recommended using nucleic acid amplification tests (NAATs) for extragenital gonorrhea (GC) and chlamydia (CT) testing because of NAATs’ improved sensitivity compared with culture. Methods In 2011, the Public Health–Seattle & King County Sexually Transmitted Disease Clinic introduced NAAT-based testing for extragenital GC and CT infection in men who have sex with men (MSM) using AptimaCombo2. We compared extragenital GC and CT test positivity and infection detection yields in the last year of culture-based testing (2010) to the first year of NAAT testing (2011). Results Test positivity of GC increased by 8% for rectal infections (9.0%–9.7%) and 12% for pharyngeal infections (5.8%–6.5%) from 2010 to 2011; CT test positivity increased 61% for rectal infections (7.4%–11.9%). Pharyngeal CT was identified in 2.3% of tested persons in 2011 (not tested in 2010). We calculated the ratio of extragenital cases per 100 urethral infections to adjust for a possible decline in GC/CT incidence in 2011; the GC rectal and pharyngeal ratios increased 77% and 66%, respectively, and the CT rectal ratio increased 127%. The proportion of infected persons with isolated extragenital infections (i.e., extragenital infections without urethral infection) increased from 43% in 2010 to 57% in 2011. Conclusions Extragenital testing with NAAT substantially increases the number of infected MSM identified with GC or CT infection and should continue to be promoted.