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 Lindley A. Barbee, MD, MPH,*Þ Julia C. Dombrowski, MD, MPH,*Þ Roxanne Kerani, PhD,*Þþ and Matthew R. Golden, MD, MPH*Þþ Background: In 2010, the Centers for Disease and Control and Pre- vention 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 HealthYSeattle & King County Sexually Transmitted Disease Clinic introduced NAAT-based testing for extra- genital GC and CT infection in men who have sex with men (MSM) using AptimaCombo2. We compared extragenital GC and CT test pos- itivity 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%Y9.7%) and 12% for pharyngeal infections (5.8%Y6.5%) from 2010 to 2011; CT test positivity increased 61% for rectal infections (7.4%Y11.9%). 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. E xtragenital gonorrhea (GC) and chlamydial (CT) infections among men who have sex with men (MSM) are common, with prevalences of rectal GC, pharyngeal GC, and rectal CT among MSM sexually transmitted disease (STD) clinic patients documented to be as high as 9.8%, 9.2%, and 8.2%, 1Y4 respec- tively. Most extragenital infections are asymptomatic, 1,5 and inadequate screening of extragenital sites in MSM is thought to be an important factor fostering the persistence of high levels of GC and CT infection in that population. 1,2 A growing body of literature supports the use of nucleic acid amplification tests (NAATs) for extragenital GC and CT screening, 6Y12 both for its increased sensitivity and ease of processing. 13 In 2010, the Centers for Disease and Control Prevention recommended the use of NAAT for testing of extragenital sites in MSM 14 ; how- ever, uptake of NAATs for extragenital testing outside specialty care settings has been limited. 13 In 2011, the Public HealthYSeattle & King County (PHSKC) STD Clinic switched from culture to NAAT for rou- tine extragenital GC and CT testing in MSM. This analysis compares clinical and laboratory data collected in the PHSKC STD Clinic in 2010, the final year in which extragenital testing was performed primarily by culture, and 2011, the first year in which our clinic used NAAT for routine extragenital testing. The primary objective was to assess how much the change in testing technology affected case finding in a real-world STD clinic setting. MATERIALS AND METHODS Study Period The PHSKC STD Clinic phased in the routine use of NAAT (Aptima Combo 2; GenProbe, San Diego, CA) for pha- ryngeal and rectal GC and CT testing in the last 2 months of 2010. By January 1, 2011, NAATs became the main method for testing for GC and CT at extragenital sites. Before that time, extragenital GC and CT testing was performed exclusively by culture. For the study period, we chose to compare 2 calendar years of data: 2010, the last year in which extragenital GC and CT testing occurred primarily by culture, and 2011, the first year in which extragenital testing was routinely performed using NAAT. (The testing technologies overlapped briefly at the end of 2010, which would potentially lead to an underestimate of the effect of the change to NAAT testing.) Study Population For purposes of this analysis, we defined any man who reported having sex with a man in the prior 12 months to be an MSM, including men who also reported having sex with wom- en. For clinic visits where data on the sex of sex partner were missing, if the participant had a prior clinic visit during which the sex partner sex was recorded, we used that information to ORIGINAL STUDY 168 Sexually Transmitted Diseases & Volume 41, Number 3, March 2014 From the *Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA; †Public HealthYSeattle & King County HIV/STD Program, Seattle, WA; and ‡Department of Epidemiology, Universityof Washington, Seattle, WA. Funding support: This work was supported by Public HealthYSeattle & King County, the National Institutes of Health Sexually Transmitted Diseases Training Grant (T32 67-4198 to L.A.B.), the National In- stitutes of Mental Health (K23MH090923 to J.C.D.), the National Institutes of Allergy and Infectious Diseases (K01 AI095060 to R.P.K.), and the University of Washington Center For AIDS Re- search, a National Institutes of HealthYfunded program (P30 AI027757) that is supported by the following National Institutes of Health institutes and centers: National Institutes of Allergy and Infec- tious Diseases, National Cancer Institute, National Institutes of Mental Health, National Institute on Drug Abuse, National Institute of Child Health and Human Development, National Heart, Lung, and Blood Institute, and National Institute on Aging Conflicts of interest: L.A.B., J.C.D., and R.P.K. have nothing to disclose. M.R.G. received research support from Genprobe Diagnostics, Cempra Pharmaceuticals, and Pfizer Pharmaceuticals. Correspondence: Lindley Barbee, MD, MPH, 325 9th Ave, Box 359777, Seattle, WA 98104. E-mail: lbarbee@u.washington.edu. Received for publication March 14, 2013, and accepted December 16, 2013. DOI: 10.1097/OLQ.0000000000000093 Copyright * 2014 American Sexually Transmitted Diseases Association All rights reserved. Copyright © 2014 by the American Sexually Transmitted Diseases Association. Unauthorized reproduction of this article is prohibited.