Background Gonorrhea (GC) and chlamydia (CT) are the most commonly reported notifiable diseases in the United States. The Centers for Disease Control and Prevention recommends that men who have sex with men (MSM) be screened for urogenital GC/CT, rectal GC/CT, and pharyngeal GC. We describe extragenital GC/CT testing and infections among MSM attending sexually transmitted disease (STD) clinics. Methods The STD Surveillance Network collects patient data from 42 STD clinics. We assessed the proportion of MSM attending these clinics during July 2011–June 2012 who were tested and positive for extragenital GC/CT at their most recent visit or in the preceding 12 months and the number of extragenital infections that would have remained undetected with urethral screening alone. Results Of 21 994 MSM, 83.9% were tested for urogenital GC, 65.9% for pharyngeal GC, 50.4% for rectal GC, 81.4% for urogenital CT, 31.7% for pharyngeal CT, and 45.9% for rectal CT. Of MSM tested, 11.1% tested positive for urogenital GC, 7.9% for pharyngeal GC, 10.2% for rectal GC, 8.4% for urogenital CT, 2.9% for pharyngeal CT, and 14.1% for rectal CT. More than 70% of extragenital GC infections and 85% of extragenital CT infections were associated with negative urethral tests at the same visit and would not have been detected with urethral screening alone. Conclusions Extragenital GC/CT was common among MSM attending STD clinics, but many MSM were not tested. Most extragenital infections would not have been identified, and likely would have remained untreated, with urethral screening alone. Efforts are needed to facilitate implementation of extragenital GC/CT screening recommendations for MSM.

Chlamydia and gonorrhea positivity was high among women reporting AI, and a large proportion of these cases would be missed in the absence of rectal testing. The high-risk behaviors of women with rectal infections highlight the need for rectal screening recommendations.

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Female meth users have high-risk behaviors that could increase their risk for STIs/HIV.

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Although TOC may be an important strategy in reducing complications and the spread of GC, low return rates may make implementation challenging. If implemented, extra efforts should be considered to enhance return rates among individuals with a history of GC. If TOCs are recommended at 1 week and NAATs are used, the interpretation of positive results, particularly those from extragenital sites, may be difficult.

Among women, risk of acquiring rectal STIs may vary by reason for engaging in unprotected AI as well as other contextual factors. Providers should consider addressing these contextual factors to reduce risk.

Remnant specimen from 1,215 women screening for chlamydia/gonorrhea at four different venue types (STD clinics, home-test kit users, juvenile and adult detention) in Los Angeles, CA, were tested for T. vaginalis. Prevalence of T. vaginalis varied by screening population and concurrent chlamydia or gonorrhea was independently associated with T. vaginalis.