Introduction The availability of extra-genital nucleic acid amplification testing (NAAT) for gonorrhoea (GC) and chlamydia (CT) is limited in many clinical and outreach settings. A recent initiative in Forsyth County, NC funded NAAT testing at oropharyngeal and rectal sites in both of these settings.

Methods A retrospective chart review was conducted for all males and females aged 12–80 who reported to an outreach site or STD clinic (MSM only) January 1, 2014 to February 28, 2015.

Results Clinic: 131 rectal, 163 pharyngeal, and 176 urethral NAAT tests were performed on 181 males. Twenty-five rectal (19.1%), 22 pharyngeal (13.5%), and 22 (12.5%) urethral specimens were GC positive. 24 rectal (18.3%) and 7 urethral (4.0%) were CT positive. 5 rectal GC (20.0%), 8 pharyngeal GC (36.4%), and 13 rectal CT (54.2%) infections would have been missed in the absence of extra-genital testing.

Outreach 47 rectal, 157 pharyngeal, and 162 urogenital NAATs were collected. For GC, 3 rectal (6.4%), 3 pharyngeal (1.9%), and 2 urogenital (1.2%) specimens were positive. Six (12.8%) and 9 (5.6%) individuals were positive for rectal and urogenital CT, respectively. 2 rectal GC (66.7%), 3 pharyngeal GC (100%), and 4 rectal CT (66.7%) infections would have been missed without extra-genital NAAT.

When NAAT and bacterial culture for GC were run on the same samples from clinic patients, culture detected 48% (12/25) of the rectal and 45.2% (10/22) of the pharyngeal infections detected by NAAT.

Conclusion A significant prevalence of extra-genital GC and CT infections were noted in both the clinic and outreach populations. In the absence of NAAT-based extra-genital testing approximately half of rectal and pharyngeal GC infections would have been missed with culture and more than half of the rectal CT infections would have been missed. Assurance of access of NAAT-based extra-genital testing is critical for STI control efforts.