Background:
Rectal infection with C. trachomatis (CT) and N. gonorrhoeae (GC) is increasing in many settings. Access to reliable diagnostics using rectal specimens is critical to both surveillance and disease management and control.

Objective:
To evaluate the relative sensitivity and specificity of NAATs compared to culture for CT & GC.

Method:
Rectal samples collected for CT culture in chlamydia transport medium were also tested for both CT and GC using BD (BD ProbeTec, Sparks, MD), AC2 (GenProbe Aptima 2 Combo, San Diego, CA), and PCR (Roche COBAS Amplicor, Indianapolis, IN). Cultures for GC were performed using a separate sample plated on modified Thayer Martin plates. κ scores and McNemar's χ2 and Cochran's Q statistics were used to compared the results with alpha=.05.

Result:
352 samples were tested by at least 2 methods for both CT and GC. An infected patient standard was used that was positive if culture and/or at least 2 NAAT assays were positive. CT or GC was identified in 31 (8.8%) and 37 (10.5%) of samples, respectively. The sensitivity and specificity of all NAATs were high (>83% and >98%, respectively) for CT while the sensitivity of culture was 54.8%. The sensitivity and specificity of all NAATs were high (>83% and >99%, respectively) for GC while the sensitivity of culture was 78.8%. All NAATS were in good agreement with the infected patient standard (all κ scores >.84 and .88 for CT and GC, respectively).

Conclusion:
NAATs offer an alternative to culture for rectal samples collected for CT and GC. These assays offer increased sensitivity compared to culture and are highly specific. These assays are less susceptible to transport conditions and sterility that is often a concern with rectal samples.

Implications:
Monitoring the prevalence of rectal infections provides useful public health information; NAAT diagnostics can facilitate this surveillance effort.