Background:
Only bacterial culture is currently approved for gonorrhea (GC) or chlamydia (CT) screening in non-genital sites. Although culture is 100% specific in this context, sensitivity varies. Nucleic acid amplification tests (NAATs) are more sensitive than culture for the detection of GC/CT in urogenital sites. If NAATs have superior performance in non-genital sites, they would facilitate the control of GC and CT infection.

Objective:
To review the performance of NAATs in the rectum and pharynx.

Method:
We searched PubMed, reviewed STD conference abstracts and elicited additional information from experts. We included only summary data with >50 positive tests and studies comparing NAATs to a reference standard consisting of culture or other nucleic acid confirmatory testing.

Result:
We found ten studies that compared NAATs to reference standards. Mean sensitivity/specificity for rectal GC polymerase chain reaction (PCR-Roche Amplicor), ligase chain reaction (LCR-Abbott LCx), strand displacement amplification (SDA-BD ProbeTec) and transcription mediated amplification (TMA-Gen-Probe Aptima) were 44.4%/98.7%, 100%/99.8%, 77.8%/100% and 100%/99.5%, respectively. Mean sensitivity/specificity for rectal CT PCR, SDA and TMA were 91.2%/95.8%, 76.5%/100% and 100%/100%, respectively (LCR was not studied). Mean sensitivity/specificity for pharyngeal GC PCR, LCR, SDA and TMA were 60%/78.9%, 95.1%/99%, 75%/99.5% and 95%/100%, respectively. Pharyngeal CT was not included as only 19 of 694 patients screened tested positive.

Conclusion:
There was variability in test performance by NAAT. PCR is less sensitive and specific than other NAATs in both sites. TMA is the most sensitive and specific for testing in both sites. Select NAATs may be useful for clinical testing.

Implications:
Because STDs are associated with HIV transmission and acquisition, improved methods for STD screening will advance medical care for groups at high risk for both STDs and HIV. In this regard, there is an important need to define performance characteristics of NAATs for GC/CT at non-genital sites.