Updated recommendations from the Centers for Disease Control and Prevention (CDC) on laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae continued prior advice that nucleic acid amplification tests (NAAT) are the best choice for detecting these pathogens (MMWR 2014;63:1–19). However, the new guidance emphasized that repeat testing of NAAT-positive genital tract specimens does not improve the positive-predictive value of the test, and discouraged this practice.

While the recommendations—an update from CDC's 2002 guidance—highlighted the overall superiority of NAAT-based testing for C. trachomatis and N. gonorrhoeae, they also stressed that labs should maintain the capability to culture for both organisms.

The best NAAT specimen types in women and in men are vaginal swabs and first urine catch, respectively. Although the Food and Drug Administration (FDA) has not cleared NAATs for detecting rectal or oropharyngeal infections caused by either C. trachomatis or N. gonorrhoeae, CDC still recommends NAAT tests for these specimen types, due to NAATs' higher sensitivity and ease of specimen transport and processing. CDC therefore cautioned that labs need to establish performance specifications for these specimen types that meet Clinical Laboratory Improvement Amendments (CLIA) regulatory requirements. In the case of commercially available moderate complexity tests, any modifications default the test to high complexity, making it necessary for the lab to meet all high-complexity CLIA requirements.

CDC identified five FDA-cleared NAAT assay platforms for detecting C. trachomatis and N. gonorrhoeae. Overall, these tests detect substantially more infections than either culture or other nonculture methods. However, NAATs also have some limitations. For example, the primers in one N. gonorrhoeae test might detect nongonococcal Neisseria species. When labs use any of the tests known to produce false positives for nongonococcal species, they might consider retesting positive specimens using a different method when dealing with oropharyngeal specimens.

Labs need to take extra care to prevent specimen contamination or spread of environmental amplicon. CDC urged that they monitor the rate of indeterminate and positive results, since any change in monthly trends might reflect a need to review the accuracy of results.

CDC acknowledged that pooling NAAT-tested specimens reduces the costs of testing, but cautioned that this practice has not been cleared by FDA, and labs that pool specimens need to comply with CLIA test modification requirements. In addition, pooled specimen NAAT testing also requires extensive sample handling, which raises the risk of sample cross-contamination.