In March, the Barnes-Jewish Hospital (BJH) Microbiology Laboratory began accepting pharyngeal (throat) and rectal swabs for nucleic acid amplification testing (NAAT) for Neisseria gonorrhoeae and Chlamydia trachomatis (GC and CT). Although the assay is not FDA approved for these specimen types, the BJH Microbiology laboratory completed verification studies demonstrating adequate analytical performance characteristics. These specimen types are accepted in addition to those specimen types that are currently acceptable for GC and CT:

  • Endocervical swabs
  • Male urethral swabs
  • Vaginal swabs (special collection kit)
  • Urine (cup specimen)

The availability of NAAT testing for these specimen types is important for diagnosis of extra-genital infection.

The 2010 Centers for Disease Control and Prevention Sexually Transmitted Disease Guidelines recommend rectal and pharyngeal testing of N. gonorrhoeae and C. trachomatis for individuals at risk for infection.

While many methodologies exist for this testing, it has been well established that NAAT has superior sensitivity compared to culture for detecting these pathogens. NAAT for GC and CT for the specimen types noted above can be ordered in COMPASS, Allscripts and HMED. Pharyngeal and rectal swab specimens should be collected using the Gen-Probe endocervical swab collection kit. Other collection kits will not be accepted. For specific instructions regarding collection of specimens for N. gonorrhoeae and C. trachomatis NAAT testing please refer to the BJH Electronic Test Catalog at

Although NAAT testing for GC and CT is more sensitive than culture for diagnosis of these agents, a limitation of NAAT is the absence of isolates for antimicrobial susceptibility testing of N. gonorrhoeae. If treatment failure secondary to antimicrobial resistance is suspected, N. gonorrhoeae culture can be ordered in parallel with NAAT using a second specimen collected in an appropriate collection device, such as the Eswab. Culture cannot be performed on the same specimen submitted for NAAT.

To speak with a representative from the laboratory call Children’s Direct at 800.678.HELP (4357).