Testing for Oral Chlamydia
Nucleic acid amplification tests (NAATs) performed on oropharyngeal swab specimens are the recommended method for diagnosing oral chlamydia, though no commercial tests are currently FDA-cleared for this specific anatomical site. 1, 2
Optimal Testing Approach
Specimen Collection and Testing Method
Collect an oropharyngeal swab specimen and test using a NAAT platform, as these demonstrate far superior sensitivity compared to culture for detecting Chlamydia trachomatis in the throat 2
The Gen-Probe APTIMA Combo 2 assay (AC2) demonstrates the highest sensitivity at 84% for oropharyngeal chlamydia detection, compared to 72% for BD ProbeTec (SDA) and only 41% for culture 2
Specificity of NAATs for oropharyngeal specimens exceeds 99.4%, making false-positive results uncommon 2
Critical Testing Considerations
Culture detects less than half of oropharyngeal chlamydia infections (41% sensitivity), making it inadequate as a standalone diagnostic method despite being the only FDA-cleared approach for extragenital sites 2
NAATs detect twice as many oropharyngeal infections as culture, representing a substantial improvement in diagnostic capability 2
Testing should be performed on all sexually active individuals with oral exposure risk, particularly those presenting with pharyngitis, oral ulcers, or cervical lymphadenopathy in the context of sexual exposure 2
Important Clinical Pitfalls
Off-Label Use Reality
All commercial NAATs used for oropharyngeal testing are technically off-label, as no FDA-cleared tests exist for pharyngeal specimens, but this represents standard clinical practice supported by research evidence 1, 2
Laboratories must validate NAATs for oropharyngeal use before offering clinical testing, though many reference laboratories have completed this validation 1
Testing Limitations to Recognize
Avoid using the Roche Amplicor PCR assay for oropharyngeal specimens, as it demonstrates unacceptably low specificity (78.9%) with high false-positive rates 2
Do not rely on point-of-care tests, which have sensitivities ranging from only 12-62.9% and are inadequate for screening or diagnosis 3
Confirmatory testing with alternate primers may be needed for discordant or unexpected positive results, particularly in low-prevalence populations 1, 4
Concurrent Testing Requirements
All patients diagnosed with oral chlamydia must be tested for urogenital chlamydia using NAAT on urine (men) or vaginal swab specimens (women), as co-infection rates are substantial 5, 6
Test for rectal chlamydia if receptive anal intercourse has occurred, using rectal swab specimens with NAAT (93% sensitivity with AC2) 1, 2
Screen for other sexually transmitted infections including gonorrhea, syphilis, and HIV at the initial visit, as co-infection rates are high 5, 7
Treatment After Positive Test
Treat immediately with azithromycin 1g orally as a single dose OR doxycycline 100mg orally twice daily for 7 days, as these regimens achieve 97-98% cure rates 5, 7
Patients must abstain from all sexual activity for 7 days after initiating treatment AND until all sexual partners complete treatment 5, 7
All sexual partners from the preceding 60 days require evaluation and empiric treatment, regardless of their symptom status 5, 7