Can Chlamydia (Chlamydial) or gonorrhea (Gonococcal) pharyngeal infections be tested using urine samples?

Testing for Pharyngeal Chlamydia and Gonorrhea Infections

Urine samples are not appropriate for detecting pharyngeal chlamydia or gonorrhea infections; direct pharyngeal swabs are required for accurate diagnosis. 1, 2

Appropriate Testing Methods for Pharyngeal Infections

• Culture has traditionally been the most widely available option for diagnosing infections in nongenital sites like the pharynx 1
• Nucleic acid amplification tests (NAATs) are increasingly being used for pharyngeal specimens due to their higher sensitivity, although they are not FDA-cleared for this purpose 2
• Many laboratories have validated NAATs for pharyngeal specimens through Clinical Laboratory Improvement Amendment (CLIA) requirements 2
• Gram stain of pharyngeal specimens is insufficient to detect infection and is not recommended 1

Site-Specific Testing Recommendations

• Specific diagnosis of gonorrhea may be performed using endocervical, vaginal, male urethral, or urine specimens for genital infections only 1
• Pharyngeal infections require direct pharyngeal swab specimens, as urine testing will miss these infections 2, 3
• The CDC recommends assessing sexual practices to determine if pharyngeal swab testing is needed (for those engaging in receptive oral sex) 2

Self-Collection vs. Clinician Collection

• Self-collected pharyngeal swabs have shown acceptable performance compared to clinician-collected swabs 4, 5
• In one study, the agreement between self-collected and clinician-collected specimens for pharyngeal gonorrhea was 96.6% and for chlamydia was 99.4% 4
• Self-collection is increasingly accepted as a viable alternative, especially in settings where reducing healthcare worker exposure is important 5

Testing Algorithm

• For patients with potential pharyngeal exposure:
  • Direct pharyngeal swab (self-collected or clinician-collected) is required 2
  • Urine testing alone will miss pharyngeal infections 3
• For men who have sex with men (MSM):
  • Annual pharyngeal screening is recommended, with more frequent screening (every 3-6 months) for those with higher risk factors 2
  • Testing should be based on exposure history rather than symptoms, as many infections are asymptomatic 2

Common Pitfalls

• Relying solely on urine or genital specimens will miss pharyngeal infections - one study found that urogenital testing alone missed 41 gonorrhea and 58 chlamydia infections that were detected with additional site testing 3
• Some NAATs have potential to cross-react with nongonococcal Neisseria and related organisms commonly found in the throat, which may affect specificity 1
• Assuming that symptoms will indicate infection is problematic, as many pharyngeal infections are asymptomatic 2, 6