What is the recommended lab test for diagnosing gonorrhea and chlamydia in a patient?

Recommended Laboratory Testing for Gonorrhea and Chlamydia

Order nucleic acid amplification tests (NAATs) as the primary diagnostic test for both gonorrhea and chlamydia, using first-void urine in men or vaginal swabs (self-collected or clinician-collected) in women, as these specimens provide the highest sensitivity and specificity while allowing simultaneous detection of both pathogens. 1, 2

Specimen Collection by Patient Population

For Women

• First-line specimen options: Vaginal swabs (self-collected or clinician-collected) or urine specimens 2
• Vaginal swabs are preferred as they maintain high sensitivity (86-100%) and specificity (>97%) 2
• The same specimen can test for both infections simultaneously 1, 2
• Endocervical specimens are acceptable alternatives but offer no advantage over vaginal swabs 1

For Men

• First-line specimen options: First-void urine or urethral swabs 2
• Urine testing with NAATs is at least as sensitive as urethral specimens 1
• When urethral discharge is present, a meatal specimen adequately substitutes for an intraurethral swab 3

For Extragenital Sites

• Rectal swabs: Collect from all patients reporting receptive anal intercourse 3, 4, 5
• Pharyngeal swabs: Collect from all patients reporting oral sex 3, 4, 6
• While not FDA-cleared for these sites, NAATs demonstrate superior sensitivity compared to culture, detecting twice as many infections 4, 5
• The Gen-Probe Aptima Combo2 shows 93-100% sensitivity for rectal specimens and 93-100% for pharyngeal specimens 4, 5, 6

Critical Testing Algorithm

Determine All Required Anatomical Sites

• Sexual history dictates testing sites: Order genital, rectal, and pharyngeal specimens based on specific sexual practices reported 3
• Do not rely solely on genital testing, as extragenital infections are common (4-9% prevalence) and frequently asymptomatic 5

Mandatory Concurrent Testing

• All patients tested for gonorrhea or chlamydia must also be tested for syphilis and HIV regardless of which diagnostic method is used 3, 2
• This is non-negotiable per CDC guidelines 3

When Culture is Necessary

Indications for Culture

• When NAATs are unavailable, use standard culture systems 3
• For antimicrobial resistance surveillance in gonorrhea-positive cases 7
• Consider deferred culture on NAAT-positive specimens stored at 4°C for 1-3 days, which yields 56-69% positivity 7

Culture Confirmation Requirements

• For gonorrhea: All presumptive isolates must be confirmed by at least two tests involving different principles 3
• For chlamydia: Isolation must be confirmed by microscopic identification using fluorescein-conjugated monoclonal antibody specific for C. trachomatis 3

Common Pitfalls to Avoid

Diagnostic Errors

• Never rely on Gram stain alone for endocervical, pharyngeal, or rectal specimens—they lack sufficient sensitivity 2
• Do not use PCR-based NAATs for oropharyngeal specimens due to poor specificity (78.9% for gonorrhea) 4
• Avoid testing only genital sites when sexual history indicates oral or anal exposure 3

Specimen Collection Mistakes

• Do not collect cervical specimens in prepubertal girls; use vaginal specimens instead 3
• Ensure first-void urine collection in men, not mid-stream specimens 2

Follow-up Failures

• Retest all positive patients at 3 months due to high reinfection rates (not test-of-cure) 2
• Test and treat all sex partners from the preceding 60 days 2
• Instruct patients to abstain from sexual intercourse until they and partners complete treatment and are asymptomatic 2

Nuances in NAAT Selection

The transcription-mediated amplification platform (Gen-Probe Aptima Combo2) demonstrates superior performance over strand displacement amplification, particularly for extragenital sites, with sensitivity of 93-100% for rectal chlamydia versus 63% for SDA 5. For pharyngeal gonorrhea, the Cepheid Xpert CT/NG shows 98% sensitivity versus 93% for Aptima, though with slightly more false positives 6. In clinical practice, the specific NAAT platform matters less than ensuring testing occurs at all anatomically relevant sites based on sexual history 3, 2.