Throat Swabs for Chlamydia and Gonorrhea Screening

Anatomical Site Distribution and Testing Recommendations

Nucleic acid amplification tests (NAATs) are the recommended diagnostic method for chlamydia and gonorrhea detection due to their high sensitivity and specificity, according to the American College of Physicians, in individuals who engage in high-risk sexual practices 1, 2
NAATs are FDA-cleared for urogenital sites, but not officially cleared for rectal and pharyngeal specimens, although many laboratories have validated NAATs for extragenital sites through Clinical Laboratory Improvement Amendment (CLIA) requirements 1, 3, 4
The Centers for Disease Control and Prevention (CDC) recommends that rectal and pharyngeal swabs can be collected from persons who engage in receptive anal intercourse and oral sex, respectively, to ensure accurate diagnosis 1, 2

The American Academy of Pediatrics recommends routine annual screening for pharyngeal gonorrhea in sexually active adolescent and young adult men who have sex with men (MSM) who engage in receptive oral intercourse, with a strength of evidence rated as strong 5, 4
The CDC recommends annual screening for chlamydia and gonorrhea in MSM based on exposure history, with more frequent screening (every 3-6 months) in higher-risk populations, with a moderate level of evidence 5, 6

Gram stain of pharyngeal specimens is not sufficient to detect infection and is not recommended, according to the CDC, due to its low sensitivity 7
Culture is traditionally the most widely available option for diagnosis of infection in nongenital sites, but NAATs are increasingly being used due to higher sensitivity, with a high level of evidence 7, 1

The CDC recommends assessing sexual practices to determine if the patient engages in receptive oral sex, and if so, to include pharyngeal swab in screening protocol, with a moderate level of evidence 5, 1
For MSM, annual pharyngeal screening is recommended, with more frequent screening (every 3-6 months) for those with higher risk factors, according to the CDC, with a strong level of evidence 5, 6

The American Academy of Pediatrics and CDC recommend annual screening at all sites of sexual contact for men who have sex with men (MSM), including pharyngeal, rectal, and urethral/urine specimens, based on the anatomical sites of sexual contact 8

For MSM, the CDC recommends pharyngeal swab for those engaging in receptive oral sex, rectal swab for those engaging in receptive anal intercourse, and urethral/urine specimen for those engaging in insertive intercourse, with increased frequency to every 3-6 months for high-risk individuals 8
For heterosexual men in high-prevalence settings, routine screening is recommended with urine NAAT as the standard specimen, and site-specific testing based on sexual practices 8

All patients with positive chlamydia or gonorrhea tests require retesting at 3 months after treatment, regardless of whether partners were treated, due to high reinfection rates, and this applies to all anatomical sites initially positive 8