Which laboratory tests should be ordered for a patient being evaluated for sexually transmitted infection (STI)?

Laboratory Testing for Sexually Transmitted Infections

For comprehensive STI evaluation, order nucleic acid amplification tests (NAATs) for gonorrhea and chlamydia from all exposure sites, syphilis serology, and HIV testing at minimum—this core panel should be expanded based on specific symptoms, anatomic sites of exposure, and patient risk factors 1.

Core STI Testing Panel

Essential Tests for All Patients Being Evaluated for STI

• Gonorrhea and Chlamydia (NAAT): Test all sites of potential exposure

  • Urogenital: First-void urine (males), vaginal swab or urine (females), or endocervical swab
  • Extragenital sites in high-risk patients (MSM, symptomatic): pharyngeal and rectal swabs 2, 1

• Syphilis Serology: Most labs use reverse algorithm—treponemal-specific test (EIA/chemiluminescence) first, followed by nontreponemal (RPR) for confirmation 1

• HIV Testing: Recommended for all sexually active patients aged 13-64 years seeking STI evaluation 1

Additional Testing Based on Clinical Presentation

For patients with genital lesions:

• Syphilis serology (as above)
• HSV testing: NAAT preferred over culture or DFA, especially for ulcerative lesions 1
• Consider H. ducreyi testing where chancroid is prevalent 1

For patients with vaginal discharge/vaginitis symptoms:

• Add Trichomonas vaginalis NAAT (vaginal or urine specimen in females) 1
• Consider bacterial vaginosis testing (Gram stain or microbiome-based assays more specific than culture) 1
• Candida culture if recurrent symptoms (10-15% have resistant species) 1

For patients with urethritis:

• Gram stain can diagnose gonorrhea in symptomatic males with urethral discharge, but negative result doesn't rule out infection 2
• NAAT for gonorrhea and chlamydia remains essential 2

Risk-Based and Population-Specific Testing

High-Risk Populations Requiring Expanded Testing

Men who have sex with men (MSM):

• Must test extragenital sites: rectal and oropharyngeal swabs for gonorrhea and chlamydia in addition to urogenital testing 1
• Consider hepatitis C screening (sexual transmission documented in MSM) 1

Pregnant patients (first prenatal visit):

• Syphilis serology (repeat third trimester and delivery in high-risk patients) 3
• Hepatitis B surface antigen 3
• HIV testing (repeat third trimester) 1
• Gonorrhea testing if at risk or high-prevalence area 3
• Chlamydia testing in third trimester if age <25 years or other risk factors 3
• Group B streptococcus at 35-37 weeks (vaginal and rectal swabs) 1

Sexual assault victims:

• Baseline testing: gonorrhea, chlamydia, trichomonas (NAATs from exposure sites), syphilis, HIV, hepatitis B 4, 5
• Follow-up testing at 1-2 weeks if no empiric treatment given and initial tests negative 4, 5
• Repeat syphilis at 4-6 weeks and 3 months if source cannot be ruled out 5
• Pregnancy test for all females of childbearing potential 4

Critical Testing Considerations

Specimen Collection Priorities

• NAATs are preferred over culture for gonorrhea and chlamydia due to superior sensitivity, especially with suboptimal specimens or asymptomatic infection 2, 1
• Vaginal swabs can be self-collected and are equivalent to clinician-collected specimens for females 1
• First-void urine acceptable for males and females, though vaginal swabs slightly more sensitive in females 2, 1
• Culture still required when antimicrobial susceptibility testing needed (treatment failures) or for legal purposes 2

Co-Testing Recommendations

Simultaneous testing for gonorrhea, chlamydia, and trichomonas is optimal for detecting the most common treatable STIs in females 1. However, current practice shows only 56% co-testing rate for trichomonas/BV when gonorrhea/chlamydia ordered 6.

All patients tested for gonorrhea should also be tested for chlamydia, syphilis, and HIV due to high co-infection rates 2.

Common Pitfalls to Avoid

• Don't rely on Gram stain alone for gonorrhea diagnosis in asymptomatic patients or for any pharyngeal/rectal specimens 2
• Don't use culture or probe testing for Gardnerella vaginalis alone to diagnose bacterial vaginosis—Gram stain or microbiome assays are more specific 1
• Don't forget extragenital sites in MSM—up to 80% of infections may be missed if only urogenital testing performed 1
• Don't use nontreponemal tests (RPR) alone for syphilis screening—less sensitive in early and late disease 1
• Don't assume negative chlamydia NAAT means no need for gonorrhea treatment—treat gonorrhea definitively when diagnosed 2

Emerging Diagnostic Considerations

• Mycoplasma genitalium: Increasingly recognized cause of urethritis and cervicitis, but testing not yet widely available 1
• Antimicrobial resistance in N. gonorrhoeae: Culture with susceptibility testing essential for treatment failures 2, 1
• HPV testing: Not recommended for routine STI screening; reserved for cervical cancer screening in women ≥30 years 1, 7