What diagnostic tests should be done for a patient presenting with symptoms or risk factors for a sexually transmitted infection (STI)?

STI Culture and Diagnostic Testing

For STI diagnosis, you should NOT rely on traditional culture methods for most infections—instead, use nucleic acid amplification tests (NAATs) for chlamydia, gonorrhea, and trichomonas, combined with serologic testing for syphilis and HIV. 1

Core Testing Approach

Primary Testing Methods

NAATs are the preferred diagnostic method for the most common bacterial STIs due to superior sensitivity (86.1%-100%) and specificity (97.1%-100%) compared to culture. 2 These tests allow non-invasive specimen collection and detect infections that culture would miss. 1

For all patients presenting with STI symptoms or risk factors, perform:

• Chlamydia and gonorrhea: NAAT testing on appropriate anatomic sites 1

  • Women: Vaginal swab (preferred), cervical swab, or urine 1
  • Men: First-void urine 1
  • High-risk individuals (MSM): Test all three sites—urogenital, rectal, and pharyngeal based on sexual practices 1, 3

• Syphilis: Reverse algorithm screening with treponemal-specific test (EIA/chemiluminescence) first, followed by nontreponemal test (RPR) for confirmation 1

• HIV: Fourth-generation antigen/antibody combination test 1, 4

• Trichomonas (women): Vaginal swab NAAT (preferred over wet mount, which misses 30-40% of infections) 1, 4

When Culture IS Still Required

Culture remains necessary in specific situations: 1

• Gonorrhea in children: Culture with antimicrobial susceptibility testing is mandatory for forensic/legal purposes in suspected sexual abuse cases 1, 5
• Treatment failures: When NAAT-positive patients fail therapy, culture with susceptibility testing guides alternative treatment due to increasing antimicrobial resistance 1, 2
• Recurrent candidiasis: Culture identifies resistant Candida species in 10-15% of patients with recurrent vulvovaginitis 1

Site-Specific Testing Based on Sexual Practices

For men who have sex with men (MSM), extragenital testing is critical because 53-100% of rectal and pharyngeal infections are asymptomatic and would be missed with urogenital-only testing. 1, 2, 3

• Pharyngeal swab for gonorrhea (culture or validated NAAT) 1
• Rectal swab for gonorrhea and chlamydia (culture or validated NAAT) 1
• Urogenital specimen (urine NAAT) 1

For patients reporting receptive oral sex: Pharyngeal gonorrhea testing 1

For patients reporting receptive anal sex: Rectal testing for both gonorrhea and chlamydia 1

Testing Frequency and Rescreening

Retest all patients treated for chlamydia or gonorrhea at 3 months post-treatment, regardless of whether partners were treated, due to reinfection rates of 25-40%. 1, 4 This is mandatory, not optional. 4

For ongoing high-risk patients, screen every 3-6 months: 1, 4

• HIV-infected individuals with multiple partners, unprotected sex, or methamphetamine use 1, 4
• MSM with multiple/anonymous partners or drug use during sex 1, 4

Common Pitfalls to Avoid

Do not use wet mount microscopy alone for trichomonas—it misses 30-40% of infections; always use NAAT. 4

Do not skip extragenital site testing in MSM—rectal and pharyngeal infections are frequently asymptomatic and represent the majority of infections in this population. 1, 3 Studies show 66.1% of chlamydia and 55.2% of gonorrhea in MSM occur at anorectal sites. 3

Do not delay treatment waiting for culture results in symptomatic patients—except in children where forensic evidence is needed. 5 However, obtain specimens before initiating therapy. 1, 5

Do not assume negative urogenital testing rules out infection in MSM—multisite infection occurs in 10.2% of chlamydia and 21.1% of gonorrhea cases. 3

Special Populations

Pregnant women require universal screening at first prenatal visit: 4

• Hepatitis B surface antigen 4
• HIV 4
• Syphilis 4
• Chlamydia and gonorrhea if age <25 years or at increased risk 4
• Repeat syphilis testing in third trimester and at delivery for high-risk women 4

Children with suspected sexual abuse: 5

• Culture (not NAAT) for gonorrhea and chlamydia from all potentially exposed sites 5
• Serology for syphilis and HIV based on risk assessment 5
• Do not initiate treatment until specimens obtained to preserve forensic evidence 5