Urethral and Cervical Swabs

Urethral and endocervical swabs are used to detect sexually transmitted pathogens causing urethritis, cervicitis and pelvic inflammatory disease: Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium, Trichomonas vaginalis, herpes simplex virus, and occasionally Ureaplasma urealyticum and Haemophilus species.

Nucleic acid amplification tests (NAAT) are the preferred method for chlamydia, gonorrhoea, trichomonas and M. genitalium (sensitivity 90 to 99%, specificity over 99%). Culture on selective media (modified Thayer-Martin) is retained for gonorrhoea when antimicrobial susceptibility is required.

Gram stain of a urethral smear in men shows intracellular Gram negative diplococci in gonorrhoea (sensitivity over 95% in symptomatic men, under 50% in women).

Chlamydia is the commonest bacterial sexually transmitted infection (about 130 million new cases a year), gonorrhoea has about 80 million new cases a year, and both are often asymptomatic in women (70%) and in 10 to 50% of men.

Untreated infection causes pelvic inflammatory disease, tubal infertility, ectopic pregnancy, epididymo orchitis, reactive arthritis, neonatal conjunctivitis and increased HIV acquisition. Gonococcal resistance to ciprofloxacin, penicillin, tetracycline and azithromycin is widespread, and resistance to ceftriaxone is emerging.

Indications. Urethral discharge, dysuria, testicular pain, vaginal discharge, intermenstrual or post-coital bleeding, mucopurulent cervicitis, pelvic pain or dyspareunia. Contact with a partner with a sexually transmitted infection. Screening of sexually active women under 25 and others at risk. Pelvic inflammatory disease.

Before termination of pregnancy or intrauterine device insertion where risk exists. Sexual assault. Antenatal screening in women at risk. Test of cure for gonorrhoea or in pregnancy.

Specimen. For NAAT: first catch urine (first 20 mL, at least 1 hour since last voiding) in men, or a self-collected vulvovaginal swab in women (preferred, equal sensitivity to clinician collected endocervical swabs). Endocervical swab after wiping the cervical os free of mucus, rotating the swab for 10 to 30 seconds.

Urethral swab in men with discharge, inserted 2 to 4 cm and rotated. Pharyngeal and rectal swabs by exposure history. For gonorrhoea culture, direct inoculation onto selective plates or transport in charcoal medium with prompt delivery (never refrigerate). Specimens from children and sexual assault need forensic handling and chain of custody.

Reference values. NAAT: Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis and Mycoplasma genitalium not detected. Culture: no gonococcus isolated. Gram stain (male urethral smear): under 5 polymorphonuclear cells in each high power field and no intracellular diplococci.

Interpretation.

• Positive gonorrhoea NAAT: infection, preferably confirmed by culture before treatment, to obtain susceptibility results where resistance is a concern (and in extragenital or low prevalence settings, where positive predictive value is lower).
• Positive chlamydia NAAT: infection (positive predictive value over 90% at prevalence over 5%), treated and partners notified.
• Gram stain showing intracellular Gram negative diplococci with neutrophils in a man with discharge: gonococcal urethritis, diagnosed at the bedside. Absence of diplococci with 5 or more polymorphs in each field: non-gonococcal urethritis (Chlamydia, M. genitalium, Ureaplasma, Trichomonas, adenovirus, herpes simplex virus).
• Mucopurulent cervicitis with negative tests: M. genitalium, Trichomonas, herpes simplex virus, bacterial vaginosis, or non-infectious causes.
• Persistent or recurrent urethritis after treatment: M. genitalium (macrolide resistance in over 50% in many regions), Trichomonas, reinfection from untreated partner, or non-compliance, and resistance testing directs therapy.
• Co-infection with chlamydia and gonorrhoea occurs in 10 to 40%, and testing for both is routine.
• Positive result in a child: sexual abuse until proven otherwise, with safeguarding procedures and culture confirmation.

Critical values and findings needing immediate action.

• Positive gonorrhoea in any patient: treatment with ceftriaxone based therapy based on local resistance, with test of cure at 2 weeks or more when pharyngeal infection is present or treatment is non-routine.
• Pelvic inflammatory disease or epididymo orchitis: immediate empirical broad antibiotics covering gonorrhoea, chlamydia and anaerobes.
• Disseminated gonococcal infection (fever, migratory arthralgia, tenosynovitis, pustular skin lesions): admission, blood and joint cultures, intravenous ceftriaxone.
• Pregnant woman with chlamydia or gonorrhoea: treatment in pregnancy, retest at 3 months, and neonatal conjunctivitis prophylaxis plan.
• Neonatal conjunctivitis within 2 days to 2 weeks of birth: urgent swab, treatment, and maternal and partner testing.
• Suspected sexual assault: forensic sampling, prophylaxis for HIV and sexually transmitted infections, emergency contraception, and psychological support.

Interferences and pitfalls.

• Urine collected after recent voiding, or a midstream sample, reduces sensitivity in men. Women should not clean the vulva before swabbing.
• Cervical mucus, blood, lubricants, spermicides and talc may inhibit NAAT or cell collection.
• Culture of gonococcus needs immediate inoculation, 5% carbon dioxide and 35 to 37 °C, and fails with delay or refrigeration.
• NAAT cannot give antimicrobial susceptibility, and culture or molecular resistance markers (for example, gyrA for ciprofloxacin) are used where resistance is a concern.
• False positive gonorrhoea NAAT in low prevalence populations because of cross-reaction with commensal Neisseria in the throat, so confirmatory testing is needed for pharyngeal specimens.
• Test of cure for chlamydia is delayed for 3 to 4 weeks after treatment (earlier tests detect non-viable DNA), and retesting at 3 months identifies reinfection.
• Doxycycline pre-exposure and post-exposure prophylaxis for sexually transmitted infections may reduce chlamydia and syphilis and select tetracycline resistant gonococci.
• Partner notification and treatment are central to control.
• Syndromic management is used without tests in resource limited settings, but it over treats and misses asymptomatic infection.

Special groups.

• Adolescents and young adults: highest incidence, and annual screening of sexually active women under 25.
• Men who have sex with men: pharyngeal and rectal swabs by exposure, and lymphogranuloma venereum (L serovars) in proctitis.
• Pregnancy: chlamydia and gonorrhoea cause preterm birth, premature rupture of membranes and neonatal infection.
• Children: any detection indicates abuse unless perinatally acquired.
• HIV-positive patients: higher prevalence and shedding, with screening at least annually.
• Regions: prevalence of gonorrhoea is highest in sub-Saharan Africa and the Western Pacific, and antimicrobial resistance surveillance directs national treatment.

Follow up tests. HIV, syphilis, hepatitis B and C serology, trichomonas and Mycoplasma genitalium NAAT with macrolide resistance testing, pharyngeal and rectal NAAT by exposure, culture for gonorrhoea susceptibility, herpes simplex virus PCR for ulcers, pregnancy test, pelvic ultrasound for suspected tubo ovarian abscess, test of cure at the right interval, repeat testing at 3 months, partner notification, and cervical screening.