The laboratory plays a central role in STI services: performing the diagnostic tests, ensuring appropriate sample handling, providing susceptibility data for gonorrhoea (where antibiotic resistance is a major concern), and generating the epidemiological data that drive public health STI control programmes.
Chlamydia trachomatis: The Most Common Bacterial STI
Chlamydia trachomatis is the most commonly diagnosed bacterial STI in England (with approximately 200,000 confirmed cases per year, predominantly in 15 to 24 year olds) and globally. It is an obligate intracellular bacterium that cannot be grown on standard bacteriological media (requires cell culture, which is too slow and technically demanding for routine use). The diagnostic revolution for chlamydia was NAAT (Nucleic Acid Amplification Test), which detects C. trachomatis DNA directly from genital swabs and first-catch urine with sensitivity above 95 per cent and specificity above 99 per cent.
Most genital chlamydial infections are asymptomatic (approximately 70 per cent of infections in women and approximately 50 per cent in men). Untreated, it can cause pelvic inflammatory disease (PID) in women, leading to infertility, ectopic pregnancy, and chronic pelvic pain. In men, it causes epididymo-orchitis.
Sample collection: first-catch urine (FCU) — the first 20 to 30 mL of urinary stream, containing the highest concentration of urethral organisms — is the recommended non-invasive sample for both male and female patients. Self-collected vulvo-vaginal swabs (SVVS) have equivalent sensitivity to clinician-collected cervical swabs and are preferred by many patients. Pharyngeal and rectal swabs for extra-genital testing in MSM (men who sex with men) and as indicated by sexual history.
Treatment: doxycycline 100 mg twice daily for 7 days (preferred, higher efficacy than single-dose azithromycin 1 g for chlamydia, which has been associated with higher treatment failure rates in rectal infection particularly).
Neisseria gonorrhoeae: The Resistant Pathogen
Neisseria gonorrhoeae (gonorrhoea) is a gram-negative diplococcus causing urethritis (men), cervicitis, and potentially disseminated gonococcal infection (DGI: septic arthritis, skin lesions, bacteraemia). It is the second most common bacterial STI. N. gonorrhoeae has an extraordinary ability to acquire antibiotic resistance: virtually every antibiotic introduced for gonorrhoea treatment has eventually been rendered ineffective by resistance emergence. The current recommended treatment in the UK and most high-income countries is ceftriaxone 1 g IM single dose (raised from 500 mg due to emerging ceftriaxone-resistant gonorrhoea, including the international "superbug" strain FC428 with ceftriaxone MIC above the clinical breakpoint).
Diagnostics: NAAT on first-catch urine, self-collected vulvo-vaginal swabs, and extra-genital swabs (pharynx, rectum) provides the highest sensitivity. Gonorrhoea culture (on selective media: Thayer-Martin or GC selective agar, incubated at 37 degrees Celsius in 5 per cent CO2 for 24 to 48 hours) is essential for susceptibility testing and for detecting emerging resistance. Culture must be performed whenever gonorrhoea is diagnosed or suspected, even when NAAT is already positive.
WHO global monitoring of gonorrhoea resistance (GASP) tracks rising MICs to ceftriaxone, azithromycin, and other agents, with routine susceptibility data from sentinel surveillance sites.
Syphilis: The Great Imitator
Treponema pallidum causes syphilis, historically called "the great imitator" because its diverse clinical manifestations (primary chancre, secondary rash, latent infection, tertiary syphilis with cardiovascular and neurosyphilis) can mimic many other diseases. Syphilis incidence has increased sharply in the UK, Europe, and North America since 2010, particularly in MSM.
Primary syphilis: a painless ulcer (chancre) at the site of inoculation, appearing 10 to 90 days after exposure. The painlessness often leads to it being missed.
Secondary syphilis: widespread maculopapular rash (characteristically involving palms and soles), condylomata lata, lymphadenopathy, and systemic features, occurring 2 to 12 weeks after the chancre.
Latent syphilis: no clinical signs, detected only by serology. Early latent (less than 1 year duration) is infectious; late latent is not infectious to sexual contacts but can be transmitted vertically to the fetus.
Congenital syphilis: T. pallidum crosses the placenta. Consequences: stillbirth, neonatal death, or Hutchinson's triad (interstitial keratitis, eighth nerve deafness, Hutchinson's teeth).
Syphilis serology uses two types of test:
Treponemal tests (TPHA, TPPA, ELISA, CIA): detect antibodies specific for Treponema pallidum antigens. These remain positive for life after infection (even after treatment), so they cannot be used to distinguish active from past treated infection.
Non-treponemal tests (RPR, VDRL): detect cardiolipin antibodies (a non-specific test that reflects the inflammatory response to active treponemal infection). RPR/VDRL titre correlates with disease activity: a rising titre indicates active infection or reinfection; a falling titre on treatment (typically a 4-fold fall by 6 to 12 months) confirms treatment response. RPR/VDRL can become negative after successful treatment (particularly in early syphilis) and can be used as a test of cure.
Treatment: benzathine penicillin G (Bicillin L-A) IM 2.4 million units single dose for primary, secondary, and early latent syphilis. Longer courses for late latent and neurosyphilis.
Other STIs: Trichomonas, Mycoplasma, and HPV
Trichomonas vaginalis: the most common curable non-viral STI globally. Causes vaginal discharge and discomfort in women; often asymptomatic in men. Diagnosed by NAAT (most sensitive) or wet preparation microscopy (sensitivity 60 to 70 per cent, requiring immediate microscopy). Treatment: metronidazole 400 mg twice daily for 7 days (or 2 g single dose for partner treatment).
Mycoplasma genitalium: an increasingly important STI causing non-gonococcal urethritis and cervicitis. High levels of macrolide resistance (azithromycin) have developed globally due to azithromycin use for chlamydia (a significant antibiotic stewardship concern). Resistance-guided therapy using moxifloxacin for azithromycin-resistant strains. Resistance testing by NAAT assay (MG NAAT with resistance marker) is now recommended before treatment.
HPV (Human Papillomavirus): over 200 HPV types; high-risk types (HPV 16, 18) cause cervical, oropharyngeal, anal, vulval, and penile cancers. Low-risk types (HPV 6, 11) cause genital warts. HPV testing on self-collected or clinician-collected cervical samples is now the primary cervical screening test in the UK (primary HPV screening, replacing cytology), with triage by cytology for HPV-positive samples.
Frequently Asked Questions
What is NAAT and why is it preferred for STI diagnosis?
NAAT (Nucleic Acid Amplification Test), including PCR, is the most sensitive method for detecting STIs like chlamydia and gonorrhoea because it detects pathogen DNA directly in the sample, even when the organism load is very low or the organism is dead (PCR does not require viability). NAAT for chlamydia has sensitivity above 95 per cent and specificity above 99 per cent, far superior to older methods like culture or antigen tests.
Why must gonorrhoea culture be done even when NAAT is positive?
Gonorrhoea culture is essential for susceptibility testing: it allows determination of the MIC of ceftriaxone and other antibiotics for the infecting strain. Since N. gonorrhoeae has high and increasing rates of antibiotic resistance, susceptibility data are essential for treatment decisions and for national resistance surveillance. NAAT cannot provide susceptibility results.
What is a first-catch urine sample?
First-catch urine (FCU) is the first 20 to 30 mL of the urinary stream, collected without prior urination for at least 1 hour. It contains the highest concentration of urethral organisms and is the recommended non-invasive sample for chlamydia and gonorrhoea NAAT. FCU has sensitivity equivalent to urethral swab in men and is the recommended self-collection sample for all patients.
What does RPR titre mean in syphilis?
The RPR (Rapid Plasma Reagin) is a non-treponemal syphilis test measuring cardiolipin-antibody titres. The titre reflects the level of inflammatory response to active syphilitic infection. A 4-fold rise in RPR titre indicates reinfection or treatment failure. A 4-fold fall by 6 to 12 months post-treatment confirms treatment response. RPR should be monitored at 3, 6, and 12 months post-treatment for early syphilis.
What is the difference between treponemal and non-treponemal syphilis tests?
Treponemal tests (TPHA, TPPA, ELISA) detect specific T. pallidum antibodies and remain positive for life after syphilis infection (they cannot distinguish past treated from active infection). Non-treponemal tests (RPR, VDRL) detect cardiolipin antibodies whose titre falls on successful treatment and can be used as a test of disease activity and treatment response.
What is gonorrhoea ceftriaxone resistance?
Ceftriaxone-resistant Neisseria gonorrhoeae strains (with MIC above 0.125 mg/L for ceftriaxone) are emerging globally. International outbreak strains (including the "FC428" cluster) with very high ceftriaxone MICs have been reported in multiple countries. This is driving the rise of the recommended ceftriaxone dose from 500 mg to 1 g IM single dose. WHO defines multi-drug resistant (MDR) gonorrhoea as resistance to ceftriaxone plus at least two other antibiotic classes.
What is Mycoplasma genitalium and why does resistance matter?
Mycoplasma genitalium is a sexually transmitted organism causing non-gonococcal urethritis and cervicitis. Azithromycin (1 g, the standard treatment for chlamydia) drives macrolide resistance in M. genitalium. Resistance rates for azithromycin now exceed 50 per cent in some populations. Resistance-guided therapy (using doxycycline first, then azithromycin if macrolide-susceptible, or moxifloxacin if resistant) is required to achieve cure.
What is primary HPV screening?
Primary HPV screening is cervical cancer screening that uses HPV NAAT as the first-line test on cervical samples, instead of cytology (Pap smear). HPV-negative samples are returned to routine recall (3 or 5 years depending on age). HPV-positive samples are triaged by cytology and colposcopy referral if cytological abnormality is present. The UK switched to primary HPV screening in 2019. HPV screening is more sensitive than cytology for detecting cervical intraepithelial neoplasia (CIN) grade 2 or above.
What is congenital syphilis and how is it prevented?
Congenital syphilis is the vertical transmission of Treponema pallidum from a syphilitic mother to her fetus, causing stillbirth, neonatal death, or severe congenital infection. It is entirely preventable by antenatal syphilis screening and treatment with benzathine penicillin G before 28 weeks gestation. Universal antenatal syphilis screening is mandated in the UK and most high-income countries. The recent rise in syphilis incidence in women of childbearing age has caused a parallel rise in congenital syphilis cases in the UK and US.
What is the window period for STI testing?
The window period is the time between exposure and when the test can reliably detect the infection. For chlamydia and gonorrhoea NAAT: approximately 2 weeks post-exposure. For syphilis serology: 2 to 6 weeks (treponemal EIA) to up to 3 months (older tests). For HIV fourth-generation Ag/Ab test: approximately 18 to 21 days. Testing before the relevant window period produces unreliable negative results and should be repeated after the window has passed.