01Purpose and principlesWhat the assessment is for and the core concepts behind it.
An STI screen is not a single panel. It is a set of specimen and assay decisions based on anatomical exposure, symptoms, timing, pregnancy, previous treatment and local laboratory validation. Begin by defining the clinical question: asymptomatic screening, diagnosis of a syndrome or lesion, testing after a partner notification, baseline after a recent exposure, or follow-up after treatment. Each purpose has different interpretation and urgency.
For chlamydia and gonorrhoea NAAT, choose the sample with the best performance at each exposed site. A self-taken vulvovaginal swab is usually the preferred genital specimen in people with a vagina; urine is an alternative but may be less sensitive. First-catch urine or urethral sampling suits urethral exposure in people with a penis. Rectal and pharyngeal swabs are separate specimens. A negative urine NAAT does not exclude a rectal or pharyngeal infection.
Gonorrhoea requires resistance surveillance. Collect culture before antibiotics from a NAAT-positive or clinically suspected site where feasible, and obtain culture when treatment failure is possible. Culture is less sensitive than NAAT but can prove viable organisms and provide susceptibility. Under the 2025 BASHH guideline, everyone with urogenital gonorrhoea and every gonorrhoea contact should receive pharyngeal testing regardless of reported pharyngeal exposure because silent throat infection matters to transmission and resistance.
Timing changes negative and positive results. For people aged 16 years or older, the 2026 BASHH chlamydia guidance advises repeating NAAT at two weeks after exposure if the first test occurred inside that interval. Blood tests have assay-specific windows; record the exact test and exposure date rather than quoting one universal HIV or syphilis number. After treatment, non-viable nucleic acid can persist, so test-of-cure timing follows the pathogen, site, symptoms, pregnancy, regimen and assay.
Symptoms may need more than screening. Ulcers require fresh-lesion sampling and syphilis assessment; vaginal discharge can require microscopy or validated tests for trichomonas and bacterial vaginosis; urethritis may need microscopy and pathogen-specific NAAT; PID remains a clinical diagnosis and lower-tract negative results do not exclude it. Pregnancy testing can redirect urgency and treatment. Avoid broad unvalidated multiplex panels that detect organisms without a clear disease or treatment pathway.
Self-sampling can widen access when the kit, instructions, packaging and support are usable and the right sites are included. It does not suit every problem: severe symptoms, examination need, culture requirement, lesion sampling, safeguarding or inability to complete the kit may require face-to-face care. State what self-sampling can and cannot answer, how transport affects validity and where the patient can obtain help.
A result is complete only when someone acts on it. Agree a confidential communication route, set expectations for timing and document who reviews results. Positive results require pathogen-specific treatment, partner notification and follow-up. Negative results require interpretation against window, site and assay. Indeterminate, rejected or missing samples need active recall rather than being silently treated as negative.
Key points
- Use a private exposure history to choose genital, rectal, pharyngeal, lesion and blood tests; one negative anatomical site does not clear another.
- For chlamydia and gonorrhoea, a self-taken vulvovaginal swab is generally more sensitive than urine in people with a vagina; first-catch urine is commonly used in people with a penis.
- Sample rectal and pharyngeal sites according to exposure and pathogen guidance. Current gonorrhoea guidance adds pharyngeal testing for every urogenital case and contact.
- Obtain gonococcal culture from NAAT-positive or clinically suspected sites before treatment where feasible because NAAT does not provide antimicrobial susceptibility.
- Explain diagnostic windows and post-treatment residual nucleic acid. An early negative or an early repeat positive may be a timing problem.
- Add HIV, syphilis, hepatitis, pregnancy and other pathogen tests according to exposure, symptoms, programme criteria and local validated assays.
- Give every result a named owner, safe contact route, treatment or referral action, partner plan and date for repeat or test of cure when indicated.
02Indications, selection and cautionsWhen it is useful, when urgency changes and important limitations.
Exposure at mouth, genitals, rectum or a lesion selects distinct samples; testing one site cannot infer the status of another.
Suspected or confirmed gonorrhoea requires culture where feasible before treatment, especially at a positive site or when failure is possible.
A test obtained soon after exposure may precede reliable detection and needs an explicit assay- and pathogen-specific repeat plan.
A molecular test repeated too soon after therapy may detect non-viable material rather than persistent infection.
Pregnancy changes antimicrobial choices, urgency, neonatal implications and test-of-cure requirements for several infections.
Pelvic pain, testicular pain, ulceration, systemic illness or neuro-ocular symptoms needs clinical assessment in addition to specimens.
03Method and interpretationA systematic approach to the test and its findings.
Read from the initial assessment onwards. Tests may run in parallel in urgent care; first-line, preferred, confirmatory, definitive and gold-standard labels appear only when the chapter explicitly states them.
- 01
Site-specific chlamydia and gonorrhoea NAATFirst step - Why
- Detect common bacterial STIs sensitively at every exposed anatomical site.
- Interpretation and limitations
- A positive result directs care; a negative result excludes only the tested infection, site and reliable time window.
- 02
Gonococcal culture and susceptibility - Why
- Recover viable gonococci and guide treatment when resistance or failure matters.
- Interpretation and limitations
- Collect before antibiotics where feasible. A negative culture does not overturn a valid positive NAAT, while NAAT alone cannot provide susceptibility.
- 03
HIV and syphilis blood testing - Why
- Detect blood-borne or systemic infection and establish a baseline after exposure.
- Interpretation and limitations
- Interpret against the assay and exposure date; repeat after the relevant window and escalate symptoms suggestive of acute HIV or neuro-ocular syphilis.
- 04
Fresh-lesion sampling - Why
- Diagnose herpes or direct-test suspected early syphilis when a lesion is present.
- Interpretation and limitations
- Yield falls as lesions heal. A negative old-lesion swab may be non-excluding and serum HSV antibody is not a substitute for lesion diagnosis.
- 05
Pregnancy test and pelvic assessment - Why
- Identify pregnancy and upper-tract complications that change management.
- Interpretation and limitations
- A very early negative urine test may not exclude pregnancy; pelvic tenderness can justify empirical PID treatment despite negative lower-tract NAAT.
- 06
Specimen integrity check - Why
- Confirm the correct container, label, site, collection technique and transport conditions.
- Interpretation and limitations
- Rejected, leaked, insufficient or delayed samples are not negative results and require recollection or a different pathway.
04Clinical next stepsHow the result changes management or prompts escalation.
01Sampling planTest each exposed siteFirst stepA patient requests screening after genital, oral and anal exposure and has no acute symptoms.+
- 1Record exposure dates, anatomical sites, barrier use, pregnancy possibility, previous antibiotics and partner diagnoses.
- 2PreferredOffer the preferred genital specimen plus rectal and pharyngeal sampling as indicated, with HIV, syphilis and hepatitis tests according to risk.
- 3Explain each window and whether a repeat will be needed, then label every sample with its anatomical site.
- 4Confirm result ownership, safe communication, actions for a positive or rejected sample, and symptoms that require earlier review.
02Gonorrhoea pathwayPreserve susceptibility evidenceGonorrhoea NAAT is positive or clinical suspicion is high.+
- 1Obtain culture from each positive or suspected site before treatment where feasible and include pharyngeal testing under current guidance.
- 2Treat promptly using the current pathogen-, allergy- and pregnancy-appropriate regimen without delaying urgent care for culture.
- 3Arrange partner management and site- and risk-specific test of cure, with culture if failure is suspected.
03Very recent exposurePlan around the diagnostic windowInitial tests are taken before reliable detection can be assumed.+
- 1Record exact exposure time and the assay used, and assess whether PEP or emergency contraception is still time critical.
- 2DefinitiveTake useful baseline samples while explaining their limits; do not call an early negative definitive.
- 3Book the pathogen- and assay-specific repeat, assign ownership and give prevention and symptom safety netting.
05Risks, monitoring and follow-upComplications, safety checks and further assessment.
- Track every ordered specimen to a final result and actively recall rejected, insufficient or missing samples.
- Record the pathogen, anatomical site, assay and exposure date so a negative or positive result can be interpreted correctly.
- Ensure positive gonorrhoea NAAT triggers culture or documented susceptibility planning and specialist review for possible failure.
- Arrange organism-, site-, pregnancy- and regimen-specific test of cure or later reinfection testing without conflating the two.
- Close positive results with treatment, partner notification, abstinence advice, vaccination or HIV-prevention review and a safe contact route.
06Special situationsVariants, exceptions and circumstances that change the usual approach.
Site beats identity
Rectal and pharyngeal infections can be silent, and their detection depends on sampling the exposed anatomy.
Culture answers resistance
Molecular detection is sensitive, while viable culture provides susceptibility information needed for gonorrhoea surveillance and failure.
Rejected is unresolved
A leaked or poorly labelled specimen has produced no clinical answer and needs active correction.
Windows work both ways
Testing too soon after exposure can miss infection; testing too soon after treatment can detect residual nucleic acid.
PID remains clinical
Negative cervical or vaginal NAAT cannot by itself rule out upper-tract pelvic infection.
07Common pitfallsFrequent interpretation and management errors.
- 01
Calling a urine-only screen comprehensive when rectal, pharyngeal, lesion or blood testing is indicated.
- 02
Relying on gonorrhoea NAAT without obtaining culture when susceptibility or treatment failure is relevant.
- 03
Giving a single universal window period without naming the pathogen, assay, specimen and exposure date.
- 04
Repeating molecular testing immediately after treatment and labelling residual nucleic acid as resistance.
- 05
Treating a rejected or unreturned self-sample as a reassuring negative result.
- 06
Waiting for routine screening results before treating a clinically likely PID or addressing another urgent syndrome.