01OverviewDefinition, clinical context and the essential points that orientate the chapter.
Chlamydia trachomatis serovars D to K infect columnar or transitional epithelium of the endocervix, urethra, rectum, pharynx and conjunctiva. Infection is often silent, especially at cervical, rectal and pharyngeal sites. Urethral infection may cause dysuria and a cloudy discharge; cervicitis may produce intermenstrual or postcoital bleeding, discharge, lower abdominal discomfort or deep dyspareunia. Absence of symptoms does not imply absence of transmission or upper-tract risk.
Sampling must follow anatomy. For genital testing, BASHH recommends a vulvovaginal swab for a vagina and first-catch urine for a penile urethra. Rectal and oropharyngeal NAAT use depends on exposure and symptoms, while ocular disease requires a conjunctival NAAT. A positive result identifies infection at the sampled site; it does not prove that unsampled sites are clear. Serology and non-molecular point-of-care antigen tests do not replace NAAT for routine uncomplicated infection.
The 2026 guideline makes doxycycline 100 mg twice daily for seven days the sole preferred treatment for uncomplicated urogenital, rectal and pharyngeal infection unless contraindicated. The preference reflects stronger cure, particularly for rectal disease, and avoids selection pressure from single-dose azithromycin on Mycoplasma genitalium. An alternative macrolide regimen requires the exact BASHH qualifications; single-dose azithromycin should not be casually substituted when rectal infection or M. genitalium is relevant.
Pregnancy changes antibiotic selection and follow-up. Current BASHH options include azithromycin 1 g once followed by 500 mg daily for two days, azithromycin 1 g once, erythromycin courses, or amoxicillin 500 mg three times daily for seven days. BASHH supports doxycycline in pregnancy only when the course can finish before 15 weeks and no suitable alternative exists. A test of cure is required no earlier than three weeks after completing therapy.
Follow-up separates cure from renewed exposure. NAAT may detect residual non-viable nucleic acid for several weeks, so routine early testing creates false concern. Test of cure is reserved for pregnancy, persistent symptoms, suspected poor adherence, and selected rectal infection treated with azithromycin. Because reinfection is common, people under 25 should be offered a later retest between two and six months. For symptomatic penile urethral infection, notify partners since symptom onset and during the four weeks before it, or the last partner if longer ago; for vaginal, rectal, pharyngeal, ocular or asymptomatic penile urethral infection, use six months before presentation. Treat symptomatic contacts alongside testing. For asymptomatic contacts, consider epidemiological treatment if they present within 14 days after exposure following individual risk discussion; after 14 days, treat only a positive result, with repeat testing at two weeks after exposure when indicated.
Key points
- Many genital, rectal and pharyngeal infections are asymptomatic; test the anatomy exposed rather than relying on symptoms or identity labels.
- Use NAAT: a self-taken vulvovaginal swab is preferred for a vagina, while first-catch urine is preferred for a penile urethra; add rectal or pharyngeal samples according to exposure and symptoms.
- If an initial test follows exposure within two weeks, test now and repeat NAAT at two weeks after exposure; notify partners since and in the four weeks before symptom onset for symptomatic penile urethral infection (or the last partner if longer), and use the preceding six months for every other presentation.
- Doxycycline 100 mg orally twice daily for seven days is the sole preferred 2026 BASHH regimen for uncomplicated urogenital, rectal and pharyngeal chlamydia when suitable.
- Pregnancy needs an alternative regimen, usually azithromycin under the current pathway; test of cure is performed no earlier than three weeks after treatment finishes.
- Routine test of cure is unnecessary after uncomplicated adherent non-pregnancy treatment, but it is indicated for pregnancy, persistent symptoms or suspected poor adherence.
- Retest people younger than 25 for reinfection between two and six months after treatment, which is distinct from testing for microbiological cure.
- Discuss and document confidential partner notification, offer partners full STI screening, and give exact abstinence advice through treatment and symptom resolution.
02AetiologyUnderlying causes, associations and risk factors, with why each one matters.
Mucosal transmission
C. trachomatis elementary bodies pass between susceptible mucosal surfaces during genital, anal or oral sexual contact and seed local epithelial cells.
Perinatal and ocular spread
Infected genital secretions can reach neonatal or adult conjunctiva, while autoinoculation can produce unilateral follicular conjunctivitis alongside genital infection.
Re-exposure
Limited protective immunity and untreated or new partners permit repeated infection, which increases cumulative risk to the upper reproductive tract.
03PathophysiologyThe causal sequence from the underlying abnormality to symptoms and harm.
- 1Intracellular developmental cycle
Infectious elementary bodies enter epithelial cells and convert into replicating reticulate bodies before reorganising and infecting neighbouring cells.
- 2Local inflammatory response
Epithelial cytokines and recruited neutrophils cause urethritis or cervicitis, although inflammation may remain clinically silent despite viable organisms.
- 3Ascending tubal injury
Endocervical organisms can reach endometrium and fallopian tubes, where repeated inflammation damages cilia and promotes fibrosis, ectopic implantation and infertility.
- 4Ductal male complication
Ascending urethral infection can involve the epididymis, generating unilateral pain and swelling that must still be distinguished from testicular torsion.
04Clinical features and red flagsSymptoms, examination findings, patterns of presentation and time-critical warnings.
Screening or partner notification detects many cases because cervical, rectal and pharyngeal chlamydia commonly causes no symptoms.
Dysuria, urethral discomfort and scant cloudy discharge developing after sexual exposure supports urethral inflammation but does not identify the organism alone.
Mucopurulent discharge, contact bleeding, postcoital bleeding or intermenstrual bleeding may accompany endocervical infection and should trigger pelvic assessment.
Lower abdominal pain, deep dyspareunia and cervical or adnexal tenderness suggests PID and needs immediate broad syndrome treatment.
Proctitis with severe pain, discharge, bleeding, tenesmus, ulcers or lymphadenopathy requires LGV testing and a longer treatment pathway.
05InvestigationsWhat to request, why it matters and how to interpret it.
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 NAATFirst step - Why
- Detect C. trachomatis at genital, rectal, pharyngeal or ocular sites selected from anatomy and exposure.
- Interpretation and limitations
- A reactive result supports treatment and partner action; a negative test clears only the sampled site at the tested time.
- 02
Timed repeat NAAT after recent exposure - Why
- Reduce false reassurance when the first sample was taken during the early detection interval.
- Interpretation and limitations
- If exposure was within the previous two weeks, test initially and repeat at two weeks after that exposure if concern remains.
- 03
Gonorrhoea NAAT and culture where indicated - Why
- Detect common co-infection and obtain gonococcal susceptibility before antibiotics when gonorrhoea is possible.
- Interpretation and limitations
- NAAT detects gonorrhoea sensitively, while culture supplies resistance data; use all exposed sites and do not delay urgent treatment.
- 04
Pregnancy test and pelvic examination - Why
- Identify pregnancy, ectopic risk and clinical PID that changes antibiotic choice and setting.
- Interpretation and limitations
- A positive hCG with pain requires localisation; pelvic tenderness can justify empirical PID treatment despite a negative cervical NAAT.
- 05
HIV and syphilis testing - Why
- Complete broader STI care and identify infections with different diagnostic windows and consequences.
- Interpretation and limitations
- Interpret results against exposure timing and arrange repeat serology when the initial sample cannot exclude recent acquisition.
06Differential diagnosisRealistic alternatives and the features that help distinguish them.
Gonorrhoea
Purulent discharge and rapid urethritis may be more prominent, but symptoms overlap and dual NAAT with gonococcal culture is required.
Mycoplasma genitalium
Persistent urethritis or cervicitis may reflect M. genitalium, for which indiscriminate azithromycin encourages resistance and specific testing is needed.
Pelvic inflammatory disease
Pelvic tenderness or deep pain represents upper-tract inflammation requiring immediate broad treatment even when the cervical chlamydia result is unavailable.
Non-infective bleeding
Cervical ectropion, polyps, trauma and malignancy can cause contact or intermenstrual bleeding and require examination when infection testing is negative.
07ManagementImmediate care, first-line treatment, alternatives and escalation.
01DETECTTest the relevant anatomyFirst stepA patient has symptoms, screening eligibility, a new exposure or notification as a chlamydia contact.+
- 1Take a private sexual history that records anatomy, exposure sites, timing, symptoms, pregnancy possibility, contraception and recent antimicrobials.
- 2Obtain a vulvovaginal swab or first-catch urine as appropriate, adding rectal, pharyngeal or conjunctival NAAT when exposure or presentation requires it.
- 3Test for gonorrhoea and offer HIV, syphilis and other tests according to risk, with a written repeat plan for samples taken inside a detection window.
- 4Assess pelvic, scrotal, rectal or ocular complications before categorising the result as uncomplicated infection.
02TREATTreat uncomplicated infectionA site-specific NAAT confirms uncomplicated chlamydia and doxycycline is suitable.+
- 1Prescribe doxycycline 100 mg orally twice daily for seven days and explain dose spacing, oesophageal irritation, photosensitivity and completion.
- 2Advise abstinence from sexual intercourse, including oral sex, until the course is completed and symptoms have resolved; align partner treatment timing.
- 3AlternativeUse the pregnancy-specific alternative list or specialist advice when doxycycline is contraindicated rather than defaulting to an unqualified single dose.
- 4EscalationEscalate PID, epididymo-orchitis, LGV, ocular infection or another complication to its longer or broader regimen.
03CLOSEPrevent missed persistence and reinfectionTreatment has been supplied and the transmission chain and follow-up plan require closure.+
- 1With a trained professional, notify partners since and during the four weeks before symptom onset for symptomatic penile urethral infection (or the last partner if longer ago), and partners from the preceding six months for all other presentations; offer every contact full STI screening.
- 2Arrange test of cure at least three weeks after completion for pregnancy, persistent symptoms, suspected poor adherence or another defined indication.
- 3Offer people under 25 a reinfection retest between two and six months and reassess renewed exposure rather than calling every positive result treatment failure.
- 4Provide rapid return instructions for pelvic pain, acute scrotal pain, rectal bleeding, eye symptoms or systemic illness.
Key medicines and prescribing safety3 treatments · regimens, roles and cautions+
Doxycycline
Take 100 mg orally twice daily for seven days for uncomplicated genital, rectal or pharyngeal infection.Review pregnancy, allergy and interactions with antacids or iron; counsel on water, remaining upright after dosing, photosensitivity and course completion.
Azithromycin in pregnancy
Give 1 g orally once followed by 500 mg daily for two days when this current pregnancy regimen is selected.Check QT risk, macrolide interactions and vomiting; a one-dose alternative is separately graded and requires the guideline context and test of cure.
Amoxicillin in pregnancy
Give 500 mg orally three times daily for seven days as a listed pregnancy alternative.Check immediate penicillin allergy, explain the theoretical persistence concern described by BASHH, and arrange test of cure after treatment.
08ComplicationsImportant consequences, why they occur and why they matter clinically.
Pelvic inflammatory disease
Ascending infection can cause endometritis and salpingitis with later chronic pelvic pain, ectopic pregnancy or tubal-factor infertility.
Epididymo-orchitis
Urethral organisms may ascend through genital ducts to the epididymis, producing pain, swelling and possible abscess or fertility impairment.
Reactive arthritis
Immune activation after genital infection can produce asymmetric arthritis, enthesitis, urethritis and ocular inflammation in a susceptible host.
Ocular and neonatal disease
Conjunctival inoculation causes adult follicular conjunctivitis and can expose a neonate to conjunctival or respiratory infection during birth.
09Monitoring and follow-upTreatment response, safety checks and longer-term review.
- Confirm that the course was completed, symptoms resolved, and no pelvic, rectal, scrotal or ocular complication has emerged.
- Perform test of cure no earlier than three weeks after treatment finishes when pregnancy, poor adherence or persistent symptoms makes it necessary.
- Retest people younger than 25 between two and six months to detect reinfection after successful therapy.
- Track partner notification and screening outcomes: treat symptomatic contacts; for asymptomatic contacts at or within 14 days after exposure consider epidemiological treatment after individual risk discussion, while those presenting more than 14 days later are treated only if positive and receive repeat testing at two weeks after exposure when indicated.
- Interpret a later positive NAAT using adherence, treatment, sexual re-exposure and test timing rather than assuming antimicrobial failure.
10Special situationsVariants, exceptions and circumstances that change the usual approach.
Window timing matters
Testing immediately is reasonable, but an exposure inside two weeks requires a planned repeat because early NAAT can be negative.
Rectal infection drives regimen choice
Doxycycline outperforms azithromycin at the rectal site, including when rectal infection was not predicted from reported anal exposure.
Cure differs from reinfection
An early test of cure assesses eradication; the later two-to-six-month test in younger people seeks infection acquired again.
Pregnancy requires closure
A pregnancy-compatible regimen must be followed by properly timed test of cure rather than assumed microbiological success.
Complications change treatment
PID, epididymo-orchitis, LGV and ocular disease are not managed by simply extending an uncomplicated seven-day prescription without reassessment.
11Common pitfallsFrequent interpretation and management errors.
- 01
Using urine to screen a vagina when a vulvovaginal swab gives better diagnostic sensitivity.
- 02
Calling a negative NAAT definitive when it was taken less than two weeks after exposure.
- 03
Substituting single-dose azithromycin routinely despite the 2026 doxycycline preference and macrolide-resistance concerns.
- 04
Performing NAAT too soon after treatment and misreading residual non-viable nucleic acid as persistent infection.
- 05
Forgetting a pregnancy test, pregnancy-specific regimen and test-of-cure appointment.
- 06
Treating cervicitis alone when pelvic tenderness indicates clinical PID requiring broader immediate therapy.