Chlamydial Infections: Complete Clinical Guide to Urogenital, Rectal, Ocular and Systemic Disease

Clinical Medicine Year 3 • sexually transmitted, perinatal and intracellular infection

Confidentiality and partner care are part of treatment. Obtain consent, protect privacy, test for other STIs, treat partners according to local policy and prevent reinfection. Use the current Uganda STI guidelines for drug choice, pregnancy and neonatal treatment.

Why chlamydia matters

Chlamydia trachomatis is frequently asymptomatic but can silently damage the upper genital tract. Untreated infection may cause pelvic inflammatory disease, infertility, ectopic pregnancy, chronic pelvic pain, epididymitis and neonatal conjunctivitis or pneumonia. Rectal infection, lymphogranuloma venereum (LGV), trachoma and respiratory chlamydial disease require different questions and treatment durations.

Learning outcomes

Describe chlamydial structure, elementary/reticulate bodies and the intracellular life cycle.
Relate serovars to trachoma, urogenital infection and LGV.
Recognise cervical, urethral, rectal, pharyngeal, ocular, neonatal, PID and epididymal syndromes.
Choose NAAT specimens from every exposed site and understand test-of-cure indications.
Provide pregnancy-safe treatment, partner management, retesting, screening and prevention.
Identify PID, tubo-ovarian abscess, testicular torsion, neonatal pneumonia and LGV complications requiring referral.

1. Organism and life cycle

Chlamydiae are obligate intracellular bacteria with a biphasic life cycle:

Elementary body (EB): small, metabolically inactive, extracellular and infectious; attaches to columnar epithelial cells.
Endocytosis and inclusion: the EB enters a host cell and remains within a membrane-bound inclusion.
Reticulate body (RB): metabolically active form that divides inside the inclusion.
Reorganisation: RBs convert back to infectious EBs.
Release: host-cell lysis or extrusion spreads EBs to neighbouring cells and new hosts.

Persistence can occur during immune stress or antibiotic pressure, helping explain chronic inflammation and recurrent symptoms.

2. Serovars and related species

Organism/serovar	Main syndrome	Clinical focus
C. trachomatis A–C	Trachoma	Repeated conjunctival infection, scarring and blindness
C. trachomatis D–K	Urogenital, rectal, pharyngeal and neonatal infection	PID, infertility, epididymitis and infant disease
C. trachomatis L1–L3	Lymphogranuloma venereum	Invasive lymphatic infection, proctitis and buboes
C. pneumoniae	Respiratory infection	Pharyngitis, bronchitis and atypical pneumonia
C. psittaci	Psittacosis	Bird exposure, atypical pneumonia, hepatitis/myocarditis/encephalitis

3. Transmission and risk factors

Urogenital, rectal and pharyngeal infection spreads through vaginal, anal or oral sexual contact. Perinatal transmission occurs during delivery. Reinfection is common when partners are untreated. Risk is increased by a new/multiple partner, inconsistent condom use, previous STI, limited screening access, sexual violence, young age and lack of partner treatment. Trachoma spreads through close contact, secretions, hands, clothing and flies in settings with inadequate water and sanitation.

4. Clinical syndromes

4.1 Cervicitis

Many women are asymptomatic. Possible findings include mucopurulent endocervical discharge, easily induced cervical bleeding, post-coital bleeding, dysuria, intermenstrual bleeding and lower abdominal discomfort. Untreated ascending infection may be silent until infertility or ectopic pregnancy occurs.

4.2 Urethritis in men and women

Dysuria, urethral irritation, scant mucous discharge and urinary frequency may occur. Gonorrhoea often produces more purulent discharge, but co-infection is common and cannot be excluded clinically.

4.3 Pelvic inflammatory disease

Lower abdominal pain, cervical motion tenderness, uterine/adnexal tenderness, fever, dyspareunia, abnormal bleeding, nausea and vomiting indicate possible PID. Chlamydia may coexist with gonorrhoea and anaerobes. Delay increases tubal damage, ectopic pregnancy and infertility.

4.4 Epididymitis and male upper-tract disease

Unilateral scrotal pain, epididymal tenderness/swelling, dysuria and fever can occur. Always exclude testicular torsion in sudden severe pain, high-riding testis, absent cremasteric reflex or vomiting.

4.5 Rectal and pharyngeal infection

Rectal infection may be asymptomatic or cause proctitis—pain, discharge, bleeding, tenesmus and painful defecation. Pharyngeal infection is often asymptomatic but can contribute to transmission; test the site when exposed.

4.6 LGV

L1–L3 infection may begin with a small painless genital/rectal papule or ulcer that resolves, followed by painful inguinal/femoral lymphadenopathy (“buboes”), fever and proctitis. Chronic infection can cause strictures, fistulas, lymphoedema and genital/rectal destruction.

4.7 Neonatal infection

Conjunctivitis typically begins 5–14 days after birth with eyelid swelling and mucopurulent discharge. Pneumonia may develop at several weeks with an afebrile staccato cough, tachypnoea and wheeze. Topical drops alone do not eradicate nasopharyngeal infection.

4.8 Trachoma and respiratory chlamydiae

Repeated trachoma causes conjunctival follicles, scarring, entropion and corneal damage. C. pneumoniae causes pharyngitis/atypical pneumonia; C. psittaci follows bird exposure with fever, headache, myalgia, dry cough, interstitial pneumonia and occasional hepatitis, myocarditis or encephalitis.

Urgent referral: severe pelvic pain, fever and vomiting, pregnancy with suspected PID, adnexal mass/tubo-ovarian abscess, acute scrotum, visual threat, neonatal respiratory distress, meningitis or disseminated infection.

5. History and examination

Ask sensitively

Symptoms, onset, sites of sexual exposure and condom use; ask separately about vaginal, anal and oral exposure.
Partners in the previous 60 days, previous STI/PID, infertility, ectopic pregnancy, contraception, pregnancy possibility and antibiotics.
Consent, safety, sexual violence, confidentiality and ability to notify/treat partners.
HIV, syphilis, hepatitis and gonorrhoea risk; bird exposure for atypical pneumonia; water/sanitation for trachoma.

Examination

Inspect external genitalia, discharge, ulcers and nodes. Perform speculum examination where indicated, looking for mucopurulent cervicitis and contact bleeding. Bimanual examination assesses cervical motion, uterine and adnexal tenderness. Examine testes/epididymis and inguinal nodes. Assess rectum, pharynx, eyes, chest and neurological system according to symptoms. Obtain consent and protect privacy throughout.

6. Diagnosis

6.1 NAAT is preferred

Nucleic acid amplification testing is the most sensitive routine test. Use first-catch urine or a vaginal/cervical swab, and obtain rectal or pharyngeal swabs from every exposed site. Self-collected vaginal swabs are acceptable where validated. A negative urine test does not exclude rectal or pharyngeal infection.

6.2 Other tests

Culture is specialised and mainly useful for research or selected resistance/forensic questions.
Microscopy is not sensitive for chlamydia; intracellular inclusions are not a reliable routine diagnosis.
Test for gonorrhoea, HIV, syphilis and hepatitis according to risk and local policy.
Pregnancy test before selecting treatment; urine dip/culture when UTI is a competing diagnosis.
PID: diagnosis is clinical; ultrasound supports tubo-ovarian abscess or ectopic pregnancy but a normal scan does not exclude early PID.
Neonate: conjunctival swab/NAAT and respiratory assessment; evaluate for pneumonia and sepsis.

7. Differential diagnosis

Syndrome	Differentials	Key distinction
Cervicitis/urethritis	Gonorrhoea, Mycoplasma genitalium, trichomoniasis, BV, candidiasis, HSV, UTI	NAAT/culture and discharge pattern; co-infection common
Pelvic pain/PID	Ectopic pregnancy, appendicitis, ovarian torsion, endometriosis, UTI	Pregnancy test, pelvic examination, ultrasound and inflammatory signs
Acute scrotum	Testicular torsion, hernia, mumps orchitis, trauma	Urgent Doppler/surgical review if torsion cannot be excluded
Proctitis	Gonorrhoea, HSV, syphilis, IBD, trauma	Site-specific NAAT, ulcer/vesicle examination and endoscopy when chronic
Neonatal conjunctivitis	Gonococcal, bacterial, HSV, chemical	Onset, Gram stain/culture/NAAT and corneal examination

8. Treatment principles

Use current Uganda STI guidelines, local resistance information, pregnancy status, infection site and adherence capacity. Doxycycline is commonly preferred for uncomplicated urogenital and rectal infection in non-pregnant adults because rectal cure is higher; azithromycin or another guideline-approved agent may be used when pregnancy, contraindication or adherence makes it appropriate. LGV requires a longer course. Treat gonorrhoea when it has not been excluded and use a full PID regimen when upper-tract disease is suspected.

Uncomplicated urogenital/rectal infection

Use the current recommended doxycycline-based or alternative regimen; take the full course and avoid sex until treatment is complete and partners are treated.

Pregnancy

Use a guideline-approved pregnancy-safe option such as azithromycin or amoxicillin where appropriate; avoid contraindicated tetracyclines and arrange test of cure at the recommended interval.

PID

Start broad empiric treatment covering chlamydia, gonorrhoea and anaerobes without waiting for NAAT. Admit for severe illness, pregnancy, tubo-ovarian abscess, vomiting or failed outpatient treatment.

Epididymitis

Cover chlamydia/gonorrhoea according to age and risk, exclude torsion, provide analgesia/scrotal support and review response promptly.

LGV

Use the longer guideline-directed doxycycline-based regimen, assess for proctitis/buboes and aspirate fluctuant nodes when indicated rather than repeatedly incising them.

Neonate

Systemic treatment is required for conjunctivitis or pneumonia; topical drops alone are inadequate. Evaluate for complications and treat mother/partners.

9. Partner management and follow-up

Notify and treat recent sexual partners under local law and service policy; preserve confidentiality and offer assisted notification.
Abstain from sex until the patient and partners have completed treatment and symptoms have resolved.
Retest around three months because reinfection is common, even after cure.
Perform test of cure at the guideline interval for pregnancy, persistent symptoms, suspected poor adherence, rectal infection when recommended or non-standard treatment.
Persistent symptoms require examination and tests for gonorrhoea, M. genitalium, trichomoniasis, PID, reinfection and non-infectious causes—not automatic repeated antibiotics.

10. Complications

PID, tubal scarring, infertility, ectopic pregnancy and chronic pelvic pain.
Tubo-ovarian abscess, peritonitis, Fitz-Hugh–Curtis perihepatitis and sepsis.
Epididymo-orchitis, chronic scrotal pain and possible infertility.
LGV strictures, fistulas, lymphoedema and genital/rectal destruction.
Neonatal conjunctival scarring, pneumonia and otitis.
Reactive arthritis/sexually acquired reactive arthritis.
Trachomatous conjunctival scarring and blindness.
Rare disseminated or respiratory disease with hepatitis, myocarditis or encephalitis.

11. Prevention

Condoms, mutual testing, reduction of concurrent partners and prompt treatment.
Confidential, consent-based screening of sexually active young people, pregnant patients and high-risk groups according to Uganda policy.
Integrated HIV/syphilis/gonorrhoea/hepatitis services and vaccination where indicated for other STIs.
Partner treatment and retesting prevent the reinfection “ping-pong” cycle.
For trachoma: facial cleanliness, environmental improvement, water/sanitation and programme-based antibiotic/surgical measures.
For psittacosis: use respiratory protection and safe cleaning around birds; report occupational clusters.

12. Clinical reasoning examples

Example A: asymptomatic risk

A young woman has no symptoms but a new partner and a partner diagnosed with chlamydia. Offer confidential NAAT, pregnancy/STI testing, partner treatment and prevention counselling; do not wait for cervicitis.

Example B: pelvic pain

A patient has lower abdominal pain, cervical motion tenderness and fever. Treat as PID promptly while testing; rule out ectopic pregnancy, torsion and appendicitis and assess for abscess.

Example C: neonatal cough

A three-week-old has an afebrile staccato cough and tachypnoea. Ask about maternal STI treatment, assess oxygenation and sepsis, obtain appropriate samples and provide systemic neonatal therapy.

13. Examination pearls

Most urogenital infection is asymptomatic; absence of symptoms does not mean absence of harm.
NAAT is preferred and must sample every exposed site.
Rectal infection responds differently from some urogenital infections; use the current site-specific regimen.
Partner management and retesting are part of treatment.
Never miss ectopic pregnancy, testicular torsion, tubo-ovarian abscess or neonatal respiratory disease.

14. References

SlideShare: Chlamydia — serovars, life cycle, urogenital disease, LGV and respiratory chlamydial infection.
WHO sexually transmitted infection guidance and current Uganda STI/Clinical Guidelines.
Current neonatal, trachoma and public-health protocols.