Chlamydia

Clinical Snapshot

Chlamydia, caused by Chlamydia trachomatis, is one of the 2 major causes of urethritis and cervicitis (the other is gonorrhea). It is frequently asymptomatic, which is why screening — not just symptom-triggered testing — is central to management. Untreated infection can ascend to cause pelvic inflammatory disease, ectopic pregnancy, and infertility, and can cause epididymitis in people with a penis. Because chlamydia and gonorrhea commonly co-occur, always assess for both when either is suspected.^[1]

Recognize the Condition

Typical Presentation

Often silent — this is the single most important fact about chlamydia.

Frequently entirely asymptomatic — a normal examination does not exclude infection.
In people with a penis: purulent urethral discharge, dysuria.
In people with a vagina: increased or altered vaginal discharge, dysuria, intermenstrual bleeding, or menorrhagia; cervicitis on examination.
Anorectal or pharyngeal infection can occur from the corresponding exposure site and is often asymptomatic as well.
Complications when untreated: epididymitis, pelvic inflammatory disease, ectopic pregnancy, infertility.

Risk Factors

Sexually active and under 30 years of age — the group in whom opportunistic annual screening is recommended.
New or multiple sexual partners.
A sexual partner with confirmed or suspected chlamydia or gonorrhea.
Inconsistent barrier protection.
Pregnancy — universal screening is recommended regardless of other risk factors.

Red Flags & Refer

Escalate or refer for any of the following:

Signs of pelvic inflammatory disease (pelvic pain, fever, cervical motion tenderness).
Suspected epididymo-orchitis with testicular pain — rule out testicular torsion urgently, a surgical emergency, not a chlamydia presentation.
Disseminated symptoms.
Prepubertal children with confirmed chlamydia — refer for assessment of possible sexual abuse.

Assessment & Diagnosis

Testing

NAAT is the test of choice. First-void urine or vaginal self-collected swab both perform well; clinician-collected cervical or vaginal swabs are also acceptable.
Test extragenital sites (pharynx, rectum) when exposure history indicates — do not limit testing to genital sites based on assumption alone.
If a rectal specimen is positive for chlamydia, test for lymphogranuloma venereum serovars — some laboratories trigger this automatically on a positive rectal result, others require a specific request.
Because co-infection with gonorrhea is common, test for both whenever either is suspected, and screen for syphilis and HIV at the same visit.

^[1]

Treatment Targets

Eradicate C. trachomatis in the patient.
Eradicate infection in all recent (under 60 days) sexual partners.
Prevent ascending complications: pelvic inflammatory disease, epididymitis, ectopic pregnancy, infertility.
Prevent vertical transmission when the patient is pregnant.

Choose Initial Treatment

Direct treatment rule

Use doxycycline 100 mg PO BID for 7 days as the preferred regimen for uncomplicated chlamydia — it has a cure rate similar to azithromycin and is specifically favoured over azithromycin for rectal infection, where it has a higher cure rate.^[2]

Use azithromycin 1 g PO as a single dose as the alternative when adherence to a 7-day course is a genuine concern, or when doxycycline cannot be used.

In pregnancy or breastfeeding, azithromycin is preferred (doxycycline is contraindicated); amoxicillin 500 mg PO TID for 7 days is a second alternative in pregnancy.^[1]

Gonorrhea co-treatment rule

If chlamydia has not been excluded by a negative test in a patient being treated for gonorrhea, treat for chlamydia at the same time.

Non-Pharmacologic Treatment

Abstain from sexual intercourse for 7 days after starting adequate treatment, and until all sexual partners have also been treated.
Refer all recent (under 60 days) sexual partners for testing and empiric treatment.
Use barrier protection consistently going forward to reduce reinfection risk — reinfection rates are high enough that repeat screening at 6 months is routinely recommended (see Monitoring).

Pharmacologic Treatment Options

Drug / intervention	Role	Dose / use	Important adverse effects	Teaching points
Doxycycline Preferred	First-line for genital, pharyngeal, and rectal infection	100 mg PO BID for 7 days	GI upset, rash, candidal vaginitis, photosensitivity	Favoured over azithromycin for rectal infection specifically — higher cure rate at this site. Contraindicated in pregnancy and breastfeeding.
Azithromycin Alternative	When adherence to a 7-day course is a concern, or doxycycline cannot be used	1 g PO as a single dose	GI upset; rare QT prolongation	Preferred specifically in pregnancy and breastfeeding. Repeat the dose if vomiting occurs within 1 hour.
Amoxicillin Special situation	Second-line option in pregnancy/breastfeeding	500 mg PO TID for 7 days	Rash, GI upset	Main advantage is safety in pregnancy and breastfeeding; not recommended as an alternative otherwise.

Erythromycin is an alternative regimen, but oral tablets/capsules are no longer commercially available in Canada — a compounded course can be used, but choose doxycycline or azithromycin when either can be used instead.^[1]

Special Populations

Pregnancy: screen every pregnant patient at the first prenatal visit. Untreated infection can cause preterm birth and premature rupture of membranes, and can cause neonatal conjunctivitis and pneumonia. Azithromycin 1 g PO single dose is the preferred antibiotic in pregnancy; amoxicillin 500 mg PO TID x 7 days can also be used. Doxycycline is contraindicated in pregnancy and breastfeeding. Abstain from intercourse for 7 days after treatment and until partners are treated. Arrange test-of-cure 3-4 weeks after completing therapy for the patient and for any ongoing sexual partner.^[1]

Children

In children 9-18 years, doxycycline is dosed at 5 mg/kg/day PO in divided doses (maximum 100 mg BID) for 7 days. Doxycycline is contraindicated in children 8 years and under. A confirmed diagnosis in a prepubertal child should prompt assessment for possible sexual abuse.

Monitoring & Follow-Up

Repeat screening is recommended for all treated patients 6 months after treatment, regardless of whether test-of-cure was performed — reinfection risk is high enough to warrant this routinely.^[3]
Perform test-of-cure 3-4 weeks after completing therapy specifically when: the preferred regimen (doxycycline or azithromycin) was not used, symptoms persist, reinfection is suspected, adherence is in question, or the patient is a prepubertal child or is pregnant.
Confirm partner treatment at follow-up — this is as important as confirming the patient's own treatment.

Treatment Failure / Next Step

Confirm the regimen was completed correctly and on schedule.
Confirm all recent partners were tested and treated, and ask specifically about re-exposure.
Perform test-of-cure with NAAT (allow the recommended 3-4 week interval after treatment to avoid a false positive from residual nucleic acid).
If reinfection is excluded and nonadherence is excluded, treat with an alternative regimen from a different class (e.g., switch from doxycycline to azithromycin, or vice versa) rather than repeating the same drug.
Reassess for pelvic inflammatory disease or epididymitis if pelvic or scrotal pain has developed since initial treatment.

Common Errors to Avoid

Assuming a normal examination or absence of symptoms rules out infection — most chlamydia is asymptomatic.
Using azithromycin for rectal infection when doxycycline is available and not contraindicated — doxycycline has a higher cure rate at this site.
Using doxycycline in a pregnant or breastfeeding patient.
Skipping the 6-month repeat screen because a test-of-cure was already done — these serve different purposes (cure versus reinfection).
Treating the patient without arranging testing and empiric treatment for recent sexual partners.

Clinical Decision Algorithm

Chlamydia: site-specific treatment and pregnancy branch

NAAT-confirmed chlamydia, or presumptive treatment indicated (gonorrhea diagnosed, chlamydia not excluded)

Pregnant or breastfeeding

Azithromycin 1 g PO single dose (preferred); amoxicillin 500 mg PO TID x 7 days (alternative)

Test of cure 3-4 weeks after completion, for the patient and any ongoing partner

Not pregnant/breastfeeding

Rectal infection confirmed or strongly suspected?

Rectal infection

Doxycycline 100 mg PO BID x 7 days — higher cure rate than azithromycin at this site

Genital/pharyngeal infection

Doxycycline 100 mg PO BID x 7 days (preferred)

Adherence to a 7-day course is a genuine concern: use azithromycin 1 g PO single dose instead

Refer all recent (under 60 days) sexual partners for testing and empiric treatment

Repeat screening at 6 months for every treated patient, regardless of test-of-cure result

Drug Tables

How to use this table: Doses are adult doses unless a pediatric dose is stated, and require patient-specific confirmation. Treat sexual partners. Select any drug name to open its complete Pharmasist Drug Database page.

Tetracyclines

Preferred regimen for most patients; contraindicated in pregnancy, breastfeeding, and children 8 years and under.

Drug	Dosage	Adverse effects	Comments
Doxycycline generics	Adults: 100 mg PO BID x 7 days. Children 9-18 years: 5 mg/kg/day PO in divided doses (maximum 100 mg BID) x 7 days.	GI upset, rash, candidal vaginitis, photosensitivity.	Favoured over azithromycin specifically for rectal infection — higher cure rate at this site. Contraindicated in pregnancy, breastfeeding, and children 8 years and under.

Macrolides

Alternative regimen; preferred specifically in pregnancy and breastfeeding, and useful when adherence to a multiday course is a concern.

Drug	Dosage	Adverse effects	Comments
Azithromycin Zithromax, generics	Adults: 1 g PO as a single dose. Children 1 month-18 years: 12-15 mg/kg (maximum 1 g) PO as a single dose.	GI upset; rare QT prolongation.	Preferred in pregnancy and breastfeeding. Useful when poor adherence to a 7-day course is expected. Repeat the dose if vomiting occurs within 1 hour of administration.
Erythromycin Eryc, generics	Adults: erythromycin base 500 mg PO QID x 7 days, or 250 mg PO QID x 14 days if tolerance is a concern. Children 1 month-18 years: 40 mg/kg/day PO in divided doses (maximum 500 mg QID x 7 days or 250 mg QID x 14 days).	GI upset; rare QT prolongation. High incidence of GI effects.	Oral tablets/capsules are no longer commercially available in Canada — a compounded course can be used, but choose a suitable alternative when possible. Do not use the estolate salt in pregnancy (cholestatic hepatitis risk). Use systemic therapy for conjunctivitis — topical treatment is not adequate. Monitor infants under 6 weeks for pyloric stenosis if exposed via breastfeeding.

Penicillins

Second-line option specifically for use in pregnancy and breastfeeding.

Drug	Dosage	Adverse effects	Comments
Amoxicillin generics	500 mg PO TID x 7 days.	Rash, GI upset.	Main advantage is safety in pregnancy and breastfeeding; not recommended as an alternative outside that context.

Evidence note: Drug inventory, dosing, adverse effects, and comments reflect standard Canadian practice per current PHAC guidance.^[1]

References

Sexually transmitted and blood-borne infections: Guides for health professionals — Public Health Agency of Canada. Canadian Guidelines on Sexually Transmitted Infections
Doxycycline versus azithromycin for the treatment of rectal chlamydia in men who have sex with men: a randomized controlled trial — Clinical Infectious Diseases (Dombrowski JC, Wierzbicki MR, Newman LM, et al.). Clin Infect Dis 2021
Recommendation on screening for chlamydia and gonorrhea in primary care for individuals not known to be at high risk — Canadian Medical Association Journal (Moore A, Traversy G, Reynolds D, et al.; Canadian Task Force on Preventive Health Care). CMAJ 2021;193(16):E549-E559

Professional reference only. Apply clinical judgment and verify patient-specific decisions against current authoritative guidance and product information.