Clinician reference — not medical advice. Default lens: PHAC Canadian STI guidelines. Verify doses against the current PHAC statement and product monographs before prescribing.

Evidence: PHAC / NAC-STBBI 2026 · sources last checked 2026-08-31

Clinician reference

Organized by decision. Jump to a section:

Routine screening standard

Who to screen, how often — and the 3-site question up front.

Test the sites that were exposed — 3-site testing

For anyone with receptive anal or oral sex, urogenital-only NAAT misses extragenital chlamydia and gonorrhea (often asymptomatic — a reservoir for reinfection and transmission).

GBMSM: 3-site NAAT (urogenital + rectal + pharyngeal) is the standard at every comprehensive screen.
Apply the same site-appropriate logic to anyone reporting anal/oral exposure, regardless of gender.
For gonorrhea, add culture where feasible (susceptibility), especially pharyngeal / suspected failure.

Full screening standard (who / how often / pregnancy / co-testing): routine screening standard →

Specimen & window-period reference

Generated from each infection's front matter — never hand-duplicated.

Organism	Specimen & site	Test	Window	Reportable
Chlamydia	first-void urine or self-collected vaginal swab (NAAT) urogenital rectal swab (NAAT) if exposed rectal throat swab (NAAT) if exposed pharyngeal	NAAT (nucleic acid amplification test)	~14 daysNAAT is reliable by about 2 weeks after exposure.	Yes
Gonorrhea	first-void urine or self-collected vaginal swab (NAAT) urogenital rectal swab (NAAT) — part of 3-site testing for GBMSM rectal throat swab (NAAT) — part of 3-site testing for GBMSM pharyngeal culture for antimicrobial susceptibility (esp. pharyngeal / suspected failure) any positive site	NAAT (plus culture for susceptibility)	~14 daysNAAT is reliable by about 2 weeks after exposure.	Yes
Hepatitis B	serology — HBsAg, anti-HBc, anti-HBs (surface antigen, core antibody, surface antibody) blood	serology (HBsAg / anti-HBc / anti-HBs)	~56 daysHBsAg is usually detectable within about 1–2 months (up to ~9 weeks) after exposure; interpret the three-marker panel together.	Yes
HIV	4th-generation Ag/Ab combination immunoassay (lab) blood rapid point-of-care or self-test (screening; confirm reactive results) blood	4th-generation antigen/antibody test	~18 days4th-gen Ag/Ab is usually reactive by ~2–3 weeks; confirm a negative result at 3 months (day 90).	Yes
HPV & genital warts	HPV-based cervical screening through the provincial cervical screening program (CTFPHC / provincial programs) — NOT a routine STI swab cervix clinical (visual) diagnosis; biopsy only if atypical or diagnosis uncertain visible wart	No routine STI swab — clinical diagnosis of warts; HPV testing is via cervical screening programs	~0 daysThere is no STI "window period" test for HPV. Screening for cervical HPV/cancer follows CTFPHC / provincial program schedules, not STI testing.	No
Genital herpes (HSV)	swab of an ulcer/vesicle for HSV PCR (NAAT) — type the virus (HSV-1 vs HSV-2) active lesion	PCR (NAAT) swab of an active lesion — test lesions when present	~0 daysThere is no "window period" to wait out — swab a lesion while it is present. Do NOT type-specific-serology-screen asymptomatic people.	No
Mycoplasma genitalium	first-void urine or vaginal/cervical swab (NAAT) — ideally with macrolide-resistance testing urogenital rectal swab (NAAT) where clinically indicated rectal	NAAT (with macrolide-resistance marker testing where available)	~14 daysTest for persistent/recurrent urethritis or cervicitis — NOT a screening test for asymptomatic people (screening drives resistance).	No
Syphilis	serology — treponemal + non-treponemal (RPR/VDRL) blood swab of any ulcer for PCR (or dark-field) if present lesion	serology (treponemal + non-treponemal) ± lesion PCR	~21 daysSerology can be reactive from ~2–6 weeks (up to 12); if early exposure, repeat at 12 weeks (day 84) before ruling out.	Yes
Trichomoniasis	self-collected or clinician-collected vaginal swab (NAAT) vagina first-void urine or urethral swab (NAAT) — for symptomatic men urethra/urine	NAAT (nucleic acid amplification test)	~7 daysNAAT is the most sensitive test; wait roughly a week after exposure for reliable detection.	No

Window = earliest reliable detection; confirm negatives per note (HIV at 3 months; syphilis repeat at 12 weeks after early exposure).

Empiric treatment by syndrome

Treat before results return, guided by presentation. Verify doses against the current PHAC statement.

Urethritis (male)

Work-up: NAAT for gonorrhea + chlamydia; add Mycoplasma genitalium and trichomonas NAAT if symptoms persist or recur.
Empiric Rx: Ceftriaxone 500 mg IM × 1 + doxycycline 100 mg PO BID × 7 days (covers GC + CT).

Cervicitis

Work-up: NAAT for chlamydia + gonorrhea; consider trichomonas and M. genitalium; assess for PID.
Empiric Rx: Doxycycline 100 mg PO BID × 7 days; ADD ceftriaxone 500 mg IM × 1 if gonorrhea risk / local prevalence is significant.

Pelvic inflammatory disease (PID)

Work-up: NAAT (GC/CT), pregnancy test, pelvic exam; imaging if abscess suspected. Treat empirically — do NOT delay for results.
Empiric Rx: Ceftriaxone 500 mg IM (single dose) + doxycycline 100 mg PO BID × 14 days + metronidazole 500 mg PO BID × 14 days.
Admit / escalate: Admit if: severe illness (high fever, vomiting), pregnancy, tubo-ovarian abscess, unable to tolerate or failed outpatient oral therapy, or surgical emergency cannot be excluded.

Epididymo-orchitis

Work-up: NAAT (GC/CT) + urinalysis/urine culture; assess age and sexual history to weigh STI vs enteric organisms.
Empiric Rx: Sexually active < 35 / STI risk: ceftriaxone 500 mg IM × 1 + doxycycline 100 mg PO BID × 10 days. Enteric-organism risk (older age, insertive anal sex): cover with a fluoroquinolone (e.g. levofloxacin) ± ceftriaxone if GC also possible.

Proctitis

Work-up: Rectal NAAT (GC/CT, with LGV typing if CT-positive), anoscopy; consider HSV PCR and syphilis serology.
Empiric Rx: Ceftriaxone 500 mg IM × 1 + doxycycline 100 mg PO BID × 7 days. If LGV suspected (proctocolitis in GBMSM) → extend doxycycline to × 21 days. Consider HSV coverage if ulceration present.

Genital ulcer

Work-up: Work up BOTH syphilis (serology + lesion PCR/darkfield) AND HSV (lesion PCR). Consider LGV/chancroid by exposure history.
Empiric Rx: Treat empirically toward the most likely cause while awaiting results: syphilis → benzathine penicillin G 2.4 MU IM (by stage); HSV → antiviral (e.g. valacyclovir).

Treatment by organism

First-line dose + route; pregnancy and allergy alternatives in each full reference.

Chlamydia

Doxycycline 100 mg PO BID × 7 d OR azithromycin 1 g PO ×1 (co-equal; doxy preferred for rectal).

Full clinician reference →

Gonorrhea

Interim

Ceftriaxone 500 mg IM ×1 (add doxycycline if chlamydia not excluded). Test-of-cure all sites.

Full clinician reference →

Mycoplasma genitalium

Resistance-guided: doxycycline 100 mg BID × 7 d → azithromycin (extended) if macrolide-sensitive, OR → moxifloxacin 400 mg daily × 7 d if resistant. Do NOT screen asymptomatic.

Full clinician reference →

Trichomoniasis

Metronidazole 500 mg PO BID × 7 d (women) OR 2 g PO ×1 (men/alt). Avoid alcohol. Treat partners; retest ~3 mo.

Full clinician reference →

Syphilis

Benzathine penicillin G 2.4 MU IM — ×1 (early) / ×3 weekly (late-latent); neurosyphilis → IV penicillin.

Full clinician reference →

HIV

Start ART promptly + link to care. U=U. PEP < 72 h; PrEP; doxy-PEP (conditional).

Full clinician reference →

Genital herpes (HSV)

Episodic valacyclovir 1 g PO BID × 3 d (or acyclovir); suppressive valacyclovir 500 mg–1 g daily. Pregnancy: suppressive from ~36 wk; C-section if active lesions.

Full clinician reference →

HPV & genital warts

Warts: imiquimod, sinecatechins, or cryotherapy (Canadian-marketed agents only). Prevent with Gardasil-9. Cervical screening = CTFPHC / provincial programs.

Full clinician reference →

Hepatitis B

Acute: supportive. Chronic: refer hepatology/ID → antivirals (tenofovir / entecavir). Vaccine-preventable; infant HBIG + vaccine to prevent vertical transmission.

Full clinician reference →

Hepatitis C treatment lives in its own AHC app: hepc.ajaxharwoodclinic.com ↗

Reporting & partner notification

Reportable organisms, the public-health unit, and partner management.

Organism	Reportable	Report to
Chlamydia	Reportable	Durham Region Health Department (local PHU)
Gonorrhea	Reportable	Durham Region Health Department (local PHU)
Hepatitis B	Reportable	Durham Region Health Department (local PHU)
HIV	Reportable	Durham Region Health Department (local PHU)
HPV & genital warts	Not reportable	—
Genital herpes (HSV)	Not reportable	—
Mycoplasma genitalium	Not reportable	—
Syphilis	Reportable	Durham Region Health Department (local PHU)
Trichomoniasis	Not reportable	—

CT / GC / syphilis / HIV (and hepatitis B) are reportable to the local public-health unit. HSV and HPV are not reportable; trichomoniasis reportability is province-dependent. Partner look-back is stage/organism-specific (commonly 60 days for CT/GC); public health can assist and may notify partners anonymously.

Partner-notification templates

Give the patient a ready-made, name-optional message to send partners (letter/email + SMS), and note that public health can notify partners anonymously. Open partner-notification templates →

Test-of-cure & retest intervals

When a test-of-cure is required, and when to retest.

Organism	Test-of-cure	Retest / follow-up
Chlamydia	Not routine; required in pregnancy / persistent symptoms / non-adherence.	Repeat at 3–6 months.
Gonorrhea	Required for ALL positive sites (culture ~3–7 d, or NAAT ~2–3 wk).	Repeat at 3–6 months.
Syphilis	Follow non-treponemal titre for ≥ 4-fold drop.	Serology at 6–12 months (stage-dependent).
HIV	N/A (not cured) — follow viral load / CD4 on ART.	Per ongoing risk — commonly every 3 months on PrEP.