Clinical Guidelines

Screening, treatment, testing, and reporting protocols for STIs in SUD care.

Screening Protocols

Comprehensive screening guidelines for STIs in patients with substance use disorder. Choose an infection for its protocol. Expand the guidance below for risk assessment and testing recommendations.

By infection

Screening intervalScreen adults at increased risk using CDC criteria and local epidemiology; for sexually active MSM, at least annually and every 3–6 months when risk persists. Screen all pregnant patients for syphilis at three time points — the first prenatal visit, the third trimester, and at birth, per ACOG/ARPQC.
Risk factorsInjection drug use, transactional sex, multiple partners, prior STI, incarceration history, and inconsistent prenatal care.
TestingTreponemal or non-treponemal serologic testing (RPR/VDRL with confirmatory TP-PA) (a blood test). Reverse-sequence algorithm acceptable for high-volume settings.
Substance use & syphilisIntoxication can mean less consistent protection and more partners, raising syphilis exposure. Stigma and unstable housing also delay testing and treatment, so screen at every opportunity and re-screen after treatment.
Screening intervalAnnually for sexually active women under 25 and older women at increased risk. For MSM, at least annually at sites of exposure and every 3–6 months when risk persists. Adapt to anatomy and sexual practices.
Specimen collectionNucleic acid amplification testing (NAAT) (a urine sample or swab) is preferred. Self-collected vaginal swabs and first-catch urine are validated and acceptable.
NotesCo-test for chlamydia. Perform test-of-cure for pharyngeal infection 7–14 days after treatment.
Substance use & gonorrheaIntoxication can lower consistent condom use and increase the number of partners, while stigma and unstable housing can impede access to care. Choose testing intervals and specimen sites from the patient’s exposures and the infection-specific guidance.
Screening intervalAnnual screening for sexually active women under 25 and older women at increased risk; for MSM, at least annually at indicated exposure sites and every 3–6 months when risk persists. Adapt to anatomy and sexual practices.
TestingNAAT on first-catch urine or self/clinician-collected swabs. Consider rectal testing by exposure. Routine throat screening for chlamydia is not recommended; combined GC/CT assays may detect it when testing for pharyngeal gonorrhea.
Follow-upRetest 3 months after treatment to detect reinfection. Evaluate and treat partners from the prior 60 days; include the most recent partner even if contact was earlier.
Substance use & chlamydiaLess consistent protection and more partners during intoxication raise chlamydia risk, and unstable housing can delay retesting — driving reinfection. Pair screening with a substance use screen and retest at 3 months.
Screening intervalRoutine opt-out screening at least once for ages 13–64 and at least annually for people with ongoing risk, including sharing injection equipment. More frequent testing may be appropriate based on exposure or a PrEP protocol.
Testing4th-generation Ag/Ab combination immunoassay (a blood test) preferred. Rapid point-of-care tests acceptable with confirmatory follow-up.
PreventionOffer PrEP to all eligible patients. Link confirmed positives to care within 72 hours.
Substance use & HIVSharing injection equipment transmits HIV directly through the blood, and intoxication can reduce consistent protection. Offer at least annual testing when risk continues, assess recent exposures, and discuss PrEP.
Screening intervalOne-time screening for all adults; at least annual screening for people who inject drugs and patients with ongoing risk.
TestingHCV antibody test (a blood test) with reflex to HCV RNA for confirmation of active infection.
Treatment accessRefer RNA-positive patients for direct-acting antiviral (DAA) therapy. Active substance use is not a contraindication to treatment.
Substance use & hepatitis CHepatitis C spreads readily through shared needles and injection equipment, so people who inject drugs are at the highest risk. Active substance use is not a barrier to cure — screen at least annually and refer for DAA therapy.
When to testSwab active lesions for HSV NAAT/PCR or culture. Routine serologic screening of asymptomatic people is not recommended. Type-specific HSV-2 serology may help with recurrent or atypical symptoms and negative lesion tests, an unconfirmed clinical diagnosis, or a partner with genital herpes.
TestingPCR or viral culture (a swab test) from an active lesion. Discuss the indications and false-positive risk of type-specific HSV-2 serology; confirm low-positive results with an appropriate second method when available.
Substance use & herpesIntoxication can mean more partners and less consistent protection, while stigma can delay assessment of symptoms. Test lesions promptly and counsel on suppression.
ScreeningRoutine cervical cancer screening (Pap and/or HPV co-testing) per age-based guidelines. There is no routine HPV test for people without a cervix.
PreventionHPV vaccination is recommended through age 26 and may be offered through age 45 based on shared clinical decision-making.
Substance use & HPVMore partners during intoxication raise HPV exposure, and unstable housing or stigma can delay cervical screening and vaccination. Offer HPV vaccination and keep patients on schedule for cervical screening.
ScreeningScreen all adults at least once with the three-test panel (HBsAg, anti-HBs, total anti-HBc). Screen pregnant patients with HBsAg at each pregnancy.
PreventionUniversal hepatitis B vaccination is recommended for all adults aged 19–59, and for those 60+ with risk factors — including people who inject drugs.
Substance use & hepatitis BHepatitis B spreads through both shared injection equipment and sex, so people who inject drugs face compounded risk. Vaccinate all unvaccinated SUD patients — it is the most effective protection.
ScreeningNAAT on vaginal swab or urine. Screen symptomatic patients and consider routine screening for women receiving care in high-prevalence settings (including SUD programs).
Follow-upRetest sexually active women approximately 3 months after treatment. Evidence is insufficient to recommend routine retesting in men.
Substance use & trichomoniasisLess consistent protection and more partners during intoxication raise trichomoniasis risk, and unstable housing can delay retesting and compound already-high reinfection rates. Retest sexually active women approximately 3 months after treatment.

Who to screen & the Five Ps

If a patient has had sex, has a new partner, has multiple partners, shares injection equipment, is pregnant, has symptoms, or thinks they've been exposed to an STI, talk with them about testing. Screening always begins with a sexual history — many STIs and HIV can be asymptomatic in people of any gender. Offer a sexual health assessment without assumptions; choose tests and intervals using infection-specific recommendations, age, anatomy, exposures, pregnancy, and local epidemiology.

To further guide your dialogue with your patient, the 5 "Ps" may be a useful way to remember the major aspects of a sexual history:

1Partners
2Practices
3Protection from STIs
4Past history of STIs
5Pregnancy intention

These are the areas to openly discuss with your patients. You'll likely need additional questions appropriate to each patient's situation — but the goal of the 5 Ps is to improve patient health, not simply to solicit full disclosure of sexual practices, especially if patients are not comfortable.

Several indicated STI tests can be collected at the same visit; there is no universal panel for every infection. Symptoms require diagnostic assessment. Bacterial vaginosis (BV) is a vaginal bacterial imbalance associated with sexual activity. Routine HSV serologic screening is not recommended, but type-specific HSV-2 testing has selected indications even without lesions.

Substance use & STI risk: the connection

Substance use raises STI risk through several pathways, not only injection. Understanding them helps target screening and counseling for patients with substance use disorder (SUD).

BehavioralIntoxication and disinhibition can mean less consistent protection, more partners, and transactional sex.
BiologicalShared injection equipment transmits bloodborne HIV & hep C. Stimulant use and dehydration can dry mucosal tissue, and small tears make STI transmission more likely.
StructuralStigma, unstable housing, and incarceration delay testing and treatment and raise reinfection risk.

Clinical takeaway: screen patients with SUD more frequently, pair STI screening with a substance use screen, and treat both without judgment. Use the SBIRT framework below to structure that conversation.

SBIRT: screening & brief intervention for substance use

SBIRT (Screening, Brief Intervention, and Referral to Treatment) is an evidence-based approach for identifying and addressing substance use in any care setting: primary care, emergency departments, and SUD or STI programs. It pairs naturally with the sexual-history screening above.

ScreeningA brief assessment to detect substance use risk and identify who may benefit from intervention or treatment.
Brief InterventionA short, motivational conversation to raise awareness of substance use and encourage change.
Referral to TreatmentConnect higher-risk patients to substance use treatment (e.g., FindTreatment.gov or the SAMHSA Helpline).

Treatment Protocols

First-line treatment regimens for common STIs in SUD populations, consistent with current CDC STI Treatment Guidelines. Always confirm allergies and drug interactions before prescribing.

By infection

Early syphilisBenzathine penicillin G 2.4 million units IM single dose. (Children: 50,000 units/kg IM, up to the 2.4 million-unit adult dose.)
Late / unknownBenzathine penicillin G 2.4 million units IM weekly for 3 weeks.
In pregnancyPenicillin is the only recommended therapy; patients with allergy require desensitization and treatment with penicillin.
First-lineCeftriaxone 500 mg IM single dose (1 g if ≥150 kg). If chlamydia not excluded, add doxycycline 100 mg PO twice daily for 7 days.
Cephalosporin allergyGentamicin 240 mg IM single dose PLUS azithromycin 2 g PO single dose.
If ceftriaxone unavailableCefixime 800 mg PO single dose (plus chlamydia treatment if not excluded).
Partner therapyEvaluate and treat partners from the prior 60 days, including the most recent partner if earlier; expedited partner therapy is permitted in Arkansas for gonorrhea and chlamydia.
PreferredDoxycycline 100 mg PO twice daily for 7 days.
AlternativeAzithromycin 1 g PO single dose (preferred in pregnancy), or levofloxacin 500 mg PO once daily for 7 days.
TreatmentInitiate antiretroviral therapy (ART) in all cases, regardless of co-occurring infections. Refer immediately to Ryan White services (through ARCare) for holistic support.
Prevention (TasP)Counsel on “Treatment as Prevention” (U=U). If the patient has sexual partners who do not have HIV, counsel those partners on PrEP.
PrEP optionsDaily oral options include F/TAF (Descovy), which is not indicated for people at risk through receptive vaginal sex, and F/TDF (Truvada). Eligibility depends on exposure route, age/weight, renal function, and other clinical factors. Descovy prescribing information. Long-acting injectable: Apretude (every 2 months) or Yeztugo (twice yearly). Find a prescriber near the patient at preplocator.org.
Cost / accessPatient-assistance programs are available through Gilead and ViiV Healthcare, including for people without insurance.
Current guidanceHCV regimens change frequently — lead with the live source: hcvguidelines.org (AASLD/IDSA)
TreatmentDirect-acting antivirals (DAAs) — protease inhibitors, nucleoside analog polymerase inhibitors, and NS5A inhibitors. Treatment-naive means no prior HCV treatment; treatment-experienced refers to prior treatment history, not simply reinfection. Distinguish relapse from reinfection and select the appropriate initial-treatment or retreatment guidance.
PregnancyTest for HCV with each pregnancy, ideally at the first visit. Defer DAA treatment until after delivery. Include hepatitis C counseling in family planning regardless of the patient's own injection history.
WomenMetronidazole 500 mg PO twice daily for 7 days.
MenMetronidazole 2 g PO single dose.
AlternativeTinidazole 2 g PO single dose.

Where can I get the medicine? (patient assistance & access)

Cost should not be a barrier to treatment. Many STI/HIV/HCV medications are available at low or no cost through manufacturer patient-assistance programs (PAPs), 340B pricing at qualifying clinics, and state programs — often including people who are uninsured.

Full treatment guidelines

The regimens below summarize first-line therapy. Always confirm current dosing, alternatives, and pediatric/pregnancy considerations against the source guidelines.

Quick treatment summary — all STIs

A plain-language overview, including infections managed rather than cured. Always confirm against CDC guidance before prescribing.

Curablea full course of medicine clears the infection
ChlamydiaTreated with antibiotics — usually cured with medicine.
GonorrheaTreated with antibiotics — usually cured with medicine.
SyphilisTreated with antibiotics — early treatment can cure the infection.
TrichomoniasisTreated with antibiotics — usually cured with medicine.
Hepatitis CTreated with medication (DAAs) — most people can be cured.
Managed, not curedtreatment controls the infection long-term
HIVTreated with daily medication (ART) — helps people live long, healthy lives.
Herpes (HSV)Treated with antiviral medication — reduces outbreaks and symptoms (not curable).
HPVNo cure for the virus; treatments are available for warts and related health problems. Vaccination prevents most high-risk types.
Hepatitis BSome people recover without treatment; others need medication to manage the infection. Vaccine-preventable.

Testing & Diagnostics

When to test, which tests to use, and how to collect and handle specimens — plus Arkansas testing and referral resources.

Recommended Tests

TEST NAME

Nucleic Acid Amplification Test (NAAT)

SAMPLE TYPE

  • Male: First-catch urine (15-30 mL)
  • Female: Vaginal swab (self or provider collected) or endocervical swab
  • Extragenital: Rectal or pharyngeal swab

TURNAROUND TIME

2-5 business days

NOTES

NAAT is the gold standard. Self-collected vaginal swabs have equivalent sensitivity to provider-collected specimens and may improve patient comfort and screening uptake.

CDC referenceCDC — Chlamydia

TEST NAME

Nucleic Acid Amplification Test (NAAT)

SAMPLE TYPE

  • Male: First-catch urine or urethral swab
  • Female: Vaginal or endocervical swab
  • Extragenital: Rectal or pharyngeal swab (especially for MSM)

TURNAROUND TIME

2-5 business days

NOTES

Culture with antimicrobial susceptibility testing recommended for treatment failures or suspected resistance. Extragenital testing important for MSM and individuals reporting receptive anal/oral sex.

CDC referenceCDC — Gonorrhea (adults)

TEST NAME

Screening: Treponemal (TP-PA, FTA-ABS) or Nontreponemal (RPR, VDRL)
Confirmatory: Opposite test type + quantitative titer

SAMPLE TYPE

  • Serology: Venous blood (serum or plasma)
  • Lesion: Darkfield microscopy or PCR from ulcer exudate (if available)

TURNAROUND TIME

2-5 business days

NOTES

Pregnancy Priority
All pregnant individuals require syphilis screening at three time points — the first prenatal visit, the third trimester, and at birth (universal, not risk-based). Quantitative titers essential for monitoring treatment response.

CDC referenceCDC — Primary & Secondary Syphilis

ArkansasARPQC — Congenital Syphilis Prevention · ADH — Syphilis in Pregnancy & Congenital Syphilis

TEST NAME

4th Generation Antigen/Antibody Combination Immunoassay
Confirmatory: HIV-1/HIV-2 Differentiation Immunoassay + HIV-1 RNA if needed

SAMPLE TYPE

  • Laboratory: Venous blood (serum or plasma)
  • Rapid test: Fingerstick blood or oral fluid

TURNAROUND TIME

Laboratory: 2-5 business days
Rapid test: 10-20 minutes

NOTES

4th generation tests detect HIV 18-45 days post-exposure. Reactive rapid tests require laboratory confirmation. Consider RNA testing for acute HIV if high suspicion and negative antibody test.

ReferenceHHS — Adult & Adolescent ARV Guidelines

TEST NAME

Screening: HCV Antibody (anti-HCV)
Confirmatory: HCV RNA (quantitative viral load)
Additional: Genotype, liver function tests, fibrosis assessment

SAMPLE TYPE

  • Serology: Venous blood (serum or plasma)
  • RNA: Venous blood (plasma or serum)

TURNAROUND TIME

Antibody: 2-5 business days
RNA: 3-7 business days

NOTES

Positive antibody requires RNA confirmation to distinguish active infection from past resolved infection. Reflex RNA testing (automatic RNA if antibody positive) streamlines diagnosis. Universal screening recommended in SUD settings.

ReferenceAASLD/IDSA — hcvguidelines.org

TEST NAME

Symptomatic: Viral culture or PCR from lesion
Asymptomatic: Type-specific HSV-1/HSV-2 serology (if clinically indicated)

SAMPLE TYPE

  • Lesion: Swab from vesicle fluid or ulcer base
  • Serology: Venous blood

TURNAROUND TIME

PCR: 2-5 business days
Culture: 3-7 business days
Serology: 2-5 business days

NOTES

CDC does not recommend routine serologic screening for asymptomatic individuals. PCR preferred over culture for lesion diagnosis (higher sensitivity). Test within 48 hours of lesion onset for best yield.

CDC referenceCDC — Genital Herpes (HSV)

How STI Testing Works

STIs are tested by urine sample, blood sample, swab, or saliva, depending on the infection and test type. Available tests vary by clinic. HIV, hepatitis C, and syphilis may have rapid options; gonorrhea, chlamydia, and trichomoniasis use assay-appropriate urine or swab specimens.

TURNAROUND

  • Rapid tests: results may be available during the visit; timing depends on the assay
  • Laboratory tests: often several days; some point-of-care GC/CT tests return results during the visit

CONFIRMATORY TESTING

  • Reactive HIV/hepatitis C rapid tests need a confirmatory blood draw
  • Syphilis: titer (RPR) (a blood test) — look for a fourfold decline over 6–24 months; in a previously cured, asymptomatic patient a titer that plateaus at a low level (≤1:8) is medically acceptable (serofast)
  • Previously treated syphilis/hepatitis C may stay antibody-reactive — use RNA (hepatitis C) or titer (syphilis)

Nuances & Common Pitfalls

False positives

  • Suspect a false positive when the result doesn't match the clinical picture or sexual history (more common with autoimmune conditions).
  • Confirmatory testing, a thorough sexual history, and counseling are advised before acting on an unexpected result.
  • Counsel every patient on prevention regardless of whether the result is a true or false positive.

Rural & resource-limited settings

  • Where diagnostic testing isn't readily available, consider the syndromic approach — classifying and treating based on symptoms and signs rather than lab confirmation.
  • Reference: PAHO — Syndromic Management of STIs

Common clinician errors to avoid

  • Inadequate sexual-history taking, personal bias, misinterpreting the window period, and overlooking concurrent screenings.
  • Use the CDC’s Five Ps framework on every sexually active patient. CDC — Taking a Sexual History

When to Test

AT PROGRAM INTAKE

  • All individuals entering SUD treatment program
  • Review prior testing; offer indicated STI, HIV, and hepatitis C screening
  • Document sexual health history and risk factors
  • Discuss pregnancy possibility and offer a pregnancy test when indicated

PERIODIC RESCREENING

  • Use infection-specific intervals and reassess after a new exposure
  • At least annual HIV testing with ongoing risk; at least annual HCV testing with ongoing injection drug use
  • 3 months post-treatment for bacterial STIs (chlamydia, gonorrhea)
  • Pregnancy: infection-specific schedule; syphilis at first visit, third trimester, and birth per ACOG/ARPQC

Arkansas testing & referral resources

High-Risk Population Indicators

Injection Drug Use

Current or recent history of injection drug use increases risk for HIV, Hepatitis C, and bacterial STIs.

Use infection-specific intervals

Multiple Partners

More than one sexual partner in past 3-6 months, or partner with multiple concurrent partners.

Use infection-specific intervals

Pregnancy

All pregnant individuals require comprehensive STI screening to prevent congenital infections.

Follow pregnancy guidance by infection

Inconsistent Condom Use

Condomless sex with partners of unknown STI status or known risk factors.

Use infection-specific intervals

MSM

Men who have sex with men have elevated risk for HIV, syphilis, and extragenital gonorrhea/chlamydia.

Assess current exposure and testing history

Prior STI Diagnosis (lifetime)

A prior STI prompts a review of recommended post-treatment retesting and current exposures. A lifetime history alone does not establish a three-month schedule.

Assess current exposure and testing history

Lab & Specimen Guidance

Specimen Collection Best Practices

URINE COLLECTION

  • First-catch urine: Collect first 15-30 mL of voided urine stream (not midstream)
  • Timing: Patient should not have urinated for at least 1-2 hours prior to collection
  • Container: Use sterile urine collection cup provided by laboratory
  • Storage: Refrigerate if not processed within 2 hours; stable for 24 hours refrigerated

VAGINAL SWAB COLLECTION

  • Self-collection: Patient inserts swab 2 inches into vagina, rotates 10-30 seconds, removes without touching skin
  • Provider-collection: Visualize cervix with speculum, swab vaginal walls or endocervix
  • Swab type: Use manufacturer-provided swab (typically Dacron or rayon, not cotton)
  • Note: Self-collected vaginal swabs have equivalent sensitivity to provider-collected for NAAT testing

EXTRAGENITAL SWAB COLLECTION (RECTAL, PHARYNGEAL)

  • Rectal: Insert swab 2-3 cm into anal canal, rotate gently for 10-30 seconds to sample crypts
  • Pharyngeal: Swab posterior pharynx and tonsillar crypts bilaterally, avoid tongue and buccal mucosa
  • Important: Verify laboratory accepts extragenital specimens for NAAT testing before collection

BLOOD COLLECTION (SEROLOGY)

  • Volume: Typically 5-10 mL venous blood in serum separator tube (SST) or plasma tube
  • Processing: Allow to clot (SST) or centrifuge (plasma), separate serum/plasma within 2 hours
  • Storage: Refrigerate if not processed immediately, stable 7 days refrigerated

LESION SWAB COLLECTION (HSV, SYPHILIS)

  • HSV: Unroof vesicle if present, swab base of lesion or ulcer vigorously to collect cellular material
  • Timing: Collect within 48 hours of lesion onset for best yield (viral load highest early)
  • Transport: Place swab in viral transport medium immediately, keep refrigerated or on ice

Specimen Handling & Transport

Labeling Requirements

  • Patient name and date of birth
  • Unique patient identifier or medical record number
  • Date and time of collection
  • Specimen source (e.g., urine, vaginal swab, rectal swab)
  • Collector initials

Storage & Temperature

  • NAAT specimens: Follow the specific assay’s collection kit, temperature, and transport-time requirements
  • Viral culture: Use the laboratory’s required transport medium and handling instructions
  • Serology: Follow the laboratory’s separation, storage, and transport instructions
  • Freezing: Requirements vary by assay and specimen; some NAAT specimens may be frozen. Check the manufacturer’s instructions and receiving laboratory before storage

Packaging

  • Place specimens in leak-proof primary container
  • Use absorbent material between primary container and outer packaging
  • Include laboratory requisition form in separate compartment
  • Mark outer package as "Diagnostic Specimen" if required

Transport Timing

  • Same-day preferred: Transport specimens to laboratory same day of collection
  • Weekend collection: Confirm an acceptable collection, storage, and pickup plan with the laboratory first
  • Viral culture: Follow the laboratory’s transport-time and temperature requirements
  • Coordinate with laboratory for pickup schedule and requirements

Prevention, Partner Services & Data

Vaccination guidance, partner notification, and Arkansas surveillance data to support prevention in SUD treatment settings.

Vaccination Recommendations

VaccineWho & when
HPVRoutine through age 26; may offer to age 45 via shared decision-making. Prevents most cervical and other HPV-related cancers.
Hepatitis BUniversal for adults 19–59; 60+ with risk factors. Strongly recommended for people who inject drugs.
Hepatitis ARecommended for people who inject drugs and others at risk.
MpoxOffer to eligible at-risk patients per current ADH guidance.

Partner Services & Notification

Partner management depends on the infection: chlamydia/gonorrhea generally use a 60-day window, including the most recent partner if earlier. Syphilis uses stage-specific windows: primary, 3 months plus symptom duration; secondary, 6 months plus symptom duration; early latent, 1 year. Follow CDC syphilis guidance for evaluation and presumptive treatment. Expedited Partner Therapy (EPT) is permitted in Arkansas for gonorrhea and chlamydia. The state health department offers confidential partner notification — partners can be notified without revealing the index patient’s identity.

Arkansas STI Data & Surveillance

Arkansas has consistently reported STI rates above the national average, and congenital syphilis has risen sharply in recent years — mirroring a national increase reported by the CDC. Confirm current figures against the ADH and CDC data linked below, and use state surveillance data to target prevention efforts.

Reporting Requirements

STIs are reportable conditions in Arkansas. Submit case reports to the Arkansas Department of Health within the required timeframe to support partner services and surveillance.

Reportable in ArkansasSyphilis, congenital syphilis, gonorrhea, chlamydia, HIV, chancroid, lymphogranuloma venereum, granuloma inguinale, and ophthalmia neonatorum (per Arkansas Code 20 CAR § 102-122). Report within 24 hours of diagnosis. Hepatitis (A, B, C and E) is also reportable within 24 hours under ADH’s reportable-diseases list.
How to reportFax the ADH Communicable Disease Reporting Form to 501-661-2428. Report immediately by phone at 501-280-4115 (M–F) or 1-800-554-5738 (holidays & weekends). HIV also requires the confidential HIV case report form in addition to the communicable disease form.
ComplianceReporting is mandatory public health policy. Failure to report diagnosed reportable STIs may result in professional license discipline, civil liability, and misdemeanor charges. There is no incentive for reporting — it is public health policy.
Reporting setupUse ADH’s reporting forms and instructions. Contact the program about your facility’s Electronic Laboratory Reporting (ELR) setup and Disease Intervention Specialist (DIS) coordination; start with ADH Public Health Reporting.