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Infectious Diseases

Sexually Transmitted Infections

Use exposure-site testing, syndrome-directed empiric treatment when indicated, pregnancy-specific screening, partner management, and targeted prevention to interrupt transmission while preventing pelvic inflammatory disease, adverse pregnancy outcomes, and neonatal infection.

Clinical question: How should clinicians test, triage, treat, and prevent common sexually transmitted infections across exposure sites and risk groups?

First encounter

Triage urgent syndromes and test the exposed sites

Use symptoms and anatomy to select immediate testing and empiric coverage.

Prioritize same-day evaluation for pelvic or lower-abdominal pain with concern for pelvic inflammatory disease, pregnancy with suspected or confirmed STI, acute proctitis, genital ulceration, ocular symptoms after sexual exposure, sexual assault, and possible disseminated infection. Untreated STIs in women are associated with pelvic inflammatory disease, infertility, chronic pelvic pain, ectopic pregnancy, pregnancy loss, stillbirth, and neonatal transmission. PubMedClinical Updates in Sexually Transmitted Infections, 2024PubMedSexually Transmitted Infections - StatPearls - NCBI Bookshelf

Take a site-specific sexual exposure history rather than inferring exposure from identity: urethral/penile, vaginal/cervical, rectal, pharyngeal, ocular, and skin-to-skin exposure. Obtain NAAT specimens from each exposed mucosal site for gonorrhea and chlamydia when testing is indicated; NAATs are the diagnostic standard and have reported sensitivity and specificity of 95% to 99%. Extragenital infection is frequently asymptomatic, so urine-only testing can miss rectal or pharyngeal infection. WileyDiagnosing sexually transmitted infections in resourceScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirect

For symptomatic patients, add HIV testing and testing for other prevalent STIs at the same encounter. In patients with urethritis, cervicitis, proctitis, pharyngitis, vaginitis, or genital lesions, interpret a positive organism-specific test in an anatomic and syndromic context because concurrent infection with more than one pathogen is common. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectPubMedSexually Transmitted Infections - StatPearls - NCBI Bookshelf

Exposure-directed diagnostic framework for common sexually transmitted syndromes. WileyDiagnosing sexually transmitted infections in resourceScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectPubMedClinical Updates in Sexually Transmitted Infections, 2024
Clinical patternImmediate testsInterpretation and next action
Urethral discharge or dysuriaUrethral or urine gonorrhea/chlamydia NAAT; HIV and other prevalent STI testing. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectPubMedSexually Transmitted Infections - StatPearls - NCBI BookshelfManage as urethritis while test results identify gonorrhea, chlamydia, or another cause. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirect
Cervical inflammation, postcoital bleeding, or mucopurulent dischargeVaginal/cervical gonorrhea/chlamydia NAAT; assess for trichomoniasis and other causes based on syndrome. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectPubMedClinical Updates in Sexually Transmitted Infections, 2024Do not rely on discharge alone to exclude infection; chlamydial and gonococcal infections are commonly asymptomatic. WHOSexually Transmitted Infections - IRIS
Rectal pain, discharge, or tenesmusRectal gonorrhea/chlamydia NAAT; assess for syphilis, herpes simplex virus, and lymphogranuloma venereum. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectUse results and severity to direct therapy; evaluate promptly when severe symptoms or systemic illness are present. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirect
Pharyngeal exposure or symptomsPharyngeal gonorrhea/chlamydia NAAT when indicated by exposure. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectA negative urine test does not exclude pharyngeal infection. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirect
Genital ulcerSyphilis and herpes simplex virus evaluation; HIV testing. PubMedClinical Updates in Sexually Transmitted Infections, 2024PubMedSexually Transmitted Infections - StatPearls - NCBI BookshelfTreat based on confirmed or strongly suspected cause and arrange follow-up for serologic and lesion-response assessment. PubMedClinical Updates in Sexually Transmitted Infections, 2024

Cause-directed care

Match treatment to the organism and syndrome

Avoid a single empiric regimen for all mucosal complaints.

Gonorrhea, chlamydia, syphilis, trichomoniasis, Mycoplasma genitalium, herpes simplex virus, lymphogranuloma venereum, and noninfectious conditions can produce overlapping urethral, cervical, rectal, pharyngeal, and genital symptoms. When quality-assured molecular testing is available, use laboratory-supported diagnosis to select current evidence-based treatment rather than relying on syndromic management alone. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectWHOSexually transmitted infections (STIs)

Use the current CDC STI treatment guideline or its current updates to select organism-specific regimen, dose, route, and follow-up because resistance patterns and recommendations change. This is particularly important for gonorrhea, where antimicrobial susceptibility is a continuing clinical and public-health concern, and for persistent Mycoplasma genitalium infection. JAMADiagnosis and Treatment of Sexually Transmitted InfectionsJAMASexually Transmitted InfectionsPubMedClinical Updates in Sexually Transmitted Infections, 2024PubMedSexually Transmitted Infections Treatment Guidelines, 2021

For patients with genital herpes, routine serologic screening is not recommended, including during pregnancy. Evaluate clinically apparent lesions and use the CDC STI treatment guidance for antiviral treatment and counseling. PubMedClinical Updates in Sexually Transmitted Infections, 2024

Persistent or recurrent symptoms after treatment should trigger reassessment of adherence, re-exposure from an untreated partner, infection at an untested anatomic site, coinfection, and an alternative infectious or noninfectious diagnosis. Do not assume microbiologic failure solely from ongoing symptoms. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectPubMedClinical Updates in Sexually Transmitted Infections, 2024

Clinical branches that should change diagnostic and management actions. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectPubMedClinical Updates in Sexually Transmitted Infections, 2024PubMedSexual Assault Infectious Disease Prophylaxis - StatPearls - NCBI Bookshelf
BranchWhat changes the planAction
Symptomatic mucosal syndromeSite-specific inflammation or discharge with relevant exposure. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectCollect site-specific NAATs and treat empirically only when syndrome severity or follow-up limitations justify it. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectPubMedSexual Assault Infectious Disease Prophylaxis - StatPearls - NCBI Bookshelf
Genital ulcer syndromeUlcerative lesion rather than isolated discharge syndrome. PubMedClinical Updates in Sexually Transmitted Infections, 2024Test for syphilis and herpes simplex virus and include HIV testing. PubMedClinical Updates in Sexually Transmitted Infections, 2024PubMedSexually Transmitted Infections - StatPearls - NCBI Bookshelf
Persistent symptomsSymptoms after treatment or after renewed sexual exposure. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectPubMedClinical Updates in Sexually Transmitted Infections, 2024Check reinfection, untreated partners, untested sites, coinfection, adherence, and alternative diagnoses before changing therapy. ScienceDirectSexually transmitted causes of urethritis, proctitis, pharyngitis, vaginitis and cervicitis - ScienceDirectPubMedClinical Updates in Sexually Transmitted Infections, 2024
Sexual assaultHigh probability of missed follow-up. PubMedSexual Assault Infectious Disease Prophylaxis - StatPearls - NCBI BookshelfProvide indicated presumptive antimicrobial prophylaxis, emergency contraception, immunization assessment, and HIV evaluation at the initial encounter. PubMedSexual Assault Infectious Disease Prophylaxis - StatPearls - NCBI Bookshelf

Sexual assault

After sexual assault, use a trauma-informed examination and minimize retraumatization while obtaining indicated baseline testing. Because follow-up adherence is often low, CDC-based guidance recommends presumptive antimicrobial treatment for chlamydia, gonorrhea, and trichomoniasis, plus emergency contraception, hepatitis B and HPV vaccination assessment, and HIV exposure evaluation. PubMedSexual Assault Infectious Disease Prophylaxis - StatPearls - NCBI Bookshelf

Asymptomatic infection

Screen by pregnancy status, age, risk, and exposure anatomy

Screening finds infection that symptom-based care routinely misses.

Routine laboratory screening is indicated for sexually active adolescents, and screening strategies should account for age, pregnancy, sexual practices, community prevalence, and disease-specific sequelae. An opt-out approach can reduce dependence on sexual-history disclosure and may improve case detection among adolescents and young adults. PubMedSexually Transmitted Infections Treatment Guidelines, 2021PubMedUpdates on Testing, Treatment, and Prevention of Sexually Transmitted Infections in the United States, 2025

During pregnancy, screen at the first prenatal visit according to CDC recommendations. For gonorrhea, screen pregnant patients at risk, including those younger than 25 years and those 25 years or older with a new sex partner, multiple partners, a partner with concurrent partners, a partner with an STI, or residence in a community with high gonorrhea rates. Treat identified infection during pregnancy and retest in 3 months, in the third trimester, or at delivery as indicated. PubMedSexually Transmitted Infections Treatment Guidelines, 2021

Do not use routine serologic screening for genital herpes in pregnancy. CDC-based pregnancy screening guidance does not recommend routine testing for bacterial vaginosis, herpes, HPV, or trichomoniasis in pregnancy. PubMedClinical Updates in Sexually Transmitted Infections, 2024PubMedSexually Transmitted Infections - StatPearls - NCBI Bookshelf

For persons with ongoing exposure risk, align repeat STI screening with the risk pattern and anatomic exposure sites. In people using doxycycline postexposure prophylaxis, perform syphilis and gonorrhea/chlamydia screening at all sites of exposure every 3 to 6 months. Oxford AcademicUtilization of Doxycycline Postexposure Prophylaxis at a Midwestern United States HIV/PrEP Clinic | Open Forum Infectious Diseases | Oxford Academic

Pregnancy-focused STI screening and follow-up decisions. PubMedClinical Updates in Sexually Transmitted Infections, 2024PubMedSexually Transmitted Infections - StatPearls - NCBI BookshelfPubMedSexually Transmitted Infections Treatment Guidelines, 2021
SituationActionFollow-up
Pregnant patient younger than 25 yearsScreen for gonorrhea at the first prenatal visit. PubMedSexually Transmitted Infections Treatment Guidelines, 2021Treat infection during pregnancy; retest in 3 months, in the third trimester, or at delivery as indicated. PubMedSexually Transmitted Infections Treatment Guidelines, 2021
Pregnant patient 25 years or older with gonorrhea risk factorsScreen for gonorrhea at the first prenatal visit. PubMedSexually Transmitted Infections Treatment Guidelines, 2021Treat infection and test/treat sex partners; repeat testing as indicated. PubMedSexually Transmitted Infections Treatment Guidelines, 2021
Pregnant patient without symptoms requesting herpes screeningDo not perform routine genital herpes serologic screening. PubMedClinical Updates in Sexually Transmitted Infections, 2024Evaluate and manage clinically suspected herpes according to current STI guidance. PubMedClinical Updates in Sexually Transmitted Infections, 2024
Pregnant patient without symptoms requesting routine BV, HPV, or trichomonas testingRoutine testing is not recommended. PubMedSexually Transmitted Infections - StatPearls - NCBI BookshelfTest when symptoms or another clinical indication is present. PubMedSexually Transmitted Infections - StatPearls - NCBI Bookshelf

Transmission prevention

Build prevention around barriers, vaccination, HIV prevention, and partner treatment

Pair each STI diagnosis with a prevention and reinfection plan.

Recommend condoms for vaginal, oral, and anal sex; consistent correct use provides effective protection against STIs, including HIV, but does not fully protect against infections transmitted from uncovered ulcerated skin, including syphilis and genital herpes. WHOSexually transmitted infections (STIs)

Review hepatitis B and HPV immunization status. Safe and effective vaccines are available for hepatitis B and HPV, and vaccination should be incorporated into STI prevention visits rather than reserved for primary care follow-up. WHOSexually transmitted infections (STIs)

Use each bacterial STI diagnosis as a prompt to assess HIV testing needs and HIV prevention, including preexposure prophylaxis when risk warrants. All patients presenting with STI symptoms should be screened for HIV and other prevalent STIs. PubMedSexually Transmitted Infections - StatPearls - NCBI Bookshelf

Address sex partners at the same visit: identify recent partners, facilitate notification, arrange testing and treatment, and counsel patients that untreated partners are a major driver of reinfection. Partner notification and partner treatment are established elements of STI case management. PubMedUpdates on Testing, Treatment, and Prevention of Sexually Transmitted Infections in the United States, 2025WHOSexually Transmitted Infections - IRIS

Prevention interventions selected by clinical scenario. Oxford AcademicUtilization of Doxycycline Postexposure Prophylaxis at a Midwestern United States HIV/PrEP Clinic | Open Forum Infectious Diseases | Oxford AcademicPubMedSexually Transmitted Infections - StatPearls - NCBI BookshelfWHOSexually transmitted infections (STIs)
ScenarioInterventionKey limitation or monitoring step
Any patient at risk for STI acquisitionRecommend condoms for vaginal, oral, and anal sex. WHOSexually transmitted infections (STIs)Condoms do not fully prevent syphilis or genital herpes when lesions occur outside the covered area. WHOSexually transmitted infections (STIs)
Eligible or incompletely immunized patientAssess and provide hepatitis B and HPV vaccination as indicated. PubMedSexual Assault Infectious Disease Prophylaxis - StatPearls - NCBI BookshelfWHOSexually transmitted infections (STIs)Address vaccination during the STI encounter to avoid missed prevention opportunities. PubMedSexual Assault Infectious Disease Prophylaxis - StatPearls - NCBI Bookshelf
Symptomatic STI presentationTest for HIV and other prevalent STIs. PubMedSexually Transmitted Infections - StatPearls - NCBI BookshelfLink HIV prevention needs to the exposure pattern and test results. PubMedSexually Transmitted Infections - StatPearls - NCBI Bookshelf
Confirmed bacterial STIInitiate partner notification, testing, and treatment processes. PubMedUpdates on Testing, Treatment, and Prevention of Sexually Transmitted Infections in the United States, 2025WHOSexually Transmitted Infections - IRISPartner management reduces reinfection risk and should not be deferred. PubMedUpdates on Testing, Treatment, and Prevention of Sexually Transmitted Infections in the United States, 2025

Selected bacterial STI prevention

Use doxycycline PEP selectively and monitor for benefit and resistance concerns

Doxycycline PEP is an exposure-linked intervention, not universal prophylaxis.

CDC guidance released in 2024 recommends counseling gay, bisexual, and other men who have sex with men and transgender women with a bacterial STI diagnosed during the past 12 months about doxycycline postexposure prophylaxis and offering it through shared decision-making. The regimen evaluated in trials is doxycycline 200 mg orally within 72 hours after sex. JAMADoxycycline Postexposure Prophylaxis and Bacterial Sexually Transmitted Infections Among Individuals Using HIV

Doxycycline PEP has reduced chlamydia and syphilis incidence in trials among persons assigned male sex at birth who were living with HIV or using HIV PrEP; gonorrhea benefit has been less consistent, plausibly reflecting tetracycline resistance in Neisseria gonorrhoeae. JAMADoxycycline Postexposure Prophylaxis and Bacterial Sexually Transmitted Infections Among Individuals Using HIVNEJMDoes Meningococcal Group B Vaccination in the Setting of DoxyPEP Reduce Incidence of Gonorrhea? | NEJM Clinician

At initiation and every 3 to 6 months, reassess ongoing use, perform syphilis serology and gonorrhea/chlamydia testing at every exposed anatomic site, and test for HIV in persons without HIV according to current recommendations. Prescribe the number of doses through individualized shared decision-making. Oxford AcademicUtilization of Doxycycline Postexposure Prophylaxis at a Midwestern United States HIV/PrEP Clinic | Open Forum Infectious Diseases | Oxford Academic

Discuss antimicrobial-resistance uncertainty explicitly. Wider doxycycline PEP use may increase resistance selection, including concern about co-transmission of gonococcal cephalosporin resistance with tetracycline resistance; this risk must be balanced against prevention of syphilis and chlamydia. JAMADoxycycline Postexposure Prophylaxis Could Accelerate the Emergence of Gonococcal Ceftriaxone Resistance—Reply

Doxycycline PEP implementation framework. JAMADoxycycline Postexposure Prophylaxis Could Accelerate the Emergence of Gonococcal Ceftriaxone Resistance—ReplyJAMADoxycycline Postexposure Prophylaxis and Bacterial Sexually Transmitted Infections Among Individuals Using HIVOxford AcademicUtilization of Doxycycline Postexposure Prophylaxis at a Midwestern United States HIV/PrEP Clinic | Open Forum Infectious Diseases | Oxford Academic
Decision pointOperational actionFollow-up
Candidate selectionCounsel gay, bisexual, and other MSM and transgender women with a bacterial STI in the last 12 months; offer through shared decision-making. JAMADoxycycline Postexposure Prophylaxis and Bacterial Sexually Transmitted Infections Among Individuals Using HIVReassess whether benefit continues to justify use every 3 to 6 months. Oxford AcademicUtilization of Doxycycline Postexposure Prophylaxis at a Midwestern United States HIV/PrEP Clinic | Open Forum Infectious Diseases | Oxford Academic
Dose instructionDoxycycline 200 mg orally within 72 hours after sex. JAMADoxycycline Postexposure Prophylaxis and Bacterial Sexually Transmitted Infections Among Individuals Using HIVNEJMDoes Meningococcal Group B Vaccination in the Setting of DoxyPEP Reduce Incidence of Gonorrhea? | NEJM ClinicianPrescribe doses based on individualized patient-provider assessment. Oxford AcademicUtilization of Doxycycline Postexposure Prophylaxis at a Midwestern United States HIV/PrEP Clinic | Open Forum Infectious Diseases | Oxford Academic
Laboratory surveillanceScreen for syphilis and gonorrhea/chlamydia at all sites of exposure. Oxford AcademicUtilization of Doxycycline Postexposure Prophylaxis at a Midwestern United States HIV/PrEP Clinic | Open Forum Infectious Diseases | Oxford AcademicRepeat every 3 to 6 months; perform HIV testing in persons without HIV according to current guidance. Oxford AcademicUtilization of Doxycycline Postexposure Prophylaxis at a Midwestern United States HIV/PrEP Clinic | Open Forum Infectious Diseases | Oxford Academic
Resistance discussionExplain that gonorrhea prevention is less consistent and resistance selection is a concern. JAMADoxycycline Postexposure Prophylaxis Could Accelerate the Emergence of Gonococcal Ceftriaxone Resistance—ReplyNEJMDoes Meningococcal Group B Vaccination in the Setting of DoxyPEP Reduce Incidence of Gonorrhea? | NEJM ClinicianRevisit risks, benefits, incident STIs, and continued preference at follow-up. JAMADoxycycline Postexposure Prophylaxis Could Accelerate the Emergence of Gonococcal Ceftriaxone Resistance—ReplyOxford AcademicUtilization of Doxycycline Postexposure Prophylaxis at a Midwestern United States HIV/PrEP Clinic | Open Forum Infectious Diseases | Oxford Academic

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