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Diagnosis and management of sexually transmitted infections in adolescents

Posted: Nov 7, 2019

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Principal author(s)

Upton D Allen, Noni E MacDonald; Canadian Paediatric Society. Updated by Karina A. Top, Infectious Diseases and Immunization Committee


Sexually transmitted infections (STIs) are a growing public health concern in Canada, with rates of Chlamydia trachomatis infection, gonorrhea, and syphilis increasing among adolescents and young adults. This practice point outlines epidemiology, risk factors, laboratory testing, and management for the more common STIs in adolescents, including Chlamydia trachomatisNeisseria gonorrhoeae, Treponema pallidum (syphilis), Trichomonas vaginalis, and herpes simplex virus, with a lesser focus on HIV and human papillomavirus. The need for test-of-cure and indications for further investigations is also discussed. The importance of maximizing opportunities to screen for and treat STIs in this age group is highlighted.

Keywords: Chlamydia trachomatis; Herpes simplex virus; HIV; Human papillomavirus; Neisseria gonorrhoeae; Test-of-cure; Treponema pallidum; Trichomonas vaginalis

Sexually transmitted infections (STIs) are a growing public health concern in Canada, where detection rates for Chlamydia trachomatis infection, syphilis, and gonorrhea in adolescents and young adults have increased over the past decade.[1]


C trachomatis (non-lymphogranuloma venereum serological variants), is the most frequently reported STI in Canada, predominantly affecting women 15 to 24 years of age and men 20 to 29 years of age.[2]

N gonorrhoeae is more prevalent in men 20 to 29 years of age, particularly among men who have sex with men (MSM). Recent data show declining rates among adolescents <20 years of age, but increasing rates in older age groups.[3] The number of female cases is likely to be underestimated because, unlike males, females are often asymptomatic. Concurrent infection with C trachomatis is common.[4] Gonococcal antimicrobial resistance has been growing both in Canada and globally, which makes management with combination antimicrobial therapy and repeat testing post-treatment increasingly necessary.[5]

T pallidum infection (syphilis) most commonly affects MSM 25 to 29 years of age, sex workers and their clients, and individuals who have acquired infection in endemic regions of the world.[6] The incidence of syphilis is rising across Canada among MSM as well as in women with histories of heterosexual contact, and outbreaks have been reported in many Canadian cities. Rates of positive HIV tests vary across Canada. A downward trend in HIV rates in some regions, starting in 2008, was followed by a subsequent rise in new diagnoses from 2014 to 2016.[7] The groups affected most commonly are MSM, individuals who have acquired infection via heterosexual contact, and people who inject drugs (PWID). The largest increases in HIV rates were seen in males, especially 30 to 39 years of age, and among individuals of First Nations ethnicity.[7]

T vaginalis, herpes simplex virus (HSV), and human papillomavirus (HPV) infections are not reportable and the true incidence of these diseases in Canada is not known. Studies have suggested that T vaginalis is the most common STI causing vaginitis, affecting an estimated 2% of sexually active females 14 to 19 years of age in the United States. T vaginalis infections are asymptomatic in greater than 70% of patients.[8]

HSV is the most common cause of genital ulcer disease. Data from the United States (2015-16) estimate the prevalence of HSV-1 at 48% and HSV-2 at 12%. The prevalence of both HSV types is higher among women and increases with age.[9] At present, HSV-1 accounts for more genital infections than HSV-2.

HPV is the most common STI among males and females, with a 75% lifetime risk of infection. Infection with high-risk HPV types (e.g., 16, 18) can lead to cervical and other genital cancers, while low-risk HPV types (e.g., 6, 11) cause anogenital warts (AGWs). The prevalence of high-risk HPV types is higher among females younger than 25 years of age, those of lower socioeconomic status, and among Indigenous women.[10] The introduction of HPV immunization programs for girls has lowered rates of HPV infection, precancerous cervical abnormalities, and AGWs.[11]

STI risk factors and opportunities for assessment

During routine and incidental medical visits, health care professionals should be asking young patients open-ended questions to elicit information about sexual history, STIs, and associated risks. Because youth are not frequent users of the health care system, any visit is an opportunity for STI assessment.

Table 1 shows a list of behavioural and other factors associated with increasing risk for STIs.[1][12][13] When exploring risk factors,  clinicians should take a simple, confidential, nonjudgmental approach and use language that patients can easily understand.

Table 1. Risk Factors for STIs
Any sexually active youth < 25 years old
  • Inconsistent or no condom use
  • Contact with someone known to have STI
  • New partner
  • >2 partners in past year
  • Serial monogamy
  • No contraception or only non-barrier contraception (e.g. oral contraceptive, intrauterine device, or Depo-Provera)
  • Injection drug use
  • Any drug use (e.g. alcohol, marijuana, others – especially if associated with sex)
  • Previous STI
  • Any unsafe sexual practices (e.g. involving exchange of blood or sharing sex toys)
  • Sex workers and their clients
  • Survival sex (e.g. exchange of sex for food, shelter, or drugs)
  • Street involvement/precarious housing
  • Anonymous sex (sex with a stranger after meeting online or elsewhere)
  • Experience of sexual assault or abuse
Adapted from references [1][12][13]

Screening for STIs

Comprehensive Canadian guidelines for STI screening are available on the Public Health Agency of Canada website and via a mobile application.[1] The decision to screen is based on risk factors and symptoms, both genital and systemic, always recognizing that rectal and pharyngeal gonococcal infections are often asymptomatic. Test types and specimen requirements should be discussed with the local laboratory before collection (Tables 2 and 3). Ideally, all of a patient’s sexual contacts should be identified, tested, and treated appropriately, although ensuring full disclosure and follow-up in individuals with multiple sexual partners is challenging. Local public health units can assist in this process.

Chlamydia: All sexually active youth younger than 25 years of age should be offered screening at least annually, with more frequent screening offered to individuals with additional STI risk factors (Table 1). After treatment, screening should be repeated every six months if the risk of reinfection persists.[14][15] The nucleic acid amplification test (NAAT) is the most sensitive and specific test for C  trachomatis. First-catch void urine, vaginal (including self-collected), endocervical or urethral specimens are all suitable for NAAT testing.[16][17] Evidence suggests that a midstream urine specimen would be adequate, but first catch is preferred.[18] Serological testing should not be used for diagnostic purposes due to cross-reactivity and the associated difficulty of interpreting test results. A noninvasive screening specimen (e.g., urine or a self-collected vaginal swab) can be obtained if the patient is asymptomatic and has no risk factors or indications for a pelvic examination. A culture using cervical or urethral specimens remains the test of choice for medico-legal purposes but  is a less sensitive test than NAAT.[19] Confirmation of a positive NAAT by another NAAT using different primers may also be acceptable. Consultation with your local laboratory is advised.[4][20][21]

Test-of-cure (TOC) using NAAT three to four weeks after completion of therapy is recommended in adolescents when compliance is uncertain, an alternative treatment was used, re-exposure is likely, or the adolescent is pregnant.[22]

Gonorrhea: Screening should occur in the same groups as for chlamydial disease. A first-catch urine sample or self-collected vaginal swab is recommended for screening asymptomatic individuals, particularly when urethral and cervical samples are not practical. Pharyngeal specimens should be obtained when there is a history of oral sex, and rectal samples if there is a history of receptive anal intercourse. Cultures provide the best opportunity for determining the resistance pattern of an isolate. Culture with susceptibility testing is particularly important given the emerging antimicrobial resistance of N gonorrhoeae, and should always be performed in the following circumstances, if possible: in sexual assault cases; when treatment failure is presumed; in evaluating pelvic inflammatory disease; in symptomatic MSM; and when infection is believed to have been acquired overseas or in an area of recognized antimicrobial resistance.[1]

As the most sensitive testing method, NATT is often used in place of culture to detect gonorrhea although it does not provide antibiotic susceptibility information. NAAT is validated for urine, vaginal, urethral and cervical samples. NAATs validated for these sites can also detect rectal and oropharyngeal infections, but are currently not licensed in Canada for this purpose. However, clinicians should consult regularly with their regional laboratories because recommendations change over time.

In light of the rising rates of gonococcal resistance to cephalosporins and azithromycin and resulting treatment failures, combination therapy for gonorrhea is recommended. TOC is recommended when the following contexts apply:[22][23] a second-line or alternative treatment is used; antimicrobial resistance is suspected; high re-exposure risk exists; an adolescent is pregnant; a previous treatment has failed; in cases of pharyngeal or disseminated infection; or if signs or symptoms persist following treatment. TOC by culture performed three to seven days post-treatment is preferred. If a culture cannot be obtained, NAAT testing may be performed two to three weeks post-treatment because NAAT remains positive for longer than a culture following adequate therapy.[22] 

Repeat screening using NAAT six months after completing therapy is recommended for individuals at risk for reinfection.[24][25] Co-treatment for chlamydia is indicated for all patients with proven gonorrhea, even if chlamydia is not detected.

TABLE 2. What screening tests should be used use to detect sexually transmitted infections?
Infection Screening tests/samples Follow-up testing


NAAT is the most sensitive and specific test. Can be performed on urine, urethral swabs, vaginal, or cervical swabs*
A culture of cervical or urethral specimen is the test of choice for medico-legal cases (e.g., sexual assault). Confirmation by NAAT using a different set of primers or DNA sequencing may be used. For pharyngeal and rectal specimens, NAAT may be considered; discuss with testing laboratory

Test-of-cure 3 to 4 weeks after treatment if:

– Compliance is uncertain
– Second-line or alternative treatment was used
– Re-exposure risk is high
– An adolescent is pregnant


NAAT can be used to detect gonorrhea from urine, and from urethral, vaginal, and cervical swabs in symptomatic and asymptomatic individuals*
Culture allows for antimicrobial susceptibility testing and should be performed if a patient does not respond promptly to therapy
Cultures should be submitted for asymptomatic or symptomatic MSM, who have an increased incidence of antibiotic resistance
For rectal and pharyngeal testing, discuss preferred specimens with the testing laboratory
Culture is preferred for pharyngeal and rectal specimens
For medico-legal purposes, a positive result obtained from NAAT should be confirmed, using culture or a different set of primers, or by DNA sequencing techniques

Test-of-cure (culture 3 to 7 days post-treatment or NAAT 2 to 3 weeks later) if:

– Second-line or alternative treatment was used
– Antimicrobial resistance is a concern
– Compliance is uncertain
– Re-exposure risk is high
– An adolescent is pregnant
– Previous treatment failure
– Pharyngeal or rectal infection
– Infection is disseminated
– Signs, symptoms persist post-treatment


Serology remains the usual diagnostic test unless the patient has lesions compatible with syphilis
Treponemal-specific screening assays (e.g., EIA) are more sensitive than non-treponemal tests, though testing algorithms vary across jurisdictions
If the treponemal-specific screen is positive, a second confirmatory treponemal test is usually required

Follow-up testing depends on the nature of infection, as follows:

Primary, secondary, early latent infection: Repeat serology at 1, 3, 6, and 12 months after treatment
Late latent infection: Repeat serology 12 and 24 months after treatment
Neurosyphilis: Repeat 6, 12, and 24 months after treatment


Serology is the key diagnostic test. A screening assay is initially performed and, if positive, a Western Blot or other confirmatory test is automatically performed. Screen all patients seeking evaluation and treatment for STIs
Ensure appropriate counselling

Antibodies may be detected at 3 weeks with fourth-generation HIV antibody screening tests, but can take up to 6 months with older tests. Follow-up testing should be planned when an initial test is negative after a known exposure

Data adapted from references [1][5][22]. EIA Enzyme immunoassay; MSM Men who have sex with men; NAAT Nucleic acid amplification testing; STIs Sexually transmitted infections *Discuss specimen selection to ensure that the NAAT is validated for the specimen to be collected and the patient being tested, particularly in sexual assault cases.

Syphilis: All sexually active adolescents should be offered screening for syphilis. Screening in pregnancy should be performed at the first prenatal visit and, ideally, again at delivery. Individuals at high risk for syphilis may also be screened at 28 to 32 weeks’ gestation or at more regular intervals (e.g., monthly) when they are at very high risk (e.g., engaged in sex trade work in an area experiencing an outbreak of infectious syphilis).[20] Non-treponemal tests (such as rapid plasma reagin (RPR)) may yield false-negative results in early cases of primary syphilis. Some laboratories use a “reverse sequence algorithm”, in which a treponemal test is used for screening (e.g., treponemal-specific EIA) with positives confirmed by a nontreponemal test.[24][26] Clinicians should contact their local laboratory for more information.

Follow-up RPR testing is recommended after the treatment of all stages of syphilis with a reactive RPR.[22] Patients diagnosed with syphilis should be referred to an STI or infectious diseases clinic for treatment and follow-up.

HIV: Education about HIV prevention and testing is an essential component of routine health care for adolescents. All sexually active adolescents should be offered screening for HIV. All pregnant adolescents should be screened for HIV at the first prenatal visit. Those considered to be at ongoing risk for HIV should be retested during pregnancy and at the point of delivery.[27] In addition to testing, appropriate counselling should be arranged. Adolescents who are newly diagnosed with HIV require urgent referral to an HIV specialist for initiation of treatment.[28][29] This level of care should continue through the transition into adult care.[30][32]

Routine screening is not recommended for Trichomonas or HSV. Screening for HPV or cervical cancer is not recommended before 21 years of age. Screening for hepatitis A, B, and C may be considered for adolescents with specific risk factors as described in Table 3.

TABLE 3. What samples should be collected based on common clinical syndromes?*
Clinical syndrome Samples/screening tests

Asymptomatic males with risk factors as per Table 1

First-catch urine for Chlamydia trachomatisNeisseria gonorrhoeae

Pharyngeal and/or rectal swabs for C trachomatis, N gonorrhoeae (history of unprotected receptive oral or anal exposure)

Serology for:

Other serological tests to consider:
Hepatitis A (particularly with oral-anal contact)
Hepatitis B (if no history of vaccine)
Hepatitis C (particularly in PWIDs)

Asymptomatic females with risk factors as per Table 1

First-catch urine or
vaginal swab for C trachomatisN gonorrhoeae*

Pharyngeal and/or rectal swabs for C trachomatis, N gonorrhoeae (history of unprotected receptive oral or anal exposure)

Serology for:

Other serological tests to consider:
Hepatitis A (particularly with oral-anal contact)
Hepatitis B (if no history of vaccine)
Hepatitis C (particularly in PWIDs)

Males with symptoms of urethritis

Urethral swab for Gram stain and culture for gonorrhea (NAAT may also be used, when available)
First-catch urine for C trachomatis (NAAT)

Women with symptoms of cervicitis

Vaginal or cervical swab for Gram stain, N gonorrhoeae (culture or NAAT if culture unavailable) and C trachomatis (NAAT or culture)
Swab of cervical lesions (if present) for HSV
Vaginal swab for wet-mount

Suspected pharyngeal gonococcal infection

Swab the posterior pharynx and the tonsillar crypts
Use the swab to directly inoculate the appropriate culture medium, or place it in a transport medium

Genital ulcer disease

Swab of ulcerative, erosive, pustular, or vesicular lesions for HSV culture OR HSV polymerase chain reaction (PCR). Unroof vesicular lesions to collect fluid and place swab in viral transport medium


Serology for syphilis. If syphilis suspected (e.g., painless ulcer), send swab from ulcer for dark-field examination, direct/indirect fluorescent antibody, or NAAT test if available

Referral to an nifectious diseases or STI clinic is recommended for patients with HIV, immunosuppression, systemic symptoms, history of travel (to assess need to test for other pathogens), MSM, atypical, and/or non-healing lesions

Symptoms of vaginitis

Collect pooled vaginal secretions, if present
If no vaginal secretions are present, swab the vaginal wall in the posterior fornix to prepare a smear, or place the swab in a transport medium
Wet-mount and Gram stain smears are useful in the diagnosis of trichomonas as well as non-STI causes of vaginitis (e.g., candidiasis, bacterial vaginosis). Because of the low sensitivity of direct microscopy, culture or commercial NAATs for T vaginalis should be used, when available

If individual is at high risk for STIs as per Table 1, collect vaginal† or cervical swab for N gonorrhoeae culture, and C trachomatis (NAAT or culture)

Data adapted from reference 1. * For information on clinical syndromes not listed above, consult reference 1. † Vaginal swabs may be self- or clinician-collected. Cervical swabs may be used if a pelvic examination is performed. HSV Herpes simplex virus; NAAT Nucleic acid amplification testing; PWIDs People who inject drugs

Key issues in managing STIs

Choosing antimicrobial agents

The Canadian Paediatric Society supports treatment protocols set out in the Public Health Agency of Canada’s Canadian guidelines on sexually transmitted infections.[1] Clinicians should always consult this resource and any local public health guidelines for emerging trends and related treatment strategies. Treatment regimens for chlamydia, gonorrhea, HSV, and Trichomonas are summarized in Table 4. Patients diagnosed with syphilis and HIV require urgent specialist referral as described above. The increase in cases of quinolone-resistant gonorrhea [1] and, more recently, a rising number of isolates with reduced susceptibility to cefixime and ceftriaxone, with associated treatment failures, are cause for concern.[5]  If recommended treatments are not tolerated, or pathogens are resistant, consultation with  infectious disease specialists is recommended.

Table 4. Recommended treatment of common STIs in adolescents: Gonococcal and chlamydial co-infection, anogenital (i.e., urethral, endocervical, vaginal, rectal) infections

Preferred treatment

Ceftriaxone 250 mg IM in a single dose PLUS azithromycin 1 g PO in a single dose
OR cefixime 800 mg PO in a single dose PLUS azithromycin 1 g PO in a single dose

Pharyngeal infection
Preferred treatment Ceftriaxone 250 mg IM in a single dose PLUS azithromycin 1 g PO in a single dose
Alternative treatment Cefixime 800 mg PO in a single dose PLUS azithromycin 1 g PO in a single dose OR Azithromycin 2 g PO in a single dose
Genital /Perianal HSV infection

First episode

Valacyclovir 1000 mg PO twice daily for 10 days
Famciclovir 250 mg PO three times/day  for 5 days
Acyclovir 200 mg PO five times/day for 5 to10 days

Recurrent lesions

Valacyclovir 500 mg PO twice daily or 1000 mg PO daily for 3 days
Famciclovir 125 mg PO twice daily for 5 days
Acyclovir 200 mg PO 5 times/day for 5 days (800 mg PO three times/day for 2 days may be as efficacious)



Metronidazole 2 g PO in a single dose OR metronidazole 500 mg PO twice daily for 7 days

IM Intramuscular; PO By mouth; STIs Sexually transmitted infections;

General issues

Specific primary and secondary prevention strategies are known to decrease the risk for STIs. Clinicians should be mindful of, and counsel on, contextual issues that can impact treatment:

  • Primary prevention measures include vaccination against hepatitis B virus and HPV, condom use, and behavioural change.
  • For youth at high risk for acquiring HIV, referral to an infectious dieseases or HIV specialist may be considered for discussion of pre-exposure prophylaxis (PrEP), when available.
  • Effective secondary preventive strategies include partner notification, and treatment and screening for STIs in asymptomatic young adults.
  • Providing education and management strategies for the partners of individuals with STIs is essential for infection control and patient well-being.
  • Several of the STIs discussed above are reportable diseases, and clinicians should be familiar with the reporting process for their area and comply in a timely fashion. Public health authorities can assist with contact tracing when indicated.
  • Directly observing therapy is important to improve compliance in adolescents receiving antimicrobial treatment for STIs.
  • Check for the presence of multiple STIs, including HIV, because risk factors are similar for different STIs.
  • Retesting at six months is indicated for adolescents and adults with N gonorrhoeae and/or chlamydia because the risk for reinfection is a major concern in this age group.
  • Youth with a newly diagnosed HIV infection should be referred urgently to a specialized clinic for treatment.

Recommended resources:


This practice point was initially reviewed by the Adolescent Health and Community Paediatrics Committees of the Canadian Paediatric Society, as well as by the Public Health Agency of Canada’s Canadian STI Guidelines Expert Working Group.

Members: Natalie A Bridger MD; Jane C Finlay MD (past member); Susanna Martin MD (Board Representative); Jane C McDonald MD; Heather Onyett MD; Joan L Robinson MD (Chair); Marina I Salvadori MD (past member); Otto G Vanderkooi MD
Liaisons: Upton D Allen MBBS, Canadian Pediatric AIDS Research Group; Michael Brady MD, Committee on Infectious Diseases, American Academy of Pediatrics; Charles PS Hui MD, Committee to Advise on Tropical Medicine and Travel (CATMAT), Public Health Agency of Canada; Nicole Le Saux MD, Immunization Monitoring Program, ACTive (IMPACT); Dorothy L Moore MD, National Advisory Committee on Immunization (NACI); Nancy Scott-Thomas MD, College of Family Physicians of Canada; John S Spika MD, Public Health Agency of Canada
Consultant: Noni E MacDonald MD
Principal authors: Upton D Allen MD, Noni E MacDonald MD
Updated by: Updated by Karina A. Top MD


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Disclaimer: The recommendations in this position statement do not indicate an exclusive course of treatment or procedure to be followed. Variations, taking into account individual circumstances, may be appropriate. Internet addresses are current at time of publication.

Last updated: May 27, 2021