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The objectives of this study were to determine the prevalence of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) infections among adolescents presenting to a pediatric emergency department (PED), to assess the association between these infections and certain risk factors, and to assess the feasibility of routine screening for sexually transmitted infections (STIs) in the PED.This was a prospective, observational cohort study. Three hundred seven adolescents aged 13 to 17 years in an urban PED in Bronx, NY, were enrolled in the study. Subjects provided urine samples for nucleic acid amplification testing for CT and GC and self-completed a confidential questionnaire to assess health care–seeking patterns, high-risk social behaviors, and the presence of abuse, depression, and suicidal ideation. Outcome measures include prevalence of STIs and association of STIs with responses to the confidential questionnaire.Twenty subjects (6.5%) tested positive for an STI. Seventeen (5.5%) were positive for CT, 2 (0.7%) for GC, and 1 (0.3%) for both. Fourteen adolescents (70%) with a positive test were asymptomatic. Logistic regression yielded 4 factors significantly associated with an STI: female sex (odds ratio [OR], 4.02; 95% confidence interval [CI], 1.1–15.2), illicit drug use (OR, 3.3; 95% CI, 1.1–9.3), disclosure of sexual activity (OR, 9.3; 95% CI, 1.1–76.9), and report of a sexual encounter resulting in pregnancy (OR, 3.7; 95% CI, 1.3–10.4).Sexually transmitted infections were common in asymptomatic adolescents presenting to the PED. We identified 4 risk factors that were significantly associated with STIs. Our findings may facilitate identification of adolescents at highest risk for STIs, help prevent further transmission of infection, and decrease morbidity in this marginalized population.