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Delay in current nucleic acid amplification testing for Neisseria gonorrhoeae and Chlamydia trachomatis has led to recommendations for presumptive treatment in patients with concern for infection and unreliable follow-up. In the urban setting, it is assumed that many patients have unreliable follow-up, therefore presumptive therapy is thought to be used frequently. We sought to measure the frequency of disease and accuracy of presumptive treatment for these infections.This was an observational cohort study performed at an urban academic Level 1 trauma center ED with an annual census of 95,000 visits per year. Testing was performed using the APTIMA Unisex swab assay (Gen-Probe Incorporated, San Diego, CA). Presumptive therapy was defined as receiving treatment for both infections during the initial encounter without confirmation of diagnosis.A total of 1162 patients enrolled. Infection was present in 26% of men, 14% of all women and 11% of pregnant women. Despite high frequency of presumptive treatment, > 4% of infected patients in each category went untreated.Inaccuracy of presumptive treatment was common for these sexually transmitted infections. There is an opportunity to improve diagnostic accuracy for treatment.