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For patients who are actively using a substance and experience psychotic symptoms, determining whether the psychotic symptoms are due to a primary psychotic disorder or are substance induced is challenging, especially in emergency departments, where historical information is limited. This study examined the accuracy and subsequent treatment implications of emergency department diagnoses among substance-using patients who were having their first psychotic episode.Emergency department diagnoses for 302 patients were compared with best-estimate longitudinal diagnoses (BELDs) based on research assessments at three time points (baseline, six months, and 12 months).Of the 223 patients whose symptoms were diagnosed in the emergency department as a primary psychotic disorder, one-quarter were determined by the BELD to have substance-induced psychosis or no psychosis. Overall, the diagnostic agreement was only fair (κ=.32). Patients with an emergency department diagnosis of primary psychosis were significantly more likely than those with an emergency department diagnosis of substance-induced psychosis to be hospitalized, started on antipsychotic medication, and referred to mental health services instead of treatment for substance use (p<.001). Patients given an emergency department diagnosis of primary psychosis who were found by the BELD to have substance-induced psychosis or no psychosis were significantly more likely to be treated for a psychotic disorder rather than for substance-induced psychosis (p<.001)Clinicians in psychiatric emergency departments appear to have a tendency to attribute psychotic symptoms to a primary psychotic disorder rather than to concurrent substance use. Given that the diagnosis has significant implications for future management, it is important to improve diagnostic approaches in the emergency department.