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Using data from 2003–2012, we updated a previous analysis of trends in hospitalizations of HIV-infected children and adolescents in the United States.We used data from the Kids´ Inpatient Database of the Healthcare Cost and Utilization Project to derive nationally representative estimates of the number of hospitalizations and the rates per 1000 hospitalizations of select discharge diagnoses and procedures in 2003, 2006, 2009 and 2012 among HIV-infected and HIV-uninfected children and adolescents ≤18 years, excluding hospitalizations for conditions related to pregnancy/delivery and neonatal diagnoses. We also examined trends in the prevalence of select discharge diagnoses and procedures using multivariable logistic regression models.During 2003–2012, the number of hospitalizations for HIV-infected children declined 58% versus 17% for uninfected, but the odds of having discharge codes for most of the diagnoses and procedures studied, including death during hospitalization, remained higher among HIV-infected compared with uninfected children. Among HIV-infected children, the prevalence of discharge diagnoses for pneumonia, pneumococcal disease and varicella/herpes zoster infections and odds of death during hospitalization decreased over time, while bacterial infections/sepsis and methicillin-resistant Staphylococcus aureus increased. Among HIV-uninfected children, there was no increase in diagnoses of bacterial infection/sepsis, but otherwise trends were similar.The number of hospitalizations for HIV-infected children declined from 2003 to 2012. The decreased prevalence of several discharge diagnoses and lower risk of death during hospitalization likely reflect improvements in HIV therapies and increased uptake of other preventive strategies. However, the increasing prevalence of discharge diagnoses for bacterial infections/sepsis warrants further attention and monitoring.