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To determine the association of maternal substance use disorders (SUDs) during pregnancy with adverse neonatal outcomes and infant hospital re-admissions, observational stays, and emergency department utilization in the first year of life.We analyzed 2 linked statewide datasets from 2002 to 2010: the Massachusetts Pregnancy to Early Life Longitudinal data system and the Massachusetts Bureau of Substance Abuse Services Management Information System. Generalized estimating equations were used to assess the association of maternal SUDs and neonatal outcomes and infant hospital-based care in the first year of life, controlling for maternal and infant characteristics.Maternal SUDs increased from 19.4 per 1000 live births in 2003 to 31.1 per 1000 live births in 2009. In the adjusted analysis, exposed neonates were more likely to be born preterm (aOR 1.85; 95% CI 1.75–1.96) and low birthweight (aOR 1.94; 95% CI 1.80–2.09). After controlling for maternal characteristics and preterm birth, SUD-exposed neonates were more likely to have intrauterine growth restriction, cardiac, respiratory, neurologic, infectious, hematologic, and feeding/nutrition problems, prolonged hospital stay, and higher mortality (aOR range 1.26–3.80). Exposed infants were more likely to be rehospitalized (aOR 1.10; 95% CI 1.04–1.17) but less likely to have an observational stay (aOR 0.90; 95% CI 0.82–0.99) or use the emergency department (aOR 0.87; 95% CI 0.83–0.90) in the first year of life.Infants born to mothers with SUD are at higher risk for adverse health outcomes in the perinatal period and are also more likely to be rehospitalized in the first year of life.