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In a multicenter cohort of neonates recovering from cardiac surgery, we sought to describe the epidemiology of extubation failure and its variability across centers, identify risk factors, and determine its impact on outcomes.We analyzed prospectively collected clinical registry data on all neonates undergoing cardiac surgery in the Pediatric Cardiac Critical Care Consortium database from October 2013 to July 2015. Extubation failure was defined as reintubation less than 72 hours after the first planned extubation. Risk factors were identified using multivariable logistic regression with generalized estimating equations to account for within-center correlation.The cohort included 899 neonates from 14 Pediatric Cardiac Critical Care Consortium centers; 14% were premature, 20% had genetic abnormalities, 18% had major extracardiac anomalies, and 74% underwent surgery with cardiopulmonary bypass. Extubation failure occurred in 103 neonates (11%), within 24 hours in 61%. Unadjusted rates of extubation failure ranged from 5% to 22% across centers; this variability was unchanged after adjusting for procedural complexity and airway anomaly. After multivariable analysis, only airway anomaly was identified as an independent risk factor for extubation failure (odds ratio, 3.1; 95% confidence interval, 1.4–6.7; P = .01). Neonates who failed extubation had a greater median postoperative length of stay (33 vs 23 days, P < .001) and in-hospital mortality (8% vs 2%, P = .002).This multicenter study showed that 11% of neonates recovering from cardiac surgery fail initial postoperative extubation. Only congenital airway anomaly was independently associated with extubation failure. We observed a 4-fold variation in extubation failure rates across hospitals, suggesting a role for collaborative quality improvement to optimize outcomes.