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Differing pathological haemodynamics in cardiac malformations lead to varying modes and timings of presentation. This study identifies historical trends in presentation of congenital heart disease in a population-based study. All patients diagnosed as having congenital heart disease in Malta between 1960–1994 were included (n = 868). Analysis was carried out on trends in referral sources, modes of presentation and birth prevalence. The number of patients diagnosed with congenital heart disease increased over the period under study. For both patients not requiring intervention (n = 283) and those requiring intervention (n = 585), the proportion diagnosed prior to hospital discharge increased (p ≤ 0.005). There was a decreasing trend for general practitioners to refer cases (p < 0.0001), and an increasing trend for paediatricians to refer such patients (p ≤ 0.0003). The commonest presentation to the general practitioner was an incidental finding (92%), while paediatricians referred more patients for cyanosis or heart failure (p ≤ 0.005). For lesions not requiring intervention, the commonest lesion referred was ventricular septal defect from all sources. For lesions requiring intervention, the commonest lesion detected prior to hospital discharge was tetralogy of Fallot. Atrial septal defects were the commonest lesions detected after discharge by both paediatricians and general practitioners. An increase in the proportion of hospital diagnoses is attributed to increasing rate of hospital delivery, and greater training and experience in doctors performing neonatal examinations prior to discharge. Patients diagnosed after discharge are increasingly diagnosed by paediatricians due to an increasing pool of paediatricians and better parent awareness and education.