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Breakthrough fungaemias due to Candida albicans and Candida parapsilosis appearing during fluconazole therapy in neonates and infants were assessed for risk factors and outcome. Forty fungaemias occurred during therapy with fluconazole within a 12 year national survey and were compared with 161 cases of non-breakthrough paediatric fungaemias. The agar disc diffusion test method was used for antifungal susceptibility testing and the Vitek system for species identification. Univariate and multivariate analysis for risk factors for breakthrough fungaemia were carried out. All the fungaemias were a result of strains susceptible to fluconazole at 0.25-4 mg/L in vitro [C. albicans (85%) and C. parapsilosis (15%)]. The mean number of positive blood cultures per episode was 2.2. Sixteen children had 'early' breakthrough fungaemias (within 4-5 days) and 24 fungaemias appeared on day 6 and later. Mean fluconazole MICs in the 'early' group were 1.2, and 2.8 mg/L in the 'late' group (P < 0.03, t-test). However, no difference was observed in the average dose of fluconazole used in the two groups. Neonatal age, total parenteral nutrition, very low birth weight, before surgery, central or umbilical venous catheterization and artificial ventilation were all significantly related to breakthrough fungaemia in univariate analysis but only central or umbilical venous catheterization were significant in multivariate analysis. The outcome of breakthrough fungaemia was better overall and attributable mortalities in non-breakthrough fungaemia was significantly higher in comparison with breakthrough fungaemia.