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Fungal colonization during cytotoxic chemotherapy was studied in 42 patients with a recent diagnosis of a haematological malignancy. In total, 2759 surveillance cultures were taken from the nostrils, throat, urine, stool and perineal region. Seven hundred and ninety-six positive surveillance cultures (28.9%) yielded 968 fungal isolates. The rate of fungal colonization did not differ between patients with acute leukaemia, patients with other haematological malignancies and control patients in the same ward at admission (71% vs. 67% vs. 80%). Patients with acute leukaemia were colonized at a significantly lower rate in samples from the throat (32%), urine (10%), stool (45%) and perineum (29%) taken during hospitalization when compared with other haematological patients (respective values 58%, 21%, 67% and 45%; P-values 0.001). This could be attributed to differences in the use of antifungal drugs. Although 21/42 (50%) of our patients had multiple-site fungal colonization at the end of follow-up, only one systemic Candida infection was diagnosed. Extensive use of antifungal treatment may have influenced the low incidence of systemic fungal infections during the follow-up. In addition to Candida species, Malassezia furfur, Geotrichum candidum and Saccharomyces cerevisiae were frequently isolated. The rate of S. cerevisiae isolation increased significantly over time after admission (1%, vs. 18% of isolates, P<0.001), suggesting hospital-acquired transmission. These isolates were highly resistant to azole antifungals (MIC90 128 microg/mL for fluconazole and 16 microg/ml, for itraconazole), and caused persistent multiple site colonization in 12 patients. Extensive use of antifungal agents in a haematological ward may keep the incidence of invasive fungal infections low in spite of heavy fungal colonization. However, there may be a risk of emergence of resistant fungal strains.