Two large studies compared posaconazole and fluconazole or itraconazole for prophylaxis in subjects undergoing allogeneic hematopoietic stem cell transplantation or subjects with acute myelogenous leukemia. To assess the impact of prophylaxis on colonization and the development of resistance in Saccharomyces yeasts, identification and susceptibility testing were performed with yeasts cultured at regular intervals from mouth, throat, and stool samples. Prior to therapy, 34 to 50% of the subjects were colonized with yeasts. For all three drugs, the number of positive Candida albicans cultures decreased during drug therapy. In contrast, the proportion of subjects with positive C. glabrata cultures increased by two-and fourfold in the posaconazole and itraconazole arms, respectively. Likewise, in the fluconazole arm the proportion of subjects with positive C. krusei cultures increased twofold. C. glabrata was the species that most frequently exhibited decreases in susceptibility, and this trend did not differ significantly between the prophylactic regimens. For the subset of subjects from whom colonizing C. glabrata isolates were recovered at the baseline and the end of treatment, approximately 40% of the isolates exhibited more than fourfold increases in MICs during therapy. Molecular typing of the C. albicans and C. glabrata isolates confirmed that the majority of the baseline and end-of-treatment isolates were closely related, suggesting that they were persistent colonizers and not newly acquired. Overall breakthrough infections by Candida species were very rare (ϳ1%), and C. glabrata was the colonizing species that was the most frequently associated with breakthrough infections.Invasive fungal infections (IFIs) are a leading cause of morbidity and mortality in neutropenic patients with hematological malignancies and recipients of hematopoietic stem cell transplants (HSCT). Treatment of an established IFI is frequently very difficult, and the most effective agents have treatmentlimiting toxicities (19). Consequently, antifungal prophylaxis is increasingly being used for patients at high risk of acquiring a fungal infection; the benefits of antifungal prophylaxis include reduced mortality as well as reduced health care costs (5,6,10,12,17,18,20). However, there are concerns that the prophylactic agent may select for less susceptible isolates. Changes in susceptibility can be caused by mutations in existing colonizing isolates, through overgrowth (by a previously minor species), or by de novo colonization by inherently less susceptible species. This concern is particularly relevant for Candida, since colonization of the oral mucosa, gastrointestinal tract, and skin are risk factors associated with the acquisition of invasive Candida infections (11, 13).Two large randomized clinical trials compared orally administered posaconazole with either fluconazole or itraconazole for antifungal prophylaxis in patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS) or HSCT recipients receiving high-dose im...