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Cryptococcal meningitis (CM) is an opportunistic fungal infection that primarily affects immunocompromised individuals, particularly those with HIV/AIDS. In resource-limited countries, patients often receive antifungal drug fluconazole monotherapy; however, long-term outcomes, even at high doses, are poor. In this episode, Neil Stone and colleagues observed treatment response in a cohort of patients with HIV-associated CM given fluconazole alone or in combination with flucytosine. Patients treated with fluconazole monotherapy had an increase in resistant subpopulations in the CSF; however, combination prevented expansion of resistant populations. Fluconazole-resistant strains had high rates of aneuploidy characterized predominant diploidy of drug efflux pump-containing chromosome 1. Together, these results support combination therapy as a successful strategy for suppressing heteroresistance.