Phylogenomic diversity of clinical Saccharomyces cerevisiae and the prevalence of probiotic-derived isolates in a tertiary care center in Hungary

Abstract

Saccharomyces cerevisiae is best known for its beneficial role in beer, bread, and wine production and is generally considered a harmless microbe. A specific subtype, S. cerevisiae var. “ boulardii,” is even marketed worldwide as a probiotic for the prevention and treatment of various gastrointestinal disorders. However, in hospitalized patients—particularly in children and immunocompromised individuals—this yeast can act as an opportunistic pathogen. In our study, nearly half of all clinical isolates belonged to the probiotic lineage, and their occurrence showed a strong correlation with prior probiotic use. By integrating genome sequencing, antifungal susceptibility testing, and patient data, we demonstrate that yeasts considered safe in food and probiotic products may nevertheless cause infections in vulnerable individuals. These findings highlight the need for clade-level molecular genetic typing of Saccharomyces samples, cautious probiotic administration, and sustained clinical vigilance.