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

Abstract

Saccharomyces cerevisiae is traditionally considered a non-pathogenic microbe; however, recent evidence has established its role as an opportunistic fungal pathogen. The probiotic subtype, var. "boulardii," is widely administered for the prevention and treatment of gastrointestinal disorders. Here, we evaluated 46 clinical S. cerevisiae isolates obtained from a tertiary care center in Hungary. Conventional species identification was complemented by multiplex PCR fingerprinting and phylogenomic assignment within a global genomic framework. In addition to these approaches, antifungal susceptibility testing, agar invasiveness, and killer activity assays were performed to provide a comprehensive characterization. Of the isolates, 22 (48%) clustered within the probiotic subclade, predominantly originating from respiratory tract samples, while 15 (33%) corresponded to clades associated with commercial baker's yeasts. Probiotic-derived isolates were significantly associated with pediatric patients (<18 years; OR = 15.92, P = 0.004) and with prior probiotic administration (S. "boulardii": OR = 11.0, P = 0.003). Caspofungin and anidulafungin retained consistent in vitro activity, whereas amphotericin B and micafungin exhibited broader MIC distributions. Sporadic isolates from wine and ale yeast clades highlighted the heterogeneous origins of clinical S. cerevisiae. Regardless of their phylogenomic relationships, isolates generally lacked invasiveness or complex colony morphologies that are often regarded as potential virulence traits. This study demonstrates that clinical S. cerevisiae isolates frequently derive from probiotic or industrial lineages, with distinct patient associations. Integrating phylogenomics, antifungal profiling, and clinical parameters, all obtained in a single location, provides critical insights into the epidemiology, pathogenic potential, and therapeutic management of this potentially emerging fungal pathogen.

Importance: 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.

Keywords: Saccharomyces boulardii; invasivity; phylogenomics; probiotic; susceptibility; yeast.