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

Nearly half of clinical S. cerevisiae isolates belonged to the probiotic subclade, predominantly originating from respiratory tract samples.

• 22 of 46 clinical isolates (48%) clustered within the probiotic subclade.
• Probiotic-derived isolates predominantly originated from respiratory tract samples.
• 15 (33%) of isolates corresponded to clades associated with commercial baker's yeasts.
• Sporadic isolates from wine and ale yeast clades were also identified, highlighting heterogeneous origins.

Probiotic-derived isolates were significantly associated with pediatric patients under 18 years of age.

• OR = 15.92 for association with pediatric patients (<18 years).
• P = 0.004 for the association with pediatric patients.
• This association was identified through integration of phylogenomic data with clinical parameters.

Probiotic-derived isolates were significantly associated with prior probiotic administration.

• OR = 11.0 for association with prior S. 'boulardii' probiotic administration.
• P = 0.003 for the association with prior probiotic administration.
• The probiotic subtype S. cerevisiae var. 'boulardii' is widely administered for the prevention and treatment of gastrointestinal disorders.

Caspofungin and anidulafungin retained consistent in vitro activity against clinical S. cerevisiae isolates, while amphotericin B and micafungin exhibited broader MIC distributions.

• Antifungal susceptibility testing was performed on all 46 clinical isolates.
• Caspofungin and anidulafungin showed consistent in vitro activity.
• Amphotericin B and micafungin exhibited broader MIC distributions across isolates.
• Antifungal profiling was integrated with phylogenomic and clinical data.

Clinical S. cerevisiae isolates generally lacked invasiveness or complex colony morphologies regardless of their phylogenomic relationships.

• Agar invasiveness and killer activity assays were performed in addition to antifungal susceptibility testing.
• Isolates generally lacked invasiveness or complex colony morphologies that are often regarded as potential virulence traits.
• This finding held regardless of phylogenomic clade assignments.
• Conventional species identification was complemented by multiplex PCR fingerprinting and phylogenomic assignment within a global genomic framework.

The study evaluated 46 clinical S. cerevisiae isolates from a single tertiary care center in Hungary using a multi-method characterization approach.

• Isolates were obtained from a tertiary care center in Hungary.
• Methods included conventional species identification, multiplex PCR fingerprinting, and phylogenomic assignment within a global genomic framework.
• Antifungal susceptibility testing, agar invasiveness, and killer activity assays were also performed.
• Phylogenomic and clinical parameters were all obtained in a single location, enabling integrated epidemiological analysis.