Andrea Harmath

Bacterial–fungal polymicrobial infections are clinically important, but the early response of Candidozyma (Candida) auris to Pseudomonas aeruginosa remains incompletely understood. We investigated early fungal growth, extracellular glucose and metal availability, transcriptional adaptation, and pathogen burden using in vitro co-culture, RNA sequencing, nutrient measurements, and a murine co-infection model. Within 2 h, C. auris increased from 3.3 ± 0.6 × 10⁶ to 7.1 ± 0.8 × 10⁶ colony-forming units (CFU)/mL in monoculture, but reached only 4.9 ± 0.4 × 10⁶ CFU/mL in co-culture. At 2 h, extracellular glucose concentrations were comparable between monoculture and co-culture despite reduced accumulation of viable C. auris cells in co-culture. Transcriptomics identified 210 upregulated and 124 downregulated genes, indicating remodelling of translation, carbon metabolism, stress responses, lipid metabolism, and cell-surface organization. Although iron-homeostasis genes were regulated, extracellular iron and zinc did not differ significantly at 2 h. Subsequently, extracellular iron concentration was significantly lower in co-culture at 4 h, whereas a reduction in zinc concentration at 6 h did not remain statistically significant. In vivo, co-infection reduced C. auris kidney burden by 1.4-log₁₀, without significantly altering bacterial burden. These findings show that early bacterial interaction is associated with reduced fungal proliferation and induces transcriptional changes before detectable effects in extracellular iron and zinc, supporting a multifactorial interaction involving metabolic adaptation and subsequent environmental changes.

We present a comparative analysis of 13 yeasts available for mead (honey wine) fermentation, a source of Saccharomyces cerevisiae diversity t hat has not yet been analyzed in detail. Using genomic, phenotyping, and analytic methods, we show that currently available mead yeasts belong to various clades of the species, most commonly to the Commercial Wine clade (5 of 13 samples). Mead yeasts in this group displayed genome structure variations and occasional loss of killer activity, despite being closely related. Historic European and traditional African mead isolates with sequenced genomes were found not to be closely related to any contemporary mead yeast product. The 13 yeasts tested here displayed high variability in oenological characteristics and in aroma production. Maximum ethanol tolerance ranged from 15 to 22% v/v, however, the most tolerant strain produced lower ethanol levels and retained high fructose content in experimental meads. The most abundant aroma components produced in meads were ethyl acetate, ethyl caprylate, isoamyl alcohol, and ethyl caprate, with similar aroma profiles in members of the Commercial Wine clade, and pronounced differences among other yeasts. Our results contribute to the knowledge of Saccharomyces yeasts in various fermentation environments, adding mead to the list of alcoholic beverages with a known diversity of starter cultures. Our results may aid strain selection for honey wine fermentations and inspire strain improvement.

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 (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.

Background/Objectives: This study examines the clinical characteristics of Pneumocystis jirovecii pneumonia (PjP) in non-Human immunodeficiency virus (HIV) patients in Hungary to describe its local epidemiological properties. Methods: Our study was conducted at a clinical center with more than 1700 beds at the University of Debrecen in Hungary. We included all patients without HIV infection for whom a diagnostic evaluation for Pneumocystis infection had been requested between 1 January 2022 and 31 December 2024. Results: In total, 21 cases of PjP were identified from 122 requests at the University of Debrecen Clinical Center between 2022 and 2024. The overall 30-day mortality rate was 43% in PjP. Admission to the intensive care unit (odds ratio [OR] 5.44, 95% confidence interval [CI] 1.87–14.09, p = 0.001), the need for mechanical ventilation (OR 4.09, 95% CI 1.45–12.14, p = 0.015) and hematological malignancies (OR 3.24, 95% CI 1.23–9.18, p = 0.024), were associated with Pneumocystis PCR positivity. Furthermore, a significant association was observed between elevated levels of C-reactive protein (OR 1.01, 95% CI 1–1.01, p = 0.001), 30-day mortality (OR 2.86, 95% CI 1.09–7.92, p = 0.049), and Pneumocystis PCR positivity. Regarding diagnostic platforms used, Fujifilm Wako assay detected serum (1-3)-β-D-glucan positivity (>7 pg/mL) from 352 copies/mL in non-HIV patients with probable PJP. Conclusions: Our study serves as a gap-filling investigation, providing an overview of Pneumocystis epidemiology in the Central European region.

Leavening dough is one of the most widespread applications of fermentative yeast and the most common practice for the general public to come into contact with microbial cultures. Saccharomyces cerevisiae is the typical species used for dough making, but the evolutionary origin of strains isolated from dough is mixed. Here, using 49 newly sequenced and 183 previously described isolates from the bakery environment, we show that the traditional strains used in Europe for sourdough making are more closely related to Chinese Mantou sourdough lineages than to commercially used baker yeast strains. Surprisingly, the expansion of these traditional European strains into other human-associated niches, including the human body, has been very limited. This is in stark contrast to the Mixed-origin clade commercial baking yeasts, which consists of only a few globally distributed clonal lineages that dominate the yeast market and recurrently colonize sourdoughs and human hosts. These clonal lineages consistently maintain their ploidy, unique heterozygous chromosomal rearrangements, and stable aneuploidies in addition to several diverse structural variants. In addition to the previously known diploid and tetraploid groups of commercial isolates, we describe a widely distributed stable triploid aneuploid clonal lineage. We show that company practices and global trade help the distribution of these clonal clusters and that these yeasts are characterized by their exclusively mitotic reproduction.