Ascomycetous yeast species belonging to the subphylum Saccharomycotina (Ascomycota, Fungi) may cause a variety of pathologies in humans. Candida albicans accounts for almost half of candidemia cases but the emergence of uncommon yeasts in the clinical setting is increasing. Here, we highlight the epidemiology of Saccharomycotina budding yeasts causing bloodstream infections, address antifungal susceptibility patterns and unravel how the latter corresponds to their phylogenetic relationship. Only studies applying Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) and/or sequence-based identification methods were considered. A ribosomal DNA-based phylogeny was used to present phylogenetic relationships of yeasts pathogens and their close relatives and to show how the antifungal susceptibility patterns for amphotericin B and azole drugs correlate with the clades found. Candida albicans was still the leading cause of yeast-related sepsis, but 22 other Saccharomycotina yeast species were also identified as a common cause of sepsis based on the literature. Similar minimum inhibitory concentration (MIC) values are found between phylogenetically closely related species and appear to be clade-specific to a large extent. This demonstrates that phylogeny may serve as a first guidance for treatment of emerging yeasts with uncommon susceptibility patterns due to intrinsic resistance.

Online sequence databases such as NCBI GenBank serve as a tremendously useful platform for researchers to share and reuse published data. However, submission systems lack control for errors such as organism misidentification, which once entered in the database can be propagated and mislead downstream analyses. Here we present an illustrating case of misidentification of Candida albicans from a clinical sample as Naumovozyma dairenensis based on whole‐genome shotgun data. Analyses of phylogenetic markers, read mapping and single nucleotide polymorphisms served to correct the identification. We propose that the routine use of such analyses could help to detect misidentifications arising from unsupervised analyses and correct them before they enter the databases. Finally, we discuss broader implications of such misidentifications and the difficulty of correcting them once they are in the records.

Antifungal susceptibility profiles of rare Saccharomycotina yeasts remain missing, even though an increase in prevalence of such rare Candida species was reported in candidemia. Majority of these rare yeast species carry intrinsic resistances against at least one antifungal compound. Some species are known to be cross-resistant (against multiple drugs of the same drug class) or even multi-drug resistant (against multiple drugs of different drug classes). We performed antifungal susceptibility testing (AFST) according to EUCAST broth microdilution for 14 rare species (Clavispora lusitaniae, Candida intermedia, Candida auris, Diutina rugosa, Wickerhamiella pararugosa, Yarrowia lipolytica, Pichia norvegensis, Candida nivariensis, Kluyveromyces marxianus, Wickerhamomyces anomalus, Candida palmioleophila, Meyerozyma guilliermondii, Meyerozyma caribbica, and Debaryomyces hansenii) known to cause candidemia. In total, 234 isolates were tested for amphotericin B, fluconazole, itraconazole, voriconazole, posaconazole, anidulafungin, micafungin, and caspofungin. Amphothericin B had the broadest efficiency against the 14 tested rare yeast species, while high minimum inhibitory concentrations (MICs) against azole drugs and echinocandins were common. Voriconazole was the most efficient azole drug. Multidrug resistance was observed for the species C. auris and K. marxianus. Multidrug resistant individual isolates were found for Y. lipolytica and M. caribbica. In conclusion, the observed high MIC values of the rare Saccharomycotina species tested limit antifungal treatment options, complicating the management of such infections.