Candida metrosideri pro tempore sp. nov. and Candida ohialehuae pro tempore sp. nov., two antifungal-resistant yeasts associated with Metrosideros polymorpha flowers in Hawaii

Improvement of a MALDI-TOF database for the reliable identification of Candidozyma auris (formally Candida auris) and related species

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a promising technique for the rapid identification microorganisms. The aim of this study was to create a new database for the accurate identification of Candidozyma auris (formerly known as Candida auris) and 11 species of the Candidozyma haemuli species complex, including C. chanthaburiensis, C. duobushaemuli, C. haemuli, C. heveicola, C. khanbhai, C. konsanensis, C. metrosideri, C. ohialehuae, C. pseudohaemuli, C. ruelliae, and C. vulturna. Seventy-one Candidozyma isolates from different national institutions were studied. Thirty-seven strains were used to create a MALDI-TOF (microTyper MS) database using the formic acid extraction method. The validation of this database was performed with 34 other strains of the genus Candidozyma, and the result was compared with the identification results when using DBRs v1.0.0.4 (Tianrui, China). Our library allowed a 100% identification of the evaluated strains with all strains showing log scores of >2.0. Repeatability and reproducibility tests result showed a coefficient of variation of the log score values of less than 5%. The MALDI-TOF MS system can identify C. auris and related species quickly and accurately. This method will play a crucial role in accurately diagnosing infectious agents of the genus Candidozyma in clinical practice.

IMPORTANCE

Importance Candidozyma auris, also known as Candida auris, has quickly spread across the world, and prompt identification of C. auris from infected individuals is critical. However, a standard identification method is lacking for the identification of C. auris in clinical and public health laboratories. To make matters worse, its biochemical assimilation profile was found to be similar to that of closely related and even no-related species, leading to frequent misidentification. To improve diagnostics of this and closely related species, we created a database of reference mass spectra resulting in the efficient and correct identification of all Candidozyma species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, potential pathogenic species of Candidozyma can be effectively identified by MALDI-TOF MS, and differentiated from non-clinically relevant phylogenetic relatives. Thus, MALDI-TOF MS may help expedite laboratory diagnosis and treatment of C. auris and related species of clinical importance and help the clinician to decide on early treatment.

Molecular Epidemiology and Antifungal Susceptibility Profile of Candidozyma Isolates From Argentina

BACKGROUND

Epidemiological surveillance of Candidozyma sp. has become important because many species of this new genus have been reported to be responsible for nosocomial outbreaks and to exhibit elevated minimal inhibitory concentrations (MIC) to one or more classes of antifungal drugs.

OBJECTIVES

To describe the genetic relationships among Argentinian clinical isolates belonging to the Candidozyma genus and to study the molecular mechanisms associated with antifungal resistance.

METHODS

We performed whole-genome sequencing of 41 isolates. Identification was based on ribosomal DNA sequencing and susceptibility testing was determined according to the EUCAST document. Phylogenetic analysis, non-synonymous mutations in genes associated with antifungal resistance and the presence of copy number variations (CNVs) were investigated.

RESULTS

We identified 12 Candidozyma haemuli, 11 Candidozyma haemuli var. vulneris, 5 Cz. haemuli/ Cz. haemuli var. vulneris ITS hybrids, 8 Candidozyma duobushaemuli and 5 Candidozyma cf. pseudohaemuli. Phylogenetic analysis, together with clinical data, demonstrated nosocomial transmission events. In addition, Cz. haemuli and Cz. haemuli var. vulneris were not separated in the phylogenetic tree; the Cz. cf. pseudohaemuli isolates clustered distantly from the Cz. pseudohaemuli type strain. Most isolates were resistant to amphotericin B, and two Cz. haemuli isolates showed fluconazole resistance and Y132F mutation in ERG11. We did not find CNV in genes associated with antifungal resistance.

CONCLUSIONS

These findings highlight the need for epidemiological surveillance of these species and the study of molecular mechanisms associated with antifungal resistance. Furthermore, we propose a taxonomic revision for Cz. haemuli var. vulneris and Cz. pseudohaemuli based on genomic data.

Vishniacozyma floricola sp. nov., a flower-related tremellomycetous yeast species from Europe

During the course of two independent studies conducted in Hungary and Spain, four conspecific yeast strains were isolated from flowers of different plant species. DNA sequences of two barcoding regions, the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S rRNA gene-ITS2), revealed that the four strains represent an undescribed Vishniacozyma (family Bulleribasidiaceae, Basidiomycota) species. In terms of pairwise sequence similarities and according to our phylogenetic analyses of the concatenated DNA sequences of the ITS region and the D1/D2 domain of the LSU rRNA gene, the undescribed species is most closely related to Vishniacozyma melezitolytica, a yeast species of phylloplane origin. The novel species differs from the type strain of V. melezitolytica by 8 substitutions and 3 insertion/deletion (indels) and 11 substitutions and 5 indels along the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. In addition to the DNA sequence divergences, the two species differ in some physiological characters as well. We propose the species Vishniacozyma floricola sp. nov. to accommodate the above-noted strains (holotype, NCAIM Y.02320; isotype, CBS 18939; MycoBank number, 856028).

Candida auris from the Egyptian cobra: Role of snakes as potential reservoirs

Candida auris represents one of the most urgent threats to public health, although its ecology remains largely unknown. Because amphibians and reptiles may present favorable conditions for C. auris colonization, cloacal and blood samples (n = 68), from several snake species, were cultured and molecularly screened for C. auris using molecular amplification of glycosylphosphatidylinositol protein-encoding genes and ribosomal internal transcribed spacer sequencing. Candida auris was isolated from the cloacal swab of one Egyptian cobra (Naja haje legionis) and molecularly identified in its cloaca and blood. The isolation of C. auris from wild animals is herein reported for the first time, thus suggesting the role that these animals could play as reservoirs of this emerging pathogen. The occurrence of C. auris in blood requires further investigation, although the presence of cationic antimicrobial peptides in the plasma of reptiles could play a role in reducing the vitality of the fungus.

Analysis of the culturable gut yeast microbiota of dogs with digestive disorders

Despite the increasing interest in studying the gut mycobiota of dogs, the association between fungal colonization and the development of digestive disorders in this species remains largely understudied. On the other hand, the high prevalence of antifungal-resistant yeasts detected in previous studies in samples from animals represents a major threat to public health. We analyzed the presence of culturable yeasts in 112 rectal swab samples obtained from dogs with digestive disorders attended in a veterinary teaching hospital. Our results revealed that Malassezia pachydermatis was frequently isolated from the studied dog population (33.9% of samples), and that the isolation of this yeast was significantly associated to the age of animals, but not to their sex, disease group, or the presence of vomits and/or diarrhea. In contrast, other yeast species were less prevalent (17.9% of samples in total), and their isolation was not significantly associated to any variable included in the analysis. Additionally, we observed that 97.5% of the studied M. pachydermatis isolates (n = 158, 1-6 per positive episode) displayed a minimum inhibitory concentration (MIC) value >4 μg/ml to nystatin, 31.6% had a MIC ≥32 μg/ml to fluconazole, and 27.2% had a MIC >4 μg/ml to amphotericin B. The antifungal susceptibility profiles of non-Malassezia (n = 43, 1-7 per episode) were more variable and included elevated MIC values for some antifungal-species combinations. These results confirm that the intestine of dogs is a reservoir of opportunistic pathogenic yeasts and suggest that the prevalence of M. pachydermatis colonization depends more on the age of animals than on any specific digestive disorder.

Yeast communities related to honeybees: occurrence and distribution in flowers, gut mycobiota, and bee products

Honeybee (Apis mellifera) is an important agricultural pollinator and a model for sociality. In this study, a deep knowledge on yeast community characterizing the honeybees' environmental was carried out. For this, a total of 93 samples were collected: flowers as food sources, bee gut mycobiota, and bee products (bee pollen, bee bread, propolis), and processed using culture-dependent techniques and a molecular approach for identification. The occurrence of yeast populations was quantitatively similar among flowers, bee gut mycobiota, and bee products. Overall, 27 genera and 51 species were identified. Basidiomycetes genera were predominant in the flowers while the yeast genera detected in all environments were Aureobasidium, Filobasidium, Meyerozyma, and Metschnikowia. Fermenting species belonging to the genera Debaryomyces, Saccharomyces, Starmerella, Pichia, and Lachancea occurred mainly in the gut, while most of the identified species of bee products were not found in the gut mycobiota. Five yeast species, Meyerozyma guilliermondii, Debaryomyces hansenii, Hanseniaspora uvarum, Hanseniaspora guilliermondii, and Starmerella roseus, were present in both summer and winter, thus indicating them as stable components of bee mycobiota. These findings can help understand the yeast community as a component of the bee gut microbiota and its relationship with related environments, since mycobiota characterization was still less unexplored. In addition, the gut microbiota, affecting the nutrition, endocrine signaling, immune function, and pathogen resistance of honeybees, represents a useful tool for its health evaluation and could be a possible source of functional yeasts. KEY POINTS: • The stable yeast populations are represented by M. guilliermondii, D. hansenii, H. uvarum, H. guilliermondii, and S. roseus. • A. pullulans was the most abondance yeast detective in the flowers and honeybee guts. • Aureobasidium, Meyerozyma, Pichia, and Hanseniaspora are the main genera resident in gut tract.

Candida khanbhai sp. nov., a new clinically relevant yeast within the Candida haemulonii species complex

Invasive fungal infections caused by non-albicans Candida species are increasingly reported. Recent advances in diagnostic and molecular tools enabled better identification and detection of emerging pathogenic yeasts. The Candida haemulonii species complex accommodates several rare and recently described pathogenic species, C. duobushaemulonii, C. pseudohaemulonii, C. vulturna, and the most notorious example is the outbreak-causing multi-drug resistant member C. auris. Here, we describe a new clinically relevant yeast isolated from geographically distinct regions, representing the proposed novel species C. khanbhai, a member of the C. haemulonii species complex. Moreover, several members of the C. haemulonii species complex were observed to be invalidly described, including the clinically relevant species C. auris and C. vulturna. Hence, the opportunity was taken to correct this here, formally validating the names of C. auris, C. chanthaburiensis, C. konsanensis, C. metrosideri, C. ohialehuae, and C. vulturna.

Going wild: ecology and genomics are crucial to understand yeast evolution

Improved and more accessible genome-sequencing approaches have allowed the analysis of large sets of natural yeast isolates. As a consequence, this unprecedented level of description of yeast-genome characteristics and variations in natural environments has provided crucial insights on yeast ecology and evolution. Here, we review some of the most relevant and intriguing aspects of yeast evolution pointed out, thanks to the combination of yeast ecology and genomics, and critically examine the resulting improvement of our knowledge on this field. Only integrated approaches, taking into consideration not only the characteristics of the microbe but also those of the hosting environment, will significantly move forward the exploration of yeast diversity, ecology, and evolution.