Scanning electron microscopy and machine learning reveal heterogeneity in capsular morphotypes of the human pathogen Cryptococcus spp.

Phenotypic heterogeneity is an important trait for the development and survival of many microorganisms including the yeast Cryptococcus spp., a deadly pathogen spread worldwide. Here, we have applied scanning electron microscopy (SEM) to define four Cryptococcus spp. capsule morphotypes, namely Regular, Spiky, Bald, and Phantom. These morphotypes were persistently observed in varying proportions among yeast isolates. To assess the distribution of such morphotypes we implemented an automated pipeline capable of (1) identifying potentially cell-associated objects in the SEM-derived images; (2) computing object-level features; and (3) classifying these objects into their corresponding classes. The machine learning approach used a Random Forest (RF) classifier whose overall accuracy reached 85% on the test dataset, with per-class specificity above 90%, and sensitivity between 66 and 94%. Additionally, the RF model indicates that structural and texture features, e.g., object area, eccentricity, and contrast, are most relevant for classification. The RF results agree with the observed variation in these features, consistently also with visual inspection of SEM images. Finally, our work introduces morphological variants of Cryptococcus spp. capsule. These can be promptly identified and characterized using computational models so that future work may unveil morphological associations with yeast virulence.

Caracterização bioquímica e molecular de Cryptococcus spp. isolados de excretas ambientais de pombos (Columba livia domestica) / Biochemical and molecular characterization of Cryptococcus spp. isolates from environmental feces of pigeons (Columba livia domestic)

Os pombos possuem uma rica diversidade de microrganismo, entre eles fungos sapróbios, como do gênero Cryptococcus, que podem atuar como agentes patogênicos para o homem e animais. Objetivou-se o isolamento, a caracterização bioquímica e a molecular de amostras de Cryptococcus spp. de excretas ambientas de pombos. Foram colhidas 100 amostras ambientais de pontos equidistantes e representativos da área da cidade de Araçatuba, São Paulo. As amostras foram rasteladas do solo de vias públicas, armazenadas em frasco coletor e encaminhadas para o Laboratório de Bacteriologia e Micologia da FMVA, onde foram processadas e cultivadas em duplicata, em placas de Petri contendo ágar Sabouraud dextrose a 4% e Niger. Em seguida, foram incubadas à temperatura ambiente e a 30ºC, respectivamente, por um período não inferior a 15 dias. Após a observação diária, as colônias sugestivas para levedura foram reisoladas em ágar Niger e submetidas a testes bioquímicos para posterior caracterização molecular pela técnica da PCR. Como resultado, a caracterização bioquímica e a molecular isolaram 32 colônias leveduriformes, sendo 8% dos cultivos positivos para Cryptococcus neoformans var. neoformans, 17% para Rhodotorula rubidae e 7% Candida albicans. Pelo exposto, concluiu-se que excretas ambientais de pombos constituem um microfoco para Cryptococcus neoformans var. neoformans e outras leveduras com potencial patogênico, representando um risco à saúde pública, sendo necessárias medidas preventivas, como a higienização com a correta remoção das excretas, a fim de minimizar os riscos de exposição ambiental.

Pigeons have a rich diversity of microrganisms, including fungi saprobes such as the genus Cryptococcus that can act as a pathogen for humans and animals. The aim of this was their isolation, biochemical and molecular characterization of samples of Cryptococcus from ambientas avian excreta. One hundred environmental samples,representative of the area equidistant from Araçatuba, São Paulo points were collected. The samples were removed and stored in collection bottles, sent to the Laboratory of Bacteriology and Mycology of FMVA, where they were processed and cultivated in duplicate on Petri dishes containing Sabouraud dextrose 4% and Niger and incubated at room temperature 30° C, respectively, for a period of no less than 15 days. Colonies after daily observation which were suggestive for yeast growth were re-isolated in Niger agar and subjected to biochemical analisis for further molecular characterization by PCR tests. As results, the biochemical and molecular characterization of 32 yeast colonies revealed 8% of cultures positive for Cryptococcus neoformans var. neoformans, 17% Rhodotorula rubidae and 7% Candida albicans. It was concluded that environmental avian excreta are active sites for replication of Cryptococcus neoformans var. neoformans and other yeasts with pathogenic potential. These constitute a public health risk, and preventive measures are necessary, such as cleaning and complete removal of excreta in order to minimize the risk of environmental exposure.

Silver nanoparticle production by the fungus Fusarium oxysporum: nanoparticle characterisation and analysis of antifungal activity against pathogenic yeasts.

The microbial synthesis of nanoparticles is a green chemistry approach that combines nanotechnology and microbial biotechnology. The aim of this study was to obtain silver nanoparticles (SNPs) using aqueous extract from the filamentous fungus Fusarium oxysporum as an alternative to chemical procedures and to evaluate its antifungal activity. SNPs production increased in a concentration-dependent way up to 1 mM silver nitrate until 30 days of reaction. Monodispersed and spherical SNPs were predominantly produced. After 60 days, it was possible to observe degenerated SNPs with in additional needle morphology. The SNPs showed a high antifungal activity against Candida and Cryptococcus , with minimum inhibitory concentration values ≤ 1.68 µg/mL for both genera. Morphological alterations of Cryptococcus neoformans treated with SNPs were observed such as disruption of the cell wall and cytoplasmic membrane and lost of the cytoplasm content. This work revealed that SNPs can be easily produced by F. oxysporum aqueous extracts and may be a feasible, low-cost, environmentally friendly method for generating stable and uniformly sized SNPs. Finally, we have demonstrated that these SNPs are active against pathogenic fungi, such as Candida and Cryptococcus.

Silver nanoparticle production by the fungus Fusarium oxysporum: nanoparticle characterisation and analysis of antifungal activity against pathogenic yeasts

The microbial synthesis of nanoparticles is a green chemistry approach that combines nanotechnology and microbial biotechnology. The aim of this study was to obtain silver nanoparticles (SNPs) using aqueous extract from the filamentous fungus Fusarium oxysporum as an alternative to chemical procedures and to evaluate its antifungal activity. SNPs production increased in a concentration-dependent way up to 1 mM silver nitrate until 30 days of reaction. Monodispersed and spherical SNPs were predominantly produced. After 60 days, it was possible to observe degenerated SNPs with in additional needle morphology. The SNPs showed a high antifungal activity against Candida and Cryptococcus , with minimum inhibitory concentration values ≤ 1.68 µg/mL for both genera. Morphological alterations of Cryptococcus neoformans treated with SNPs were observed such as disruption of the cell wall and cytoplasmic membrane and lost of the cytoplasm content. This work revealed that SNPs can be easily produced by F. oxysporum aqueous extracts and may be a feasible, low-cost, environmentally friendly method for generating stable and uniformly sized SNPs. Finally, we have demonstrated that these SNPs are active against pathogenic fungi, such as Candida and Cryptococcus .

Synthesis of magneto-sensitive iron-containing nanoparticles by yeasts.

Industrial production of magneto-sensitive nanoparticles, which can be used in the production of target drug delivery carriers, is a subject of interest for biotechnology and microbiology. Synthesis of these nanoparticles by microorganisms has been described only for bacterial species. At the same time, it is well known that yeasts can form various metal-containing nanoparticles used, for instance, in semiconductors, etc. This paper describes the first results of the biosynthesis of magneto-sensitive nanoparticles by yeasts. The organisms we used-Saccharomyces cerevisiae and Cryptococcus humicola-represented two different genera. Magneto-sensitive nanoparticles were synthesized at room temperature in bench-scale experiments. The study included transmission electron microscopy of the yeast cells and their energy dispersive spectrum analyses and revealed the presence of iron-containing nanoparticles. Both yeast cultures synthesized nanoparticles at high concentrations of dissolved iron. Electron microscopy showed that nanoparticles were associated mainly with the yeast cell wall. Formation of magneto-sensitive nanoparticles was studied under conditions of applied magnetic fields; a possible stimulating role of magnetic field is suggested. On the whole, the paper reports a novel approach to green biosynthesis of magneto-sensitive nanoparticles.

The effects of palm oil breakdown products on lipid turnover and morphology of fungi.

The oleaginous fungi Cryptococcus curvatus and Mucor circinelloides were used to determine the effect of palm oil breakdown products, measured as polymerized triglycerides (PTGs), on lipid turnover and on fungal growth and morphology. In M. circinelloides, we found after 7 days of growth, a decrease in biomass and in lipid utilization and accumulation at increased PTG levels, both at low and neutral pH. In C. curvatus, there was also a decrease in lipid utilization and biomass production at increased PTG levels, at both low and neutral pH. However, an increase in oil accumulation was observed at low pH while it remained similar at neutral pH for all PTG levels tested. Hairy and warty protuberances on the cell surface were observed when C. curvatus was grown on oils with 15% and 45% PTGs, respectively. Using nano scanning Auger microscopy, we found no evidence to suggest a difference in elemental composition of the surfaces of the warty protuberances compared with the rest of the cell wall surface. We conclude that the warty protuberances are outgrowths of cell walls and that the changes observed in lipid turnover in both fungi are due to the presence of palm oil breakdown products.

Antifungal activity of the essential oil of Thymus x viciosoi against Candida, Cryptococcus, Aspergillus and dermatophyte species.

The essential oil (EO) of Thymus x viciosoi (Pau) R. Morales was isolated and analysed by GC and GC-MS. The antifungal activity of the EO and its major components against clinically relevant yeasts and molds was then measured. Their influence on the germ tube formation in Candida albicans and the influence of the EO on the metabolic function and cytoplasmic membrane integrity in the same yeast, analyzed by flow cytometry, were also studied. The EO showed high contents of carvacrol, thymol, and P-cymene. The total EO, as well as its components carvacrol and thymol, displayed very low minimum inhibitory concentrations and minimum fungicidal concentrations against all tested organisms (0.04 to 0.64 microL mL(-1)), while P-cymene showed weaker activity (2.5 to > 20.0 microL mL(-1)). They also inhibited filamentation at sub-inhibitory concentrations in C. albicans, particularly P-cymene, and the EO led to rapid metabolic arrest, disruption of the plasma membrane and consequently cell death. The EO and its main components were found to display a broad fungicidal activity through the disruption of cytoplasmic membrane integrity leading to leakage of vital intracellular compounds. In conclusion, the phenolic oil of T. x viciosoi may have potential for use in the development of clinically useful antifungal preparations.

Diversity of endophytic yeasts from sweet orange and their localization by scanning electron microscopy.

Endophytes are microorganisms that colonize plant tissues internally without causing harm to the host. Despite the increasing number of studies on sweet orange pathogens and endophytes, yeast has not been described as a sweet orange endophyte. In the present study, endophytic yeasts were isolated from sweet orange plants and identified by sequencing of internal transcribed spacer (ITS) rRNA. Plants sampled from four different sites in the state of São Paulo, Brazil exhibited different levels of CVC (citrus variegated chlorosis) development. Three citrus endophytic yeasts (CEYs), chosen as representative examples of the isolates observed, were identified as Rhodotorula mucilaginosa, Pichia guilliermondii and Cryptococcus flavescens. These strains were inoculated into axenic Citrus sinensis seedlings. After 45 days, endophytes were re-isolated in populations ranging from 10(6) to 10(9) CFU/g of plant tissue, but, in spite of the high concentrations of yeast cells, no disease symptoms were observed. Colonized plant material was examined by scanning electron microscopy (SEM), and yeast cells were found mainly in the stomata and xylem of plants, reinforcing their endophytic nature. P. guilliermondii was isolated primarily from plants colonized by the causal agent of CVC, Xylella fastidiosa. The supernatant from a culture of P. guilliermondii increased the in vitro growth of X. fastidiosa, suggesting that the yeast could assist in the establishment of this pathogen in its host plant and, therefore, contribute to the development of disease symptoms.

Distribution of 3-hydroxy oxylipins and acetylsalicylic acid sensitivity in Cryptococcus species.

Using a well tested antibody specific for 3-hydroxy oxylipins, we mapped the presence of these oxylipins in selected Cryptococcus (Filobasidiella) species. Immunofluorescence microscopy studies revealed that these compounds are deposited on cell wall surfaces, appendages, and collarettes. In vitro studies revealed that growth of Cryptococcus species was inhibited by acetylsalicylic acid (which is known to inhibit mitochondrial function, including the production of 3-hydroxy oxylipins) at concentrations as low as 1 mmol/L. The results suggest that acetylsalicylic acid is effective in controlling the growth of tested pathogens, probably by targeting their mitochondria. This study further expands the known function of this anti-inflammatory drug as anti-fungal agent.

Typing and patterns of cellular morphological alterations in Cryptococcus neoformans and Cryptococcus gattii isolates exposed to a panel of killer yeasts.

Cryptococcus neoformans and Cryptococcus gattii are encapsulated basidiomycetous yeasts that cause meningoencephalitis. The action of killer yeasts on the growth of one hundred genotypically characterized C. neoformans var. neoformans, C. neoformans var. grubii, and C. gattii clinical and environmental isolates was evaluated. Killer studies were performed on yeast malt-methylene blue (YM-MB) agar Petri dishes, and a dendrogram was obtained based on a quantitative data matrix using the diameter of the inhibition halo. The cellular morphological characteristics of dead cells within the halo were observed by means of optical and scanning electron microscopy. There was no formation of pores on the cell surface of the sensitive cells in contact with the toxins, at least for C. neoformans. The sensitivity patterns of clinical and environmental isolates to the killer toxins demonstrated that there is correlation between killer sensitivity of Cryptococcus species or varieties and some of the killer strains. In this case, the isolates were discriminated using the killer sensitivity patterns, and this could be used as a complementary tool to PCR-fingerprinting in epidemiological studies.

Osmotic shock tolerance and membrane fluidity of cold-adapted Cryptococcus flavescens OH 182.9, previously reported as C. nodaensis, a biocontrol agent of Fusarium head blight.

Cryptococcus flavescens (previously reported as C. nodaensis), a biological control agent of Fusarium head blight, has been previously shown to have improved desiccation tolerance after cold adaptation. The goal of the current study was to determine the effect of cold adaptation on the physicochemical properties of C. flavescens that may be responsible for its improved desiccation tolerance. The results show that cold adaptation improves liquid hyperosmotic shock tolerance and alters the temperature dependence of osmotic shock tolerance. Fluorescence anisotropy was used to characterize differences in the membrane fluidity of C. flavescens with and without cold adaptation. Force curves from atomic force microscopy showed a significant increase in the cell wall spring constant after cold adaptation. Cold adaptation of C. flavescens during culturing was shown to produce smaller cells and produced a trend towards higher CFU yields. These results suggest that cold adaptation significantly alters the membrane properties of C. flavescens and may be an effective method of improving the desiccation tolerance of microorganisms. In addition, we provide information on the correct naming of the isolate as C. flavescens.

Cytoskeletal structures, ultrastructural characteristics and the capsule of the basidiomycetous yeast Cryptococcus laurentii.

The cytoskeleton, capsule and cell ultrastructure were studied during the cell cycle of Cryptococcus laurentii. In an encapsulated strain, cytoplasmic microtubules and a mitotic spindle were detected. Mitosis was preceded by migration of the nucleus into the bud. F-actin failed to be visualised by rhodamine-phalloidin (RhPh) in encapsulated cells and therefore an acapsular strain was used. The following actin structures were found: actin dots, actin cables and cytokinetic ring. Ultrastructural studies showed the presence of a nucleus in the bud before mitosis. A collar-shaped structure was seen at the base of bud emergence. A lamellar cell wall and a rough outer surface of the cells were detected. Cytoskeletal structures found in C. laurentii are similar to those in Cryptococcus neoformans, which is a serious human pathogen.

Cryptococcus anemochoreius sp. nov., a novel anamorphic basidiomycetous yeast isolated from the atmosphere in central South Africa.

A novel yeast strain, CBS 10258T, was isolated from the atmosphere in central South Africa. Sequence analysis of the D1/D2 domain and internal transcribed spacer region of the novel strain indicates that it represents a novel species within the Cryptococcus laurentii complex. Phylogenetic analyses based on the D1/D2 domain revealed that the novel strain occupies a relatively isolated position within this complex with Papiliotrema bandonii, Cryptococcus perniciosus, Cryptococcus nemorosus and Cryptococcus sp. CBS 8363 being the closest relatives. However, the novel strain could be distinguished from related species by standard physiological tests including the inability to assimilate rhamnose, methyl alpha-d-glucoside, salicin, lactose, erythritol, ribitol, xylitol, citrate and ethanol. In addition, no extracellular starch production was observed and the isolate was able to grow in the absence of additional vitamins. On the basis of these results, we suggest that the new strain represents a novel species for which the name Cryptococcus anemochoreius sp. nov. is proposed [type strain CBS 10258T (=NRRL Y-27920T)].

Ultrastructural and chemotaxonomic analysis of a xylanolytic strain of Cryptococcus adeliensis isolated from sheep droppings in Spain.

Cryptococcus adeliensis was initially described as a psycrophilic species containing a single strain CBS 8351(T) isolated from decayed algae in Terre Adelie (Antartida). Later, a second strain of this species was isolated from an immunosuppressed patient affected by leukaemia in Germany and recently several strains from this species have been found in human patients and pigeon droppings of the same country. In this study, we isolated from sheep droppings in Spain a xylanolytic strain named LEVX01 that was phenotypically related to the strain CBS 8351(T) and showed a 100% similarity in the D1/D2 domain and 5.8S-ITS region sequences with respect to the remaining described strains of C. adeliensis. These findings suggest that this species has a wide geographical distribution and that the animal faeces are a common habitat for C. adeliensis. The chemotaxonomic analyses showed the absence of detectable amounts of xylose in the cell walls of the strains LEVX01 and CBS8351(T) in contrast to other Cryptococcus species. Interestingly, the ultrastructural study showed the presence of fimbriae in these two strains that could be involved in the attachment to the host cells and, as occurs in Candida albicans, they could also be a pathogenicity factor for the man.

Peroxisomal localization of D-aspartate oxidase and development of peroxisomes in the yeast Cryptococcus humicolus UJ1 grown on D-aspartate.

The peroxisomal localization of D-aspartate oxidase (EC. 1.4.3.1) was demonstrated in the yeast Cryptococcus humicolus UJ1 cells grown in the medium containing D-aspartate as a nitrogen source. The conclusion is based on the identical behavior of the enzyme with those of peroxisomal marker enzymes, catalase and urate oxidase, during all steps of subcellular fractionations. Supporting evidence was provided by the morphometric analysis of the peroxisomes with electron microscopy, showing that the cells grown on D-aspartate contained more and larger peroxisomes than those grown on L-aspartate, consistent with the 500-fold and 3-fold, higher contents of D-aspartate oxidase and catalase activities, respectively, in the former cells than the latter.

Synergism between the antifungal agents amphotericin B and alkyl glycerol ethers.

The alkyl glycerol ether rac-1-O-dodecylglycerol inhibited the growth of members of two genera of yeasts, Candida and Cryptococcus, and was strongly synergistic with amphotericin B. At one-half its MIC, dodecylglycerol decreased the MIC of amphotericin B by as much as 80-fold. This high degree of synergism between dodecylglycerol and amphotericin B was demonstrated against a number of species of yeasts including Candida albicans, Candida tropicalis, Candida parapsilosis, Cryptococcus neoformans, Cryptococcus albidus, and Cryptococcus laurentii. All fractional inhibitory concentrations (for all strains and species) were calculated to be less than 1, and most were less than 0.6, again demonstrating strong synergism. Other alkyl glycerol ethers with alkyl chain lengths ranging from 8 to 18 carbon atoms were also found to be synergistic with amphotericin B against C. neoformans and C. albicans. Electron microscopy experiments showed that C. neoformans grown in the presence of dodecylglycerol had severely abnormal, deformed capsules. Although the mechanism of action of dodecylglycerol is not known, dodecylglycerol was not simply acting as a detergent. The natural detergent sodium deoxycholate could not substitute for dodecylglycerol. At comparable and higher concentrations, sodium deoxycholate had no fungicidal effect on its own, nor did it potentiate the activity of amphotericin B. Dodecylglycerol did not interact synergistically with the water-soluble antifungal agent fluconazole. The lipid-soluble hydrophobic properties of amphotericin B appear to be important for this synergistic effect, in that alkyl glycerol ethers could promote synergism with amphotericin B by potentially increasing the interaction between membrane-bound ergosterol and amphotericin B.