Comparative Genomic Analysis of Capsule-Producing Black Yeasts Exophiala dermatitidis and Exophiala spinifera, Potential Agents of Disseminated Mycoses

In Vitro and In Vivo Evaluation of Synergistic Effects of Everolimus in Combination with Antifungal Agents on Exophiala dermatitidis

To investigate the combined function of the novel oral mTOR inhibitor, everolimus, with antifungal agents and their potential mechanisms against Exophiala dermatitidis, the CLSI microliquid-based dilution method M38-A2, chequerboard technique, and disk diffusion testing were performed. The efficacy of everolimus was evaluated in combination with itraconazole, voriconazole, posaconazole, and amphotericin B against 16 clinically isolated strains of E. dermatitidis. The synergistic effect was determined by measuring the MIC and fractional inhibitory concentration index. Dihydrorhodamine 123 was used for the quantification of ROS levels. The differences in the expression of antifungal susceptibility-associated genes were analyzed following different types of treatment. Galleria mellonella was used as the in vivo model. While everolimus alone showed minimal antifungal effects, combinations with itraconazole, voriconazole, posaconazole, or amphotericin B resulted in synergy in 13/16 (81.25%), 2/16 (12.5%), 14/16 (87.75%), and 5/16 (31.25%) of isolates, respectively. The disk diffusion assay revealed that the combination of everolimus and antifungal drugs showed no significant increase in the inhibition zones compared with the single agent, but no antagonistic effects were observed. Combination of everolimus and antifungal agents resulted in increased ROS activity (everolimus + posaconazole versus posaconazole [P < 0.05], everolimus + amphotericin B versus amphotericin B [P < 0.002]). Simultaneously, compared to mono-treatment, the combination of everolimus + itraconazole suppressed the expression of MDR2 (P < 0.05) and the combination of everolimus + amphotericin B suppressed the expression of MDR3 (P < 0.05) and CDR1B (P < 0.02). In vivo, combinations of everolimus and antifungal agents improved survival rates, particularly the combination of everolimus + amphotericin B (P < 0.05). In summary, the in vivo and in vitro experiments performed in our study suggest that the combination of everolimus with azoles or amphotericin B can have synergistic effects against E. dermatitidis, potentially due to the induction of ROS activity and inhibition of efflux pumps, providing a promising new approach for the treatment of E. dermatitidis infections. IMPORTANCE Cancer patients with E. dermatitidis infection have high mortality if untreated. Clinically, the conventional treatment of E. dermatitidis is poor due to the long-term use of antifungal drugs. In this study, we have for the first time investigated the interaction and action mechanism of everolimus combined with itraconazole, voriconazole, posaconazole, and amphotericin B on E. dermatitidis in vitro and in vivo, which provided new ideas and direction for further exploring the mechanism of drug combination and clinical treatment of E. dermatitidis.

Multifocal cutaneous phaeohyphomycosis caused by Exophiala spinifera with clinical resolution in an immunocompromised cat

Case summary

A 3-year-old neutered domestic shorthair cat with a long history of idiopathic immune-mediated haemolytic anaemia and thrombocytopenia treated with ciclosporin and prednisolone was referred 2 months after the appearance of nodular dermatitis. A single pigmented nodule was present in the lateral carpal region of the right foreleg. The lesion was 7 mm in diameter, non-exudative and cutaneous to subcutaneous. Fine-needle aspiration of the mass revealed the presence of pigmented fungal elements. Excisional surgery was planned; in the meantime, a plaque-like lesion developed in the interorbital region. Histopathological examination confirmed the presumptive diagnosis of phaeohyphomycosis, and Exophiala spinifera was identified as the aetiological agent. Itraconazole, given orally at a dose of 10 mg/kg for 8 weeks following surgery, enabled clinical resolution despite continued use of immunosuppressants. The follow-up was carried out over 14 weeks.

Relevance and novel information

This case report provides the first evidence of multifocal cutaneous phaeohyphomycosis caused by E spinifera with clinical resolution after combined surgical and itraconazole treatment in an immunocompromised cat.

Exophiala dermatitidis

Exophiala is a genus comprising several species of opportunistic black yeasts, which belongs to Ascomycotina. It is a rare cause of fungal infections. However, infections are often chronic and recalcitrant, and while the number of cases is steadily increasing in both immunocompromised and immunocompetent people, detailed knowledge remains scarce regarding infection mechanisms, virulence factors, specific predisposing factors, risk factors, and host response. The most common manifestations of Exophiala infection are skin infections, and the most frequent type of deep infection is pulmonary infection due to inhalation. The invasive disease ranges from cutaneous or subcutaneous infection to systemic dissemination to internal organs. The final identification of the causative organism should be achieved through a combination of several methods, including the newly introduced diagnostic analysis, matrix-assisted laser desorption/ ionization-time-of-flight mass spectrometry, together with sequencing of the ribosomal ribonucleic acid internal transcribed spacer region of the fungi, and histological and culture findings. Regarding treatment, because anti-infective agents and natural compounds exhibited poor antibiofilm activity, few treatments have ultimately been found to be effective for specific antifungal therapy, so the optimal antifungal therapy and duration of therapy for these infections remain unknown. Therefore, most forms of disease caused by Exophiala dermatitidis require aggressive combination therapies: Both surgical intervention and aggressive antifungal therapy with novel compounds and azoles are necessary for effective treatment.

Molecular and MALDI-ToF MS differentiation and antifungal susceptibility of prevalent clinical Fusarium species in China

BACKGROUND

Fusarium species are emerging causative agents of superficial and disseminated human infections. Early diagnosis and treatment contribute to better prognosis of severe infection.

OBJECTIVES

To detect the effectiveness of matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-ToF MS) for Fusarium identification, and evaluate the susceptibility profiles to clinical available antifungals.

METHODS

All 203 clinical Fusarium isolates and 25 environmental isolates were identified by using translation elongation factor 1-alpha (TEF1) and RNA polymerase subunit II (RPB2) sequencing and MALDI-ToF MS. Antifungal susceptibility testing was determined by a microdilution method following the CLSI approved standard M38-A3 document.

RESULTS

Correct identification rates at the species and genus levels were 89.04% (203/228) and 95.18% (217/228), respectively, using Bruker Filamentous Fungi Library 1.0 combined with the novel database. Seven species complexes with 19 Fusarium species were identified, including F. solani (59.21%, n = 135), F. verticillioides (17.54%, n = 40), F. proliferatum (6.58%, n = 15) and F. oxysporum (4.39%, n = 10). Four uncommon species complexes (F. incarnatum-equiseti SC, F. dimerum SC, F. redolens SC and F. sporotrichioides SC) were also identified. A high degree of antifungal resistance was observed. Fusarium isolates exhibited lower MICs to luliconazole and terbinafine compared with amphotericin B and voriconazole, which in turn were significantly more active than amorolfine, fluconazole and itraconazole.

CONCLUSIONS

MALDI-ToF MS showed good performance in Fusarium species with an adapted Bruker library and expanded database. Fusarium isolates exhibited lower MICs to luliconazole and terbinafine compared to amphotericin B and voriconazole.

Comparative genomics of opportunistic Phialophora species involved in divergent disease types

BACKGROUND

Black opportunists Phialophora verrucosa complex species can cause different disease types in competent and in immunocompromised individuals, but are remarkably overrepresented in CARD9-related infections.

OBJECTIVES

To better understand the ecology and potential pathogenicity of opportunistic Phialophora species and reveal eventual genetic parameters associated with the behaviour in vivo and genetic profiles in patients with CARD9 immunodeficiency.

METHODS

Genomes of 26 strains belonging to six species of the Phialophora verrucosa complex were sequenced. Using multilocus analysis, all environmental and clinical strains were identified correctly. We compared the genomes of agents from different disease types among each other including CARD9 immunodeficiency.

RESULTS

We obtained genome sizes of the 26 Phialophora strains ranged between 32 and 37 MB. Some species showed considerable intraspecific genomic variation. P americana showed the highest degree of variability. P verrucosa was variable in CAZy enzymes, whereas P americana varied in PKS-related genes. Phialophora species, particularly P verrucosa, are relatively frequent in patients with CARD9-related immunodeficiency. Different mutations in the CARD9 gene seem to increase susceptibility for infection by different groups of species, that is either Candida, dermatophytes or black fungi. A number of patients with chromoblastomycosis revealed an as yet unknown CARD9 mutation. TNFα impairment was prevalent in patients with CARD9 infections, while CBM patients were invariably IFNγ.

CONCLUSIONS

From genomic investigations, the known virulence factors between clinical and environmental strains did not reveal any significant difference. Phialophora complex has an equal chance to cause infection in humans, either healthy or CARD9-impaired.

Comparative Genomic Data Provide New Insight on the Evolution of Pathogenicity in Sporothrix Species

Sporothrix species are commonly isolated from environmental and clinical samples. As common causes of zoonotic mycosis, Sporothrix species may result in localized or disseminated infections, posing considerable threat to animal and human health. However, the pathogenic profiles of different Sporothrix species varied, in virulence, geographic location and host ranges, which have yet to be explored. Analysing the genomes of Sporothrix species are useful for understanding their pathogenicity. In this study, we analyzed the whole genome of 12 Sporothrix species and six S. globosa isolates from different clinical samples in China. By combining comparative analyses with Kyoto Encyclopedia of Genes and Genomes (KEGG), Carbohydrate-Active enZymes (CAZy), antiSMASH, Pfam, and PHI annotations, Sporothrix species showed exuberant primary and secondary metabolism processes. The genome sizes of four main clinical species, i.e., S. brasiliensis, S. schenckii, S. globosa, and S. luriei were significantly smaller than other environmental and clinical Sporothrix species. The contracted genes included mostly CAZymes and peptidases genes that were usually associated with the decay of plants, as well as the genes that were associated with the loss of pathogenicity and the reduced virulence. Our results could, to some extent, explain a habitat shift of Sporothrix species from a saprobic life in plant materials to a pathogenic life in mammals and the increased pathogenicity during the evolution. Gene clusters of melanin and clavaric acid were identified in this study, which improved our understanding on their pathogenicity and possible antitumor effects. Moreover, our analyses revealed no significant genomic variations among different clinical isolates of S. globosa from different regions in China.