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Wang Y, Guo X, Zhang X, Chen P, Wang W, Hu S, Ma T, Zhou X, Li D, Yang Y. In Vivo Microevolutionary Analysis of a Fatal Case of Rhinofacial and Disseminated Mycosis Due to Azole-Drug-Resistant Candida Species. J Fungi (Basel) 2023; 9:815. [PMID: 37623586 PMCID: PMC10455694 DOI: 10.3390/jof9080815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Ten Candida species strains were isolated from the first known fatal case of rhinofacial and rhino-orbital-cerebral candidiasis. Among them, five strains of Candida parapsilosis complex were isolated during the early stage of hospitalization, while five strains of Candida tropicalis were isolated in the later stages of the disease. Using whole-genome sequencing, we distinguished the five strains of C. parapsilosis complex as four Candida metapsilosis strains and one Candida parapsilosis strain. Antifungal susceptibility testing showed that the five strains of C. parapsilosis complex were susceptible to all antifungal drugs, while five C. tropicalis strains had high minimum inhibitory concentrations to azoles, whereas antifungal-drug resistance gene analysis revealed the causes of azole resistance in such strains. For the first time, we analyzed the microevolutionary characteristics of pathogenic fungi in human hosts and inferred the infection time and parallel evolution of C. tropicalis strains. Molecular clock analysis revealed that azole-resistant C. tropicalis infection occurred during the first round of therapy, followed by divergence via parallel evolution in vivo. The presence/absence variations indicated a potential decrease in the virulence of genomes in strains isolated following antifungal drug treatment, despite the absence of observed clinical improvement in the conditions of the patient. These results suggest that genomic analysis could serve as an auxiliary tool in guiding clinical diagnosis and treatment.
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Affiliation(s)
- Yuchen Wang
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjing 300457, China;
| | - Xinran Zhang
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
| | - Ping Chen
- Division of Dermatology and Mycological Lab, Peking University Third Hospital, Beijing 100191, China
| | - Wenhui Wang
- Division of Dermatology and Mycological Lab, Peking University Third Hospital, Beijing 100191, China
| | - Shan Hu
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
| | - Teng Ma
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
| | - Xingchen Zhou
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
- School of Life Science & Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Dongming Li
- Division of Dermatology and Mycological Lab, Peking University Third Hospital, Beijing 100191, China
| | - Ying Yang
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
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Abstract
AbstractThe order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by the keratin and cellulose degradation abilities. The present study aimed to investigate whether the ecological trends of the members of Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families, namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigoidaceae, were accepted in Onygenales, and two new families, Malbrancheaceae and Neogymnomycetaceae, were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of Onygenales, supported by multilocus analyses of ITS, LSU, TUB, TEF1, TEF3, RPB1, RPB2, and ribosomal protein 60S L10 (L1) (RP60S) sequences, combined with available data on ecology, physiology, morphology, and genomics.
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Kraková L, Šoltys K, Puškárová A, Bučková M, Jeszeová L, Kucharík M, Budiš J, Orovčík LU, Szemes T, Pangallo D. The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment. Environ Microbiol 2018; 20:3294-3308. [PMID: 30051567 DOI: 10.1111/1462-2920.14312] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 12/31/2022]
Abstract
This microbiological survey was performed to determine the conservation state of a mummy in the Slovak castle of Krásna Hôrka and its surrounding environment. Culture-dependent identification was coupled with biodegradation assays on keratin, gelatin and cellulose. Next Generation Sequencing (NGS) using Illumina platform was used for a deeper microbial investigation. Three environmental samples were collected: from the glass of the sarcophagus, from the air inside it, and from the air of the chapel where the mummy is located. Seven different samples were taken from mummy's surface: from the left ear, left-hand palm, left-hand nail, left instep, right hand, abdomen and mineral crystals embedded within the skin. Three internal organ samples, from the lung, pleura and stomach, were also included in this study. Together, the culture-dependent and culture-independent analyses revealed that the bacterial communities present had fewer taxa than the fungal ones. The mycobiome showed the largest variability and included Epicoccum nigrum, Penicillium spp., Alternaria spp., Aspergillus spp., Cladosporium spp. and Aureobasidium pullulans; many other Ascomycota and Basidiomycota genera were detected by NGS. The most interesting results came from the skin mineral crystals and the internal organs. The hydrolytic assays revealed those microorganisms which might be considered dangerous 'mummy pathogens'. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Affiliation(s)
- Lucia Kraková
- Institute of Molecular Biology, Slovak Academy of Science, Dúbravská cesta 21, Bratislava, 84551, Slovakia
| | - Katarína Šoltys
- Comenius University in Bratislava, Comenius University Science Park, Ilkovicova 8, Bratislava, 84104, Slovakia
| | - Andrea Puškárová
- Institute of Molecular Biology, Slovak Academy of Science, Dúbravská cesta 21, Bratislava, 84551, Slovakia
| | - Mária Bučková
- Institute of Molecular Biology, Slovak Academy of Science, Dúbravská cesta 21, Bratislava, 84551, Slovakia
| | - Lenka Jeszeová
- Institute of Molecular Biology, Slovak Academy of Science, Dúbravská cesta 21, Bratislava, 84551, Slovakia
| | | | - Jaroslav Budiš
- Geneton s.r.o, Galvaniho 7, Bratislava, 82104, Slovakia.,Faculty of Mathematics, Physics and Informatics, Department of Computer Science, Comenius University in Bratislava, Mlynska dolina, Bratislava, 84248, Slovakia
| | - L Ubomír Orovčík
- Institute of Materials and Machine Mechanics, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, 84513, Slovakia
| | - Tomáš Szemes
- Comenius University in Bratislava, Comenius University Science Park, Ilkovicova 8, Bratislava, 84104, Slovakia.,Geneton s.r.o, Galvaniho 7, Bratislava, 82104, Slovakia.,Faculty of Natural Sciences, Department of Molecular Biology, Comenius University in Bratislava, Mlynská dolina Ilkovičova 6, Bratislava, 84215, Slovakia
| | - Domenico Pangallo
- Institute of Molecular Biology, Slovak Academy of Science, Dúbravská cesta 21, Bratislava, 84551, Slovakia.,Caravella s.r.o., Tupolevova 2, Bratislava, 85101, Slovakia
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Abstract
In the expanding population of immunocompromised patients and those treated in intensive care units, rare fungal infectious agents have emerged as important pathogens, causing invasive infections associated with high morbidity and mortality. These infections may present either as de novo or as breakthrough invasive infections in high-risk patients with hematologic malignancies receiving prophylactic or empirical antifungal therapy or in patients with central venous catheters. Diagnosis and treatment are challenging. Physicians should have a high index of suspicion because early diagnosis is of paramount importance. Conventional diagnostic methods such as cultures and histopathology are still essential, but rapid and more specific molecular techniques for both detection and identification of the infecting pathogens are being developed and hopefully will lead to early targeted treatment. The management of invasive fungal infections is multimodal. Reversal of risk factors, if feasible, should be attempted. Surgical debridement is recommended in localized mold infections. The efficacy of various antifungal drugs is not uniform. Amphotericin B is active against most yeasts, except Trichosporon, as well as against Mucorales, Fusarium, and some species of Paecilomyces and dimorphic fungi. The use of voriconazole is suggested for the treatment of trichosporonosis and scedosporiosis. Combination treatment, though recommended as salvage therapy in some infections, is controversial in most cases. Despite the use of available antifungals, mortality remains high. The optimization of molecular-based techniques, with expansion of reference libraries and the possibility for direct detection of resistance mechanisms, is awaited with great interest in the near future. Further research is necessary, however, in order to find the best ways to confront and destroy these lurking enemies.
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Affiliation(s)
- Anna Skiada
- 1st Department of Medicine, Laiko Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Maria Drogari-Apiranthitou
- Infectious Diseases Research Laboratory, 4th Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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