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Anderson MZ, Dietz SM. Evolution and strain diversity advance exploration of Candida albicans biology. mSphere 2024:e0064123. [PMID: 39012122 DOI: 10.1128/msphere.00641-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024] Open
Abstract
Fungi were some of the earliest organismal systems used to explore mutational processes and its phenotypic consequences on members of a species. Yeasts that cause significant human disease were quickly incorporated into these investigations to define the genetic and phenotypic drivers of virulence. Among Candida species, Candida albicans has emerged as a model for studying genomic processes of evolution because of its clinical relevance, relatively small genome, and ability to tolerate complex chromosomal changes. Here, we describe major recent findings that used evolution of strains from defined genetic backgrounds to delineate mutational and adaptative processes and include how nascent exploration into naturally occurring variation is contributing to these conceptual frameworks. Ultimately, efforts to discern adaptive mechanisms used by C. albicans will continue to divulge new biology and can better inform treatment regimens for the increasing prevalence of fungal disease.
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Affiliation(s)
- Matthew Z Anderson
- Department of Medical Genetics, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Siobhan M Dietz
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Wang Y, Zhang Y, Leng H, Dong J. Segmentation of hyphae and yeast in fungi-infected tissue slice images and its application in analyzing antifungal blue light therapy. Med Mycol 2024; 62:myae050. [PMID: 38692846 DOI: 10.1093/mmy/myae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 05/03/2024] Open
Abstract
Candida albicans is a pathogenic fungus that undergoes morphological transitions between hyphal and yeast forms, adapting to diverse environmental stimuli and exhibiting distinct virulence. Existing research works on antifungal blue light (ABL) therapy have either focused solely on hyphae or neglected to differentiate between morphologies, obscuring potential differential effects. To address this gap, we established a novel dataset of 150 C. albicans-infected mouse skin tissue slice images with meticulously annotated hyphae and yeast. Eleven representative convolutional neural networks were trained and evaluated on this dataset using seven metrics to identify the optimal model for segmenting hyphae and yeast in original high pixel size images. Leveraging the segmentation results, we analyzed the differential impact of blue light on the invasion depth and density of both morphologies within the skin tissue. U-Net-BN outperformed other models in segmentation accuracy, achieving the best overall performance. While both hyphae and yeast exhibited significant reductions in invasion depth and density at the highest ABL dose (180 J/cm2), only yeast was significantly inhibited at the lower dose (135 J/cm2). This novel finding emphasizes the importance of developing more effective treatment strategies for both morphologies.
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Affiliation(s)
- Yuan Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou 215163, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yunchu Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou 215163, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Hong Leng
- The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Jianfei Dong
- School of Future Science and Engineering, Soochow University, Suzhou 215222, China
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3
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Yang Z, Zhang S, Ji N, Li J, Chen Q. The evil companion of OSCC: Candida albicans. Oral Dis 2024; 30:1873-1886. [PMID: 37530513 DOI: 10.1111/odi.14700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023]
Abstract
OBJECTIVE Microbial dysbiosis and microbiome-induced inflammation may play a role in the etiopathogenesis of oral squamous cell carcinoma (OSCC). Candida albicans (C. albicans) is the most prevalent opportunistic pathogenic fungus in the oral cavity, and Candida infection is considered as one of its high-risk factors. Although oral microbiota-host interactions are closely associated with the development of OSCC, the interrelationship between fungi and OSCC is poorly understood compared to that between bacteria and viruses. RESULTS We accumulated knowledge of the evidence, pathogenic factors, and possible multiple mechanisms by which C. albicans promotes malignant transformation of OSCC, focusing on the induction of epithelial damage, production of carcinogens, and regulation of the tumor microenvironment. In addition, we highlight the latest treatment strategies for Candida infection. CONCLUSION This review provides a new perspective on the interrelationship between C. albicans and OSCC and contributes to the establishment of a systematic and reliable clinical treatment system for OSCC patients with C. albicans infection.
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Affiliation(s)
- Zhixin Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Shiyu Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Ning Ji
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, P. R. China
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4
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Lozano-Rosas R, Ramos-Garcia R, Salazar-Morales MF, Robles-Águila MJ, Spezzia-Mazzocco T. Evaluation of antifungal activity of visible light-activated doped TiO 2 nanoparticles. Photochem Photobiol Sci 2024; 23:823-837. [PMID: 38568410 DOI: 10.1007/s43630-024-00557-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 03/04/2024] [Indexed: 06/11/2024]
Abstract
Titanium dioxide (TiO2) is a well-known material for its biomedical applications, among which its implementation as a photosensitizer in photodynamic therapy has attracted considerable interest due to its photocatalytic properties, biocompatibility, high chemical stability, and low toxicity. However, the photoactivation of TiO2 requires ultraviolet light, which may lead to cell mutation and consequently cancer. To address these challenges, recent research has focused on the incorporation of metal dopants into the TiO2 lattice to shift the band gap to lower energies by introducing allowed energy states within the band gap, thus ensuring the harnessing of visible light. This study presents the synthesis, characterization, and application of TiO2 nanoparticles (NPs) in their undoped, doped, and co-doped forms for antimicrobial photodynamic therapy (APDT) against Candida albicans. Blue light with a wavelength of 450 nm was used, with doses ranging from 20 to 60 J/cm2 and an NP concentration of 500 µg/ml. It was observed that doping TiO2 with Cu, Fe, Ag ions, and co-doping Cu:Fe into the TiO2 nanostructure enhanced the visible light photoactivity of TiO2 NPs. Experimental studies were done to investigate the effects of different ions doped into the TiO2 crystal lattice on their structural, optical, morphological, and chemical composition for APDT applications. In particular, Ag-doped TiO2 emerged as the best candidate, achieving 90-100% eradication of C. albicans.
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Affiliation(s)
- Ricardo Lozano-Rosas
- Instituto Nacional de Astrofísica, Óptica y Electrónica, Departamento de Óptica, Luis Enrique Erro #1 Sta María Tonantzintla, 72840, Puebla, Mexico
| | - Rubén Ramos-Garcia
- Instituto Nacional de Astrofísica, Óptica y Electrónica, Departamento de Óptica, Luis Enrique Erro #1 Sta María Tonantzintla, 72840, Puebla, Mexico
| | - Mayra F Salazar-Morales
- Instituto Nacional de Astrofísica, Óptica y Electrónica, Departamento de Óptica, Luis Enrique Erro #1 Sta María Tonantzintla, 72840, Puebla, Mexico
| | - María Josefina Robles-Águila
- Centro de Investigación en Dispositivos Semiconductores, Benemérita Universidad Autónoma de Puebla, Instituto de Ciencias, Edificio 105 C, Boulevard 14 Sur y Av. San Claudio, Col. San Manuel, C. P. 72570, Puebla, Puebla, Mexico
| | - Teresita Spezzia-Mazzocco
- Instituto Nacional de Astrofísica, Óptica y Electrónica, Departamento de Óptica, Luis Enrique Erro #1 Sta María Tonantzintla, 72840, Puebla, Mexico.
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5
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Schutz K, Melie T, Smith SD, Quandt CA. Patterns recovered in phylogenomic analysis of Candida auris and close relatives implicate broad environmental flexibility in Candida/Clavispora clade yeasts. Microb Genom 2024; 10. [PMID: 38630608 DOI: 10.1099/mgen.0.001233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Fungal pathogens commonly originate from benign or non-pathogenic strains living in the natural environment. The recently emerged human pathogen, Candida auris, is one example of a fungus believed to have originated in the environment and recently transitioned into a clinical setting. To date, however, there is limited evidence about the origins of this species in the natural environment and when it began associating with humans. One approach to overcome this gap is to reconstruct phylogenetic relationships between (1) strains isolated from clinical and non-clinical environments and (2) between species known to cause disease in humans and benign environmental saprobes. C. auris belongs to the Candida/Clavispora clade, a diverse group of 45 yeast species including human pathogens and environmental saprobes. We present a phylogenomic analysis of the Candida/Clavispora clade aimed at understanding the ecological breadth and evolutionary relationships between an expanded sample of environmentally and clinically isolated yeasts. To build a robust framework for investigating these relationships, we developed a whole-genome sequence dataset of 108 isolates representing 18 species, including four newly sequenced species and 18 environmentally isolated strains. Our phylogeny, based on 619 orthologous genes, shows environmentally isolated species and strains interspersed with clinically isolated counterparts, suggesting that there have been many transitions between humans and the natural environment in this clade. Our findings highlight the breadth of environments these yeasts inhabit and imply that many clinically isolated yeasts in this clade could just as easily live outside the human body in diverse natural environments and vice versa.
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Affiliation(s)
- Kyle Schutz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Tina Melie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
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Alonso-Monge R, Cortés-Prieto I, Román E, Pla J. Morphogenetic transitions in the adaptation of Candida albicans to the mammalian gut. Microbes Infect 2024; 26:105253. [PMID: 37977323 DOI: 10.1016/j.micinf.2023.105253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/06/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Candida albicans is a pathobiont in humans that forms part of the mycobiota in healthy individuals and can cause different pathologies upon alterations of the host defenses. The mammalian gut is clinically relevant as this niche is the most common pool for bloodstream-derived infections. The ability of C. albicans to switch from yeast to hypha has been related to the commensal-to-pathogen transition and is, therefore, considered relevant in virulence. Recently, filaments have been implicated in the humoral response in the gut. C. albicans exhibits other morphologies that play different roles in pathogenicity and commensalism. This review focuses on the role of these morphological transitions in C. albicans proliferation and its establishment as a commensal in the mammalian gut, paying special attention to the transcription factors involved in their regulation.
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Affiliation(s)
- Rebeca Alonso-Monge
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain.
| | - Isabel Cortés-Prieto
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain.
| | - Elvira Román
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain.
| | - Jesús Pla
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain.
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Domán M, Kaszab E, Laczkó L, Bali K, Makrai L, Kovács R, Majoros L, Bányai K. Genomic epidemiology of antifungal resistance in human and avian isolates of Candida albicans: a pilot study from the One Health perspective. Front Vet Sci 2024; 11:1345877. [PMID: 38435368 PMCID: PMC10904516 DOI: 10.3389/fvets.2024.1345877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024] Open
Abstract
Stress-induced genomic changes in Candida albicans contribute to the adaptation of this species to various environmental conditions. Variations of the genome composition of animal-origin C. albicans strains are largely unexplored and drug resistance or other selective pressures driving the evolution of these yeasts remained an intriguing question. Comparative genome analysis was carried out to uncover chromosomal aneuploidies and regions with loss of heterozygosity (LOH), two mechanisms that manage genome plasticity. We detected aneuploidy only in human isolates. Bird-derived isolates showed LOH in genes commonly associated with antifungal drug resistance similar to human isolates. Our study suggests that environmental fungicide usage might exert selective pressure on C. albicans infecting animals, thus contributing to the spread of potentially resistant strains between different hosts.
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Affiliation(s)
- Marianna Domán
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Eszter Kaszab
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- One Health Institute, University of Debrecen, Debrecen, Hungary
| | - Levente Laczkó
- One Health Institute, University of Debrecen, Debrecen, Hungary
- HUN-REN-UD Conservation Biology Research Group, University of Debrecen, Debrecen, Hungary
| | - Krisztina Bali
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | | | - Renátó Kovács
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Majoros
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Krisztián Bányai
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
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Lim SJ, Muhd Noor ND, Sabri S, Mohamad Ali MS, Salleh AB, Oslan SN. Bibliometric analysis and thematic review of Candida pathogenesis: Fundamental omics to applications as potential antifungal drugs and vaccines. Med Mycol 2024; 62:myad126. [PMID: 38061839 DOI: 10.1093/mmy/myad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 01/11/2024] Open
Abstract
Invasive candidiasis caused by the pathogenic Candida yeast species has resulted in elevating global mortality. The pathogenicity of Candida spp. is not only originated from its primary invasive yeast-to-hyphal transition; virulence factors (transcription factors, adhesins, invasins, and enzymes), biofilm, antifungal drug resistance, stress tolerance, and metabolic adaptation have also contributed to a greater clinical burden. However, the current research theme in fungal pathogenicity could hardly be delineated with the increasing research output. Therefore, our study analysed the research trends in Candida pathogenesis over the past 37 years via a bibliometric approach against the Scopus and Web of Science databases. Based on the 3993 unique documents retrieved, significant international collaborations among researchers were observed, especially between Germany (Bernhard Hube) and the UK (Julian Naglik), whose focuses are on Candida proteinases, adhesins, and candidalysin. The prominent researchers (Neils Gow, Alistair Brown, and Frank Odds) at the University of Exeter and the University of Aberdeen (second top performing affiliation) UK contribute significantly to the mechanisms of Candida adaptation, tolerance, and stress response. However, the science mapping of co-citation analysis performed herein could not identify a hub representative of subsequent work since the clusters were semi-redundant. The co-word analysis that was otherwise adopted, revealed three research clusters; the cluster-based thematic analyses indicated the severeness of Candida biofilm and antifungal resistance as well as the elevating trend on molecular mechanism elucidation for drug screening and repurposing. Importantly, the in vivo pathogen adaptation and interactions with hosts are crucial for potential vaccine development.
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Affiliation(s)
- Si Jie Lim
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Suriana Sabri
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Wang Y, Xu J, Ben Abid F, Salah H, Sundararaju S, Al Ismail K, Wang K, Sara Matthew L, Taj-Aldeen S, Ibrahim EB, Tang P, Perez-Lopez A, Tsui CKM. Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata ( Nakaseomyces glabrata) isolates causing invasive infections. Microb Genom 2024; 10:001179. [PMID: 38226964 PMCID: PMC10868614 DOI: 10.1099/mgen.0.001179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024] Open
Abstract
Candida glabrata is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common Candida pathogen causing bloodstream infections. Although there are many studies on the epidemiology of C. glabrata infections, the fine- and large-scale geographical nature of C. glabrata remain incompletely understood. Here we investigated both the fine- and large-scale population structure of C. glabrata through genome sequencing of 80 clinical isolates obtained from six tertiary hospitals in Qatar and by comparing with global collections. Our fine-scale analyses revealed high genetic diversity within the Qatari population of C. glabrata and identified signatures of recombination, inbreeding and clonal expansion within and between hospitals, including evidence for nosocomial transmission among coronavirus disease 2019 (COVID-19) patients. In addition to signatures of recombination at the population level, both MATa and MATα alleles were detected in most hospitals, indicating the potential for sexual reproduction in clinical environments. Comparisons with global samples showed that the Qatari C. glabrata population was very similar to those from other parts of the world, consistent with the significant role of recent anthropogenic activities in shaping its population structure. Genome-wide association studies identified both known and novel genomic variants associated with reduced susceptibilities to fluconazole, 5-flucytosine and echinocandins. Together, our genomic analyses revealed the diversity, transmission patterns and antifungal drug resistance mechanisms of C. glabrata in Qatar as well as the relationships between Qatari isolates and those from other parts of the world.
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Affiliation(s)
- Yue Wang
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Fatma Ben Abid
- Department of Medicine, Division of Infectious Diseases, Hamad Medical Corporation, Doha, Qatar
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Communicable Disease Centre, Hamad Medical Corporation, Doha, Qatar
| | - Husam Salah
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | | | - Khalil Al Ismail
- Communicable Disease Centre, Hamad Medical Corporation, Doha, Qatar
| | - Kun Wang
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Saad Taj-Aldeen
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Emad B. Ibrahim
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Patrick Tang
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Andres Perez-Lopez
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Clement K. M. Tsui
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
- Infectious Diseases Research Laboratory, National Center for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
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Porter R, Černoša A, Fernández-Sanmartín P, Cortizas AM, Aranda E, Luo Y, Zalar P, Podlogar M, Gunde-Cimerman N, Gostinčar C. Degradation of polypropylene by fungi Coniochaeta hoffmannii and Pleurostoma richardsiae. Microbiol Res 2023; 277:127507. [PMID: 37793281 DOI: 10.1016/j.micres.2023.127507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
The urgent need for better disposal and recycling of plastics has motivated a search for microbes with the ability to degrade synthetic polymers. While microbes capable of metabolizing polyurethane and polyethylene terephthalate have been discovered and even leveraged in enzymatic recycling approaches, microbial degradation of additive-free polypropylene (PP) remains elusive. Here we report the isolation and characterization of two fungal strains with the potential to degrade pure PP. Twenty-seven fungal strains, many isolated from hydrocarbon contaminated sites, were screened for degradation of commercially used textile plastic. Of the candidate strains, two identified as Coniochaeta hoffmannii and Pleurostoma richardsiae were found to colonize the plastic fibers using scanning electron microscopy (SEM). Further experiments probing degradation of pure PP films were performed using C. hoffmannii and P. richardsiae and analyzed using SEM, Raman spectroscopy and Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). The results showed that the selected fungi were active against pure PP, with distinct differences in the bonds targeted and the degree to which each was altered. Whole genome and transcriptome sequencing was conducted for both strains and the abundance of carbohydrate active enzymes, GC content, and codon usage bias were analyzed in predicted proteomes for each. Enzymatic assays were conducted to assess each strain's ability to degrade naturally occurring compounds as well as synthetic polymers. These investigations revealed potential adaptations to hydrocarbon-rich environments and provide a foundation for further investigation of PP degrading activity in C. hoffmannii and P. richardsiae.
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Affiliation(s)
- Rachel Porter
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Anja Černoša
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Paola Fernández-Sanmartín
- CRETUS, EcoPast Research Group (GI-1553), Departamento de Edafoloxía e Química Agrícola, Faculty of Biology, Universidade de Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain
| | - Antonio Martínez Cortizas
- CRETUS, EcoPast Research Group (GI-1553), Departamento de Edafoloxía e Química Agrícola, Faculty of Biology, Universidade de Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain
| | - Elisabet Aranda
- University of Granada, Institute of Water Research, Environmental Microbiology Group, Ramón y Cajal n4, 18071 Granada, Spain
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao 266555, China
| | - Polona Zalar
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Matejka Podlogar
- Department for Nanostructured Materials, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Cene Gostinčar
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia.
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Glazier VE, Kramara J, Ollinger T, Solis NV, Zarnowski R, Wakade RS, Kim MJ, Weigel GJ, Liang SH, Bennett RJ, Wellington M, Andes DR, Stamnes MA, Filler SG, Krysan DJ. The Candida albicans reference strain SC5314 contains a rare, dominant allele of the transcription factor Rob1 that modulates filamentation, biofilm formation, and oral commensalism. mBio 2023; 14:e0152123. [PMID: 37737633 PMCID: PMC10653842 DOI: 10.1128/mbio.01521-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/27/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Candida albicans is a commensal fungus that colonizes the human oral cavity and gastrointestinal tract but also causes mucosal as well as invasive disease. The expression of virulence traits in C. albicans clinical isolates is heterogeneous and the genetic basis of this heterogeneity is of high interest. The C. albicans reference strain SC5314 is highly invasive and expresses robust filamentation and biofilm formation relative to many other clinical isolates. Here, we show that SC5314 derivatives are heterozygous for the transcription factor Rob1 and contain an allele with a rare gain-of-function SNP that drives filamentation, biofilm formation, and virulence in a model of oropharyngeal candidiasis. These findings explain, in part, the outlier phenotype of the reference strain and highlight the role heterozygosity plays in the strain-to-strain variation of diploid fungal pathogens.
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Affiliation(s)
| | - Juraj Kramara
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Tomye Ollinger
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Norma V. Solis
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute and Harbor-UCLA Medical Center, Torrance, California, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Robert Zarnowski
- Department of Medicine, Section of Infectious Disease, University of Wisconsin, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA
| | - Rohan S. Wakade
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Min-Ju Kim
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Gabriel J. Weigel
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Shen-Huan Liang
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Richard J. Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Melanie Wellington
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - David R. Andes
- Department of Medicine, Section of Infectious Disease, University of Wisconsin, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute and Harbor-UCLA Medical Center, Torrance, California, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Damian J. Krysan
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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12
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Zuber J, Sah SK, Mathews DH, Rustchenko E. Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants. Microorganisms 2023; 11:1870. [PMID: 37630430 PMCID: PMC10458384 DOI: 10.3390/microorganisms11081870] [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: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/27/2023] Open
Abstract
Drugs from the echinocandin (ECN) class are now recommended 'front-line' treatments of infections caused by a prevailing fungal pathogen, C. albicans. However, the increased use of ECNs is associated with a rising resistance to ECNs. As the acquisition of ECN resistance in C. albicans is viewed as a multistep evolution, determining factors that are associated with the decreased ECN susceptibility is of importance. We have recently identified two cohorts of genes that are either up- or downregulated in concert in order to control remodeling of cell wall, an organelle targeted by ECNs, in laboratory mutants with decreased ECN susceptibility. Here, we profiled the global DNA sequence of four of these adapted mutants in search of DNA changes that are associated with decreased ECN susceptibility. We find a limited number of 112 unique mutations representing two alternative mutational pathways. Approximately half of the mutations occurred as hotspots. Approximately half of mutations and hotspots were shared by ECN-adapted mutants despite the mutants arising as independent events and differing in some of their phenotypes, as well as in condition of chromosome 5. A total of 88 mutations are associated with 43 open reading frames (ORFs) and occurred inside of an ORF or within 1 kb of an ORF, predominantly as single-nucleotide substitution. Mutations occurred more often in the 5'-UTR than in the 3'-UTR by a 1.67:1 ratio. A total of 16 mutations mapped to eight genomic features that were not ORFs: Tca4-4 retrotransposon; Tca2-7 retrotransposon; lambda-4a long terminal repeat; mu-Ra long terminal repeat; MRS-7b Major Repeat Sequence; MRS-R Major Repeat Sequence; RB2-5a repeat sequence; and tL (CAA) leucine tRNA. Finally, eight mutations are not associated with any ORF or other genomic feature. Repeated occurrence of single-nucleotide substitutions in non-related drug-adapted mutants strongly indicates that these DNA changes are accompanying drug adaptation and could possibly influence ECN susceptibility, thus serving as factors facilitating evolution of ECN drug resistance due to classical mutations in FKS1.
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Affiliation(s)
| | | | | | - Elena Rustchenko
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.Z.); (S.K.S.); (D.H.M.)
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13
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Glazier VE, Kramara J, Ollinger T, Solis NV, Zarnowski R, Wakade RS, Kim MJ, Weigel GJ, Liang SH, Bennett RJ, Wellington M, Andes DR, Stamnes MA, Filler SG, Krysan DJ. The Candida albicans reference strain SC5314 contains a rare, dominant allele of the transcription factor Rob1 that modulates biofilm formation and oral commensalism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.17.545405. [PMID: 37398495 PMCID: PMC10312810 DOI: 10.1101/2023.06.17.545405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Candida albicans is a diploid human fungal pathogen that displays significant genomic and phenotypic heterogeneity over a range of virulence traits and in the context of a variety of environmental niches. Here, we show that the effects of Rob1 on biofilm and filamentation virulence traits is dependent on both the specific environmental condition and the clinical strain of C. albicans . The C. albicans reference strain SC5314 is a ROB1 heterozygote with two alleles that differ by a single nucleotide polymorphism at position 946 resulting in a serine or proline containing isoform. An analysis of 224 sequenced C. albicans genomes indicates that SC5314 is the only ROB1 heterozygote documented to date and that the dominant allele contains a proline at position 946. Remarkably, the ROB1 alleles are functionally distinct and the rare ROB1 946S allele supports increased filamentation in vitro and increased biofilm formation in vitro and in vivo, suggesting it is a phenotypic gain-of-function allele. SC5314 is amongst the most highly filamentous and invasive strains characterized to date. Introduction of the ROB1 946S allele into a poorly filamenting clinical isolate increases filamentation and conversion of an SC5314 laboratory strain to a ROB1 946S homozygote increases in vitro filamentation and biofilm formation. In a mouse model of oropharyngeal infection, the predominant ROB1 946P allele establishes a commensal state while the ROB1 946S phenocopies the parent strain and invades into the mucosae. These observations provide an explanation for the distinct phenotypes of SC5314 and highlight the role of heterozygosity as a driver of C. albicans phenotypic heterogeneity. Importance Candida albicans is a commensal fungus that colonizes human oral cavity and gastrointestinal tracts but also causes mucosal as well as invasive disease. The expression of virulence traits in C. albicans clinical isolates is heterogenous and the genetic basis of this heterogeneity is of high interest. The C. albicans reference strain SC5314 is highly invasive and expresses robust filamentation and biofilm formation relative to many other clinical isolates. Here, we show that SC5314 derivatives are heterozygous for the transcription factor Rob1 and contain an allele with a rare gain-of-function SNP that drives filamentation, biofilm formation, and virulence in a model of oropharyngeal candidiasis. These finding explain, in part, the outlier phenotype of the reference strain and highlight the role of heterozygosity plays in the strain-to-strain variation of diploid fungal pathogens.
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Affiliation(s)
| | - Juraj Kramara
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
| | - Tomye Ollinger
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
| | - Norma V. Solis
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute and Harbor-UCLA Medical Center, Torrance, CA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Robert Zarnowski
- Department of Medicine, Section of Infectious Disease, University of Wisconsin, Madison WI
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison WI
| | - Rohan S. Wakade
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
| | - Min-Ju Kim
- Department of Microbiology, University of Georgia, Athens, GA
| | - Gabriel J. Weigel
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
| | - Shen-Huan Liang
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI
| | - Richard J. Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI
| | - Melanie Wellington
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
| | - David R. Andes
- Department of Medicine, Section of Infectious Disease, University of Wisconsin, Madison WI
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison WI
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute and Harbor-UCLA Medical Center, Torrance, CA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Damian J. Krysan
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City IA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City IA
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14
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Smukowski Heil C. Loss of Heterozygosity and Its Importance in Evolution. J Mol Evol 2023; 91:369-377. [PMID: 36752826 PMCID: PMC10276065 DOI: 10.1007/s00239-022-10088-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
Loss of heterozygosity (LOH) is a mitotic recombination event that converts heterozygous loci to homozygous loci. This mutation event is widespread in organisms that have asexual reproduction like budding yeasts, and is also an important and frequent mutation event in tumorigenesis. Mutation accumulation studies have demonstrated that LOH occurs at a rate higher than the point mutation rate, and can impact large portions of the genome. Laboratory evolution experiments of heterozygous yeasts have revealed that LOH often unmasks beneficial recessive alleles that can confer large fitness advantages. Here, I highlight advances in understanding dominance, fitness, and phenotypes in laboratory evolved heterozygous yeast strains. I discuss best practices for detecting LOH in intraspecific and interspecific evolved clones and populations. Utilizing heterozygous strain backgrounds in laboratory evolution experiments offers an opportunity to advance our understanding of this important mutation type in shaping adaptation and genome evolution in wild, domesticated, and clinical populations.
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Affiliation(s)
- Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
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15
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Anderson FM, Visser ND, Amses KR, Hodgins-Davis A, Weber AM, Metzner KM, McFadden MJ, Mills RE, O'Meara MJ, James TY, O'Meara TR. Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease. PLoS Biol 2023; 21:e3001822. [PMID: 37205709 DOI: 10.1371/journal.pbio.3001822] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
Candida albicans is a frequent colonizer of human mucosal surfaces as well as an opportunistic pathogen. C. albicans is remarkably versatile in its ability to colonize diverse host sites with differences in oxygen and nutrient availability, pH, immune responses, and resident microbes, among other cues. It is unclear how the genetic background of a commensal colonizing population can influence the shift to pathogenicity. Therefore, we examined 910 commensal isolates from 35 healthy donors to identify host niche-specific adaptations. We demonstrate that healthy people are reservoirs for genotypically and phenotypically diverse C. albicans strains. Using limited diversity exploitation, we identified a single nucleotide change in the uncharacterized ZMS1 transcription factor that was sufficient to drive hyper invasion into agar. We found that SC5314 was significantly different from the majority of both commensal and bloodstream isolates in its ability to induce host cell death. However, our commensal strains retained the capacity to cause disease in the Galleria model of systemic infection, including outcompeting the SC5314 reference strain during systemic competition assays. This study provides a global view of commensal strain variation and within-host strain diversity of C. albicans and suggests that selection for commensalism in humans does not result in a fitness cost for invasive disease.
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Affiliation(s)
- Faith M Anderson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Noelle D Visser
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Kevin R Amses
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea Hodgins-Davis
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Alexandra M Weber
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Katura M Metzner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Michael J McFadden
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Timothy Y James
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Teresa R O'Meara
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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16
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Bedekovic T, Usher J. Is There a Relationship Between Mating and Pathogenesis in Two Human Fungal Pathogens, Candida albicans and Candida glabrata?. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023; 10:47-54. [PMID: 37151577 PMCID: PMC10154270 DOI: 10.1007/s40588-023-00192-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/09/2023]
Abstract
Purpose of Review Human fungal pathogens are rapidly increasing in incidence and readily able to evade the host immune responses. Our ability to study the genetic behind this has been limited due to the apparent lack of a sexual cycle and forward genetic tools. In this review, we discuss the evolution of mating, meiosis, and pathogenesis and if these processes are advantageous to pathogens. Recent Findings This review summarises what is currently known about the sexual cycles of two important human fungal pathogens, Candida albicans and Candida glabrata. This includes the identification of parasexual cycle in C. albicans and the observed low levels of recombination in C. glabrata populations. Summary In this review, we present what is currently known about the mating types and mating/sexual cycles of two clinically important human fungal pathogens, Candida albicans and Candida glabrata. We discuss the evolution of meiosis using the knowledge that has been amassed from the decades of studying Saccharomyces cerevisiae and how this can be applied to fungal pathogens. We further discuss how the evolution of pathogenesis has played a role in influencing mating processes in human fungal pathogens and compare sexual cycles between C. albicans and C. glabrata, highlighting knowledge gaps and suggesting how these two fungi have evolved distinct mating niches to allow the development of disease in a human host.
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Affiliation(s)
- Tina Bedekovic
- MRC Centre for Medical Mycology, Department of Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD UK
| | - Jane Usher
- MRC Centre for Medical Mycology, Department of Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD UK
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17
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Kakade P, Sircaik S, Maufrais C, Ene IV, Bennett RJ. Aneuploidy and gene dosage regulate filamentation and host colonization by Candida albicans. Proc Natl Acad Sci U S A 2023; 120:e2218163120. [PMID: 36893271 PMCID: PMC10089209 DOI: 10.1073/pnas.2218163120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/02/2023] [Indexed: 03/11/2023] Open
Abstract
Aneuploidy is a frequent occurrence in fungal species where it can alter gene expression and promote adaptation to a variety of environmental cues. Multiple forms of aneuploidy have been observed in the opportunistic fungal pathogen Candida albicans, which is a common component of the human gut mycobiome but can escape this niche and cause life-threatening systemic disease. Using a barcode sequencing (Bar-seq) approach, we evaluated a set of diploid C. albicans strains and found that a strain carrying a third copy of chromosome (Chr) 7 was associated with increased fitness during both gastrointestinal (GI) colonization and systemic infection. Our analysis revealed that the presence of a Chr 7 trisomy resulted in decreased filamentation, both in vitro and during GI colonization, relative to isogenic euploid controls. A target gene approach demonstrated that NRG1, encoding a negative regulator of filamentation located on Chr 7, contributes to increased fitness of the aneuploid strain due to inhibition of filamentation in a gene dosage-dependent fashion. Together, these experiments establish how aneuploidy enables the reversible adaptation of C. albicans to its host via gene dosage-dependent regulation of morphology.
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Affiliation(s)
- Pallavi Kakade
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
| | - Shabnam Sircaik
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
| | - Corinne Maufrais
- Institut Pasteur Bioinformatic Hub, Université Paris Cité, Paris75015, France
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Lab, Paris75015, France
| | - Iuliana V. Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Lab, Paris75015, France
| | - Richard J. Bennett
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
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18
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Mohammadi S, Leduc A, Charette SJ, Barbeau J, Vincent AT. Amino acid substitutions in specific proteins correlate with farnesol unresponsiveness in Candida albicans. BMC Genomics 2023; 24:93. [PMID: 36859182 PMCID: PMC9979538 DOI: 10.1186/s12864-023-09174-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/09/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND The quorum-sensing molecule farnesol, in opportunistic yeast Candida albicans, modulates its dimorphic switch between yeast and hyphal forms, and biofilm formation. Although there is an increasing interest in farnesol as a potential antifungal drug, the molecular mechanism by which C. albicans responds to this molecule is still not fully understood. RESULTS A comparative genomic analysis between C. albicans strains that are naturally unresponsive to 30 µM of farnesol on TYE plates at 37 °C versus responsive strains uncovered new molecular determinants involved in the response to farnesol. While no signature gene was identified, amino acid changes in specific proteins were shown to correlate with the unresponsiveness to farnesol, particularly with substitutions in proteins known to be involved in the farnesol response. Although amino acid changes occur primarily in disordered regions of proteins, some amino acid changes were also found in known domains. Finally, the genomic investigation of intermediate-response strains showed that the non-response to farnesol occurs gradually following the successive accumulation of amino acid changes at specific positions. CONCLUSION It is known that large genomic changes, such as recombinations and gene flow (losses and gains), can cause major phenotypic changes in pathogens. However, it is still not well known or documented how more subtle changes, such as amino acid substitutions, play a role in the adaptation of pathogens. The present study shows that amino acid changes can modulate C. albicans yeast's response to farnesol. This study also improves our understanding of the network of proteins involved in the response to farnesol, and of the involvement of amino acid substitutions in cellular behavior.
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Affiliation(s)
- Sima Mohammadi
- grid.23856.3a0000 0004 1936 8390Département des sciences animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Pavillon Paul-Comtois, 2425 rue de l’Agriculture, G1V 0A6 Quebec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, QC Canada
| | - Annie Leduc
- grid.14848.310000 0001 2292 3357Département de stomatologie, Faculté de Médecine Dentaire, Université de Montréal, Montreal City, QC Canada
| | - Steve J. Charette
- grid.23856.3a0000 0004 1936 8390Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, QC Canada ,grid.421142.00000 0000 8521 1798Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, QC Canada
| | - Jean Barbeau
- grid.14848.310000 0001 2292 3357Département de stomatologie, Faculté de Médecine Dentaire, Université de Montréal, Montreal City, QC Canada
| | - Antony T. Vincent
- grid.23856.3a0000 0004 1936 8390Département des sciences animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Pavillon Paul-Comtois, 2425 rue de l’Agriculture, G1V 0A6 Quebec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, QC Canada
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19
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Genetic Diversity of Human Fungal Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023. [DOI: 10.1007/s40588-023-00188-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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20
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Ruiz-Castilla FJ, Ruiz Pérez FS, Ramos-Moreno L, Ramos J. Candida albicans Potassium Transporters. Int J Mol Sci 2022; 23:ijms23094884. [PMID: 35563275 PMCID: PMC9105532 DOI: 10.3390/ijms23094884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 12/10/2022] Open
Abstract
Potassium is basic for life. All living organisms require high amounts of intracellular potassium, which fulfils multiple functions. To reach efficient potassium homeostasis, eukaryotic cells have developed a complex and tightly regulated system of transporters present both in the plasma membrane and in the membranes of internal organelles that allow correct intracellular potassium content and distribution. We review the information available on the pathogenic yeast Candida albicans. While some of the plasma membrane potassium transporters are relatively well known and experimental data about their nature, function or regulation have been published, in the case of most of the transporters present in intracellular membranes, their existence and even function have just been deduced because of their homology with those present in other yeasts, such as Saccharomyces cerevisiae. Finally, we analyse the possible links between pathogenicity and potassium homeostasis. We comment on the possibility of using some of these transporters as tentative targets in the search for new antifungal drugs.
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21
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Genome plasticity in Candida albicans: A cutting-edge strategy for evolution, adaptation, and survival. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105256. [PMID: 35231665 DOI: 10.1016/j.meegid.2022.105256] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/12/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022]
Abstract
Candida albicans is the most implicated fungal species that grows as a commensal or opportunistic pathogen in the human host. It is associated with many life-threatening infections, especially in immunocompromised persons. The genome of Candida albicans is very flexible and can withstand a wide assortment of variations in a continuously changing environment. Thus, genome plasticity is central to its adaptation and has long been of considerable interest. C. albicans has a diploid heterozygous genome that is highly dynamic and can display variation from small to large scale chromosomal rearrangement and aneuploidy, which have implications in drug resistance, virulence, and pathogenicity. This review presents an up-to-date overview of recent genomic studies involving C. albicans. It discusses the accumulating evidence that shows how mitotic recombination events, ploidy dynamics, aneuploidy, and loss of heterozygosity (LOH) influence evolution, adaptation, and survival in C. albicans. Understanding the factors that affect the genome is crucial for a proper understanding of species and rapid development and adjustment of therapeutic strategies to mitigate their spread.
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22
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Hong N, Lei Y, Chen H, Chen X, Tsui KM, Hu D, Liao W, Yan L, Zhang H, Zhao R, Wu G, Yu N, Deng S. Genotyping and Drug Resistance Profile of Clinical Isolates of Candida albicans from Vulvovaginal Candidiasis in the Eastern China. Mycopathologia 2022; 187:217-224. [PMID: 35072854 PMCID: PMC9124162 DOI: 10.1007/s11046-022-00616-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 01/01/2022] [Indexed: 11/23/2022]
Abstract
A total of 244 Candida albicans isolates recovered from vulvovaginal candidiasis (VVC) patients in Suzhou, Eastern China, were investigated. According to CLSI documents M27-A4 and M59-3ed/M60-2ed, the MIC geometric means of nine antifungals in increasing order were micafungin (0.048 mg/L), anidulafungin (0.132 mg/L), caspofungin (0.19 mg/L), itraconazole (0.23 mg/L), posaconazole (0.25 mg/L), voriconazole (0.28 mg/L), 5-flucytosine (0.44 mg/L), amphotericin B (0.49 mg/L) and fluconazole (2.01 mg/L) respectively. Of note, 6.5% (16/244) C. albicans isolates showed resistance mainly to anidulafungin (mono-echinocandin resistance), while voriconazole had the lowest susceptibility rate of 34.8% (85/244), followed by fluconazole 59.4% (145/244), respectively. All isolates were genotyped by allelic combination of 3 microsatellite markers (CEF3, CAIII and LOC4). A total of 129 different allelic genotypes were identified, in which seven different clades were recognized with a discriminatory power of 0.96. Genotypes A-D were present in 35% of the isolates. In conclusion, decrease in antifungal drug susceptibility to C. albicans isolates from VVC is alarming. Our findings revealed the genetic diversity of C. albicans isolates among VVC patients and provided insights into the molecular epidemiology of Candida infections in China.
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Affiliation(s)
- Nan Hong
- Department of Dermatology, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China.,Department of Dermatology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Yan Lei
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huan Chen
- Department of Dermatology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xiaofei Chen
- Department of Medical Microbiology, The People's Hospital of Suzhou New District, Suzhou, Jiangsu, China
| | - Kin Ming Tsui
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada.,Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Danyang Hu
- Department of Medical Microbiology, The People's Hospital of Suzhou New District, Suzhou, Jiangsu, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Medical Molecular Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Liang Yan
- Department of Dermatology, PLA General Hospital of Central Theater Command, Wuhan, China
| | - Hong Zhang
- Department of Medical Microbiology, The People's Hospital of Suzhou New District, Suzhou, Jiangsu, China
| | - Rongfen Zhao
- Department of Medical Microbiology, The People's Hospital of Suzhou New District, Suzhou, Jiangsu, China
| | - Gang Wu
- Nanjing Chia Tai Tianqing Pharmaceutical Co., Ltd, Nanjing, China
| | - Nong Yu
- Department of Medical Microbiology, The People's Hospital of Suzhou New District, Suzhou, Jiangsu, China
| | - Shuwen Deng
- Department of Medical Microbiology, The People's Hospital of Suzhou New District, Suzhou, Jiangsu, China.
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Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary. Mycopathologia 2021; 186:237-244. [PMID: 33512664 PMCID: PMC8106574 DOI: 10.1007/s11046-021-00527-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/10/2021] [Indexed: 10/29/2022]
Abstract
The molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.
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24
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Correia I, Wilson D, Hube B, Pla J. Characterization of a Candida albicans Mutant Defective in All MAPKs Highlights the Major Role of Hog1 in the MAPK Signaling Network. J Fungi (Basel) 2020; 6:jof6040230. [PMID: 33080787 PMCID: PMC7711971 DOI: 10.3390/jof6040230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/16/2022] Open
Abstract
The success of Candida albicans as a pathogen relies on its ability to adapt and proliferate in different environmental niches. Pathways regulated by mitogen-activated protein kinases (MAPKs) are involved in sensing environmental conditions and developing an accurate adaptive response. Given the frequent cooperative roles of these routes in cellular functions, we have generated mutants defective in all combinations of the four described MAPKs in C. albicans and characterized its phenotype regarding sensitiveness to specific drugs, morphogenesis and interaction with host immune cells. We demonstrate that all MAPKs are dispensable in this yeast as a mutant defective in Cek1, Cek2, Mkc1 and Hog1 is viable although highly sensitive to oxidative and osmotic stress, displaying a specific pattern of sensitivity to antifungals. By comparing its phenotype with single, double and triple combinations of MAPK-deletion mutants we were able to unveil a Cek1-independent mechanism for Hog1 resistance to Congo red, and confirm the predominant effect of Hog1 on oxidative and osmotic adaptation. The quadruple mutant produces filaments under non-inducing conditions, but is unable to develop chlamydospores. Furthermore, cek1 cek2 mkc1 hog1 cells switch to the opaque state at high frequency, which is blocked by the ectopic expression of HOG1 suggesting a role of this kinase for phenotypic switching.
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Affiliation(s)
- Inês Correia
- iBiMED-Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Agra do Crasto, 3810-193 Aveiro, Portugal
- Correspondence: (I.C.); (J.P.); Tel.: +351-234-370-213 (I.C.); +34-913-941-617 (J.P.)
| | - Duncan Wilson
- Medical Research Council Centre for Medical Mycology, School of Biosciences, University of Exeter, Exeter EX4 4QD, UK;
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knoell-Institute, Beutenbergstraße 11A, 07745 Jena, Germany;
- Institute of Microbiology, Friedrich Schiller University, Neugasse 25, 07743 Jena, Germany
| | - Jesús Pla
- Departamento de Microbiología y Parasitología-IRYCIS, Facultad de Farmacia, Universidad Complutense de Madrid, Avda. Ramón y Cajal s/n, 28040 Madrid, Spain
- Correspondence: (I.C.); (J.P.); Tel.: +351-234-370-213 (I.C.); +34-913-941-617 (J.P.)
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25
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Wang Q, Sun M, Zhang Y, Song Z, Zhang S, Zhang Q, Xu J, Liu H. Extensive chromosomal rearrangements and rapid evolution of novel effector superfamilies contribute to host adaptation and speciation in the basal ascomycetous fungi. MOLECULAR PLANT PATHOLOGY 2020; 21:330-348. [PMID: 31916390 PMCID: PMC7036362 DOI: 10.1111/mpp.12899] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/06/2019] [Accepted: 11/28/2019] [Indexed: 05/11/2023]
Abstract
The basal ascomycetes in genus Taphrina have strict host specificity and coevolution with their host plants, making them appealing models for studying the genomic basis of ecological divergence and host adaption. We therefore performed genome sequencing and comparative genomics of different Taphrina species with distinct host ranges to reveal their evolution. We identified frequent chromosomal rearrangements and highly dynamic lineage-specific (LS) genomic regions in Taphrina genomes. The LS regions occur at the flanking regions of chromosomal breakpoints, and are greatly enriched for DNA repeats, non-core genes, and in planta up-regulated genes. Furthermore, we identified hundreds of candidate secreted effector proteins (CSEPs) that are commonly organized in gene clusters that form distinct AT-rich isochore-like regions. Nearly half of the CSEPs constitute two novel superfamilies with modular structures unique to Taphrina. These CSEPs are commonly up-regulated during infection, enriched in the LS regions, evolved faster, and underwent extensive gene gain and loss in different species. In addition to displaying signatures of positive selection, functional characterization of selected CSEP genes confirmed their roles in suppression of plant defence responses. Overall, our results showed that extensive chromosomal rearrangements and rapidly evolving CSEP superfamilies play important roles in speciation and host adaptation in the early-branching ascomycetous fungi.
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Affiliation(s)
- Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Manli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Yimei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Zhenzhen Song
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Shijie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Qiang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Jin‐Rong Xu
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteINUSA
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
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26
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Usher J. The Mechanisms of Mating in Pathogenic Fungi-A Plastic Trait. Genes (Basel) 2019; 10:E831. [PMID: 31640207 PMCID: PMC6826560 DOI: 10.3390/genes10100831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/30/2019] [Accepted: 10/17/2019] [Indexed: 01/20/2023] Open
Abstract
The impact of fungi on human and plant health is an ever-increasing issue. Recent studies have estimated that human fungal infections result in an excess of one million deaths per year and plant fungal infections resulting in the loss of crop yields worth approximately 200 million per annum. Sexual reproduction in these economically important fungi has evolved in response to the environmental stresses encountered by the pathogens as a method to target DNA damage. Meiosis is integral to this process, through increasing diversity through recombination. Mating and meiosis have been extensively studied in the model yeast Saccharomyces cerevisiae, highlighting that these mechanisms have diverged even between apparently closely related species. To further examine this, this review will inspect these mechanisms in emerging important fungal pathogens, such as Candida, Aspergillus, and Cryptococcus. It shows that both sexual and asexual reproduction in these fungi demonstrate a high degree of plasticity.
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Affiliation(s)
- Jane Usher
- Medical Research Council Centre for Medical Mycology, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, UK.
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