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Geremia N, Giovagnorio F, Colpani A, De Vito A, Caruana G, Meloni MC, Madeddu G, Panese S, Parisi SG. What do We Know about Cryptic Aspergillosis? Microorganisms 2024; 12:886. [PMID: 38792716 PMCID: PMC11124275 DOI: 10.3390/microorganisms12050886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Cryptic Aspergillus species are increasingly recognized as pathogens involved in human disease. They are ubiquitarian fungi with high tenacity in their environment and can express various resistance mechanisms, often due to exposure to antifungal agents employed in agriculture and farming. The identification of such species is increasing thanks to molecular techniques, and a better description of this type of pathogen is granted. Nevertheless, the number of species and their importance in the clinical setting still need to be well studied. Furthermore, their cross-sectional involvement in animal disease, plants, and human activities requires a multidisciplinary approach involving experts from various fields. This comprehensive review aims to provide a sharp vision of the cryptic Aspergillus species, from the importance of correct identification to the better management of the infections caused by these pathogens. The review also accentuates the importance of the One Health approach for this kind of microorganism, given the interconnection between environmental exposure and aspergillosis, embracing transversely the multidisciplinary process for managing the cryptic Aspergillus species. The paper advocates the need for improving knowledge in this little-known species, given the burden of economic and health implications related to the diffusion of these bugs.
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Affiliation(s)
- Nicholas Geremia
- Unit of Infectious Diseases, Department of Clinical Medicine, Ospedale Dell’Angelo, 30174 Venice, Italy;
- Unit of Infectious Diseases, Department of Clinical Medicine, Ospedale Civile “S.S. Giovanni e Paolo”, 30122 Venice, Italy
| | - Federico Giovagnorio
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (F.G.); (S.G.P.)
| | - Agnese Colpani
- Unit of Infectious Diseases, Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (A.D.V.); (M.C.M.); (G.M.)
| | - Andrea De Vito
- Unit of Infectious Diseases, Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (A.D.V.); (M.C.M.); (G.M.)
- Biomedical Science Department, School in Biomedical Science, University of Sassari, 07100 Sassari, Italy
| | - Giorgia Caruana
- Department of Laboratory Medicine and Pathology, Institute of microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland;
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
| | - Maria Chiara Meloni
- Unit of Infectious Diseases, Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (A.D.V.); (M.C.M.); (G.M.)
| | - Giordano Madeddu
- Unit of Infectious Diseases, Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (A.D.V.); (M.C.M.); (G.M.)
| | - Sandro Panese
- Unit of Infectious Diseases, Department of Clinical Medicine, Ospedale Dell’Angelo, 30174 Venice, Italy;
- Unit of Infectious Diseases, Department of Clinical Medicine, Ospedale Civile “S.S. Giovanni e Paolo”, 30122 Venice, Italy
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Celia-Sanchez BN, Mangum B, Gómez Londoño LF, Wang C, Shuman B, Brewer MT, Momany M. Pan-azole- and multi-fungicide-resistant Aspergillus fumigatus is widespread in the United States. Appl Environ Microbiol 2024; 90:e0178223. [PMID: 38557086 PMCID: PMC11022549 DOI: 10.1128/aem.01782-23] [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: 10/06/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Aspergillus fumigatus is an important global fungal pathogen of humans. Azole drugs are among the most effective treatments for A. fumigatus infection. Azoles are also widely used in agriculture as fungicides against fungal pathogens of crops. Azole-resistant A. fumigatus has been increasing in Europe and Asia for two decades where clinical resistance is thought to be driven by agricultural use of azole fungicides. The most prevalent mechanisms of azole resistance in A. fumigatus are tandem repeats (TR) in the cyp51A promoter coupled with mutations in the coding region which result in resistance to multiple azole drugs (pan-azole resistance). Azole-resistant A. fumigatus has been isolated from patients in the United States (U.S.), but little is known about its environmental distribution. To better understand the distribution of azole-resistant A. fumigatus in the U.S., we collected isolates from agricultural sites in eight states and tested 202 isolates for sensitivity to azoles. We found azole-resistant A. fumigatus in agricultural environments in seven states showing that it is widespread in the U.S. We sequenced environmental isolates representing the range of U.S. sample sites and compared them with publicly available environmental worldwide isolates in phylogenetic, principal component, and ADMIXTURE analyses. We found worldwide isolates fell into three clades, and TR-based pan-azole resistance was largely in a single clade that was strongly associated with resistance to multiple agricultural fungicides. We also found high levels of gene flow indicating recombination between clades highlighting the potential for azole-resistance to continue spreading in the U.S.IMPORTANCEAspergillus fumigatus is a fungal pathogen of humans that causes over 250,000 invasive infections each year. It is found in soils, plant debris, and compost. Azoles are the first line of defense antifungal drugs against A. fumigatus. Azoles are also used as agricultural fungicides to combat other fungi that attack plants. Azole-resistant A. fumigatus has been a problem in Europe and Asia for 20 years and has recently been reported in patients in the United States (U.S.). Until this study, we did not know much about azole-resistant A. fumigatus in agricultural settings in the U.S. In this study, we isolated azole-resistant A. fumigatus from multiple states and compared it to isolates from around the world. We show that A. fumigatus which is resistant to azoles and to other strictly agricultural fungicides is widespread in the U.S.
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Affiliation(s)
| | - B. Mangum
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | | | - C. Wang
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - B. Shuman
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - M. T. Brewer
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - M. Momany
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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Steenwyk JL, Balamurugan C, Raja HA, Gonçalves C, Li N, Martin F, Berman J, Oberlies NH, Gibbons JG, Goldman GH, Geiser DM, Houbraken J, Hibbett DS, Rokas A. Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus. Microbiol Spectr 2024; 12:e0398023. [PMID: 38445873 PMCID: PMC10986620 DOI: 10.1128/spectrum.03980-23] [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: 11/20/2023] [Accepted: 02/18/2024] [Indexed: 03/07/2024] Open
Abstract
Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus Aspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly available Aspergillus genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.
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Affiliation(s)
- Jacob L. Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Charu Balamurugan
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Carla Gonçalves
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Ningxiao Li
- Department of Plant Pathology, University of California, Davis, California, USA
- USDA-ARS, Salinas, California, USA
| | | | - Judith Berman
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Gustavo H. Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - David M. Geiser
- Department of Plant Pathology and Environmental Microbiology, Penn State University, University Park, Pennsylvania, USA
| | - Jos Houbraken
- Food and Indoor Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - David S. Hibbett
- Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg, Heidelberg, Germany
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Elalouf A, Elalouf H, Rosenfeld A. Modulatory immune responses in fungal infection associated with organ transplant - advancements, management, and challenges. Front Immunol 2023; 14:1292625. [PMID: 38143753 PMCID: PMC10748506 DOI: 10.3389/fimmu.2023.1292625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Organ transplantation stands as a pivotal achievement in modern medicine, offering hope to individuals with end-stage organ diseases. Advancements in immunology led to improved organ transplant survival through the development of immunosuppressants, but this heightened susceptibility to fungal infections with nonspecific symptoms in recipients. This review aims to establish an intricate balance between immune responses and fungal infections in organ transplant recipients. It explores the fundamental immune mechanisms, recent advances in immune response dynamics, and strategies for immune modulation, encompassing responses to fungal infections, immunomodulatory approaches, diagnostics, treatment challenges, and management. Early diagnosis of fungal infections in transplant patients is emphasized with the understanding that innate immune responses could potentially reduce immunosuppression and promise efficient and safe immuno-modulating treatments. Advances in fungal research and genetic influences on immune-fungal interactions are underscored, as well as the potential of single-cell technologies integrated with machine learning for biomarker discovery. This review provides a snapshot of the complex interplay between immune responses and fungal infections in organ transplantation and underscores key research directions.
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Affiliation(s)
- Amir Elalouf
- Department of Management, Bar-Ilan University, Ramat Gan, Israel
| | - Hadas Elalouf
- Information Science Department, Bar-Ilan University, Ramat Gan, Israel
| | - Ariel Rosenfeld
- Information Science Department, Bar-Ilan University, Ramat Gan, Israel
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Martins C, Piontkivska D, Mil-Homens D, Guedes P, Jorge JMP, Brinco J, Bárria C, Santos ACF, Barras R, Arraiano C, Fialho A, Goldman GH, Silva Pereira C. Increased Production of Pathogenic, Airborne Fungal Spores upon Exposure of a Soil Mycobiota to Chlorinated Aromatic Hydrocarbon Pollutants. Microbiol Spectr 2023; 11:e0066723. [PMID: 37284774 PMCID: PMC10434042 DOI: 10.1128/spectrum.00667-23] [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: 02/13/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023] Open
Abstract
Organic pollutants are omnipresent and can penetrate all environmental niches. We evaluated the hypothesis that short-term (acute) exposure to aromatic hydrocarbon pollutants could increase the potential for fungal virulence. Specifically, we analyzed whether pentachlorophenol and triclosan pollution results in the production of airborne fungal spores with greater virulence than those derived from an unpolluted (Control) condition. Each pollutant altered the composition of the community of airborne spores compared to the control, favoring an increase in strains with in vivo infection capacity (the wax moth Galleria mellonella was used as an infection model). Fungi subsisting inside larvae at 72 h postinjection with airborne spore inocula collected in polluted and unpolluted conditions exhibited comparable diversity (mainly within Aspergillus fumigatus). Several virulent Aspergillus strains were isolated from larvae infected with the airborne spores produced in a polluted environment. Meanwhile, strains isolated from larvae injected with spores from the control, including one A. fumigatus strain, showed no virulence. Potential pathogenicity increased when two Aspergillus virulent strains were assembled, suggesting the existence of synergisms that impact pathogenicity. None of the observed taxonomic or functional traits could separate the virulent from the avirulent strains. Our study emphasizes pollution stress as a possible driver of phenotypic adaptations that increase Aspergillus pathogenicity, as well as the need to better understand the interplay between pollution and fungal virulence. IMPORTANCE Fungi colonizing soil and organic pollutants often meet. The consequences of this encounter constitute an outstanding question. We scrutinized the potential for virulence of airborne fungal spores produced under unpolluted and polluted scenarios. The airborne spores showed increased diversity of strains with higher infection capacity in Galleria mellonella whenever pollution is present. Inside the larvae injected with either airborne spore community, the surviving fungi demonstrated a similar diversity, mainly within Aspergillus fumigatus. However, the isolated Aspergillus strains greatly differ since virulence was only observed for those associated with a polluted environment. The interplay between pollution and fungal virulence still hides many unresolved questions, but the encounter is costly: pollution stress promotes phenotypic adaptations that may increase Aspergillus pathogenicity.
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Affiliation(s)
- Celso Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Daryna Piontkivska
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Dalila Mil-Homens
- Institute for Bioengineering and Biosciences and Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Paula Guedes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- CENSE (Center for Environmental and Sustainability Research)/CHANGE (Global Change and Sustainability Institute), NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - João M. P. Jorge
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - João Brinco
- CENSE (Center for Environmental and Sustainability Research)/CHANGE (Global Change and Sustainability Institute), NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Cátia Bárria
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ariana C. F. Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ricardo Barras
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Arsénio Fialho
- Institute for Bioengineering and Biosciences and Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Gustavo H. Goldman
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Bosetti D, Neofytos D. Invasive Aspergillosis and the Impact of Azole-resistance. CURRENT FUNGAL INFECTION REPORTS 2023; 17:1-10. [PMID: 37360857 PMCID: PMC10024029 DOI: 10.1007/s12281-023-00459-z] [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: 03/04/2023] [Indexed: 06/28/2023]
Abstract
Purpose of Review IA (invasive aspergillosis) caused by azole-resistant strains has been associated with higher clinical burden and mortality rates. We review the current epidemiology, diagnostic, and therapeutic strategies of this clinical entity, with a special focus on patients with hematologic malignancies. Recent Findings There is an increase of azole resistance in Aspergillus spp. worldwide, probably due to environmental pressure and the increase of long-term azole prophylaxis and treatment in immunocompromised patients (e.g., in hematopoietic stem cell transplant recipients). The therapeutic approaches are challenging, due to multidrug-resistant strains, drug interactions, side effects, and patient-related conditions. Summary Rapid recognition of resistant Aspergillus spp. strains is fundamental to initiate an appropriate antifungal regimen, above all for allogeneic hematopoietic cell transplantation recipients. Clearly, more studies are needed in order to better understand the resistance mechanisms and optimize the diagnostic methods to identify Aspergillus spp. resistance to the existing antifungal agents/classes. More data on the susceptibility profile of Aspergillus spp. against the new classes of antifungal agents may allow for better treatment options and improved clinical outcomes in the coming years. In the meantime, continuous surveillance studies to monitor the prevalence of environmental and patient prevalence of azole resistance among Aspergillus spp. is absolutely crucial.
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Affiliation(s)
- Davide Bosetti
- Division of Infectious Diseases, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, Geneva, Switzerland
| | - Dionysios Neofytos
- Division of Infectious Diseases, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, Geneva, Switzerland
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Occurrence of Aflatoxins and Ochratoxin A during Merkén Pepper Powder Production in Chile. Foods 2022; 11:foods11233843. [PMID: 36496651 PMCID: PMC9739129 DOI: 10.3390/foods11233843] [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: 08/27/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
Abstract
Berry fruits of Capsicum annuum L. cv. "Cacho de Cabra" are used for the manufacture of a traditional pepper powder known as Merkén. In the present study, aflatoxins (AFs) and ochratoxin A (OTA) contamination in berry fruits of C. annuum was determined at harvest, drying, and smoking stages of Merkén production, in cumin and coriander seeds used as Merkén ingredients, and in the final packaged Merkén produced by local farmers. Additionally, Merkén samples from local markets in the region of La Araucanía (Chile) were also evaluated. Chromatographic analysis was based on a qualitative method. AFs and OTA were not detected on pepper pods and seeds. There was no detection of AFs and OTA on cultured Aspergillus and Penicillium strains isolated from pepper pods, cumin and coriander seeds and Merkén. The lack of AFs/OTA-producers among the isolated fungal species can explain and support the absence of contamination in pepper pods. In contrast, the AFB1 was detected in 75% of Merkén obtained from farmers and 46% of Merkén samples purchased from local markets; while OTA was detected in 100% of Merkén samples obtained from farmers and local markets. In the Merkén production chain, the harvest and post-harvest are key stages for fungal growth while the commercialization stage is highly susceptible to AFs and OTA contamination.
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Celia-Sanchez BN, Mangum B, Brewer M, Momany M. Analysis of Cyp51 protein sequences shows 4 major Cyp51 gene family groups across fungi. G3 (BETHESDA, MD.) 2022; 12:jkac249. [PMID: 36130263 PMCID: PMC9635630 DOI: 10.1093/g3journal/jkac249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Azole drugs target fungal sterol biosynthesis and are used to treat millions of human fungal infections each year. Resistance to azole drugs has emerged in multiple fungal pathogens including Candida albicans, Cryptococcus neoformans, Histoplasma capsulatum, and Aspergillus fumigatus. The most well-studied resistance mechanism in A. fumigatus arises from missense mutations in the coding sequence combined with a tandem repeat in the promoter of cyp51A, which encodes a cytochrome P450 enzyme in the fungal sterol biosynthesis pathway. Filamentous members of Ascomycota such as A. fumigatus have either 1 or 2 of 3 Cyp51 paralogs (Cyp51A, Cyp51B, and Cyp51C). Most previous research in A. fumigatus has focused on Cyp51A due to its role in azole resistance. We used the A. fumigatus Cyp51A protein sequence as the query in database searches to identify Cyp51 proteins across fungi. We found 435 Cyp51 proteins in 295 species spanning from early-diverging fungi (Blastocladiomycota, Chytridiomycota, Zoopagomycota, and Mucormycota) to late-diverging fungi (Ascomycota and Basidiomycota). We found these sequences formed 4 major Cyp51 groups: Cyp51, Cyp51A, Cyp51B, and Cyp51C. Surprisingly, we found all filamentous Ascomycota had a Cyp51B paralog, while only 50% had a Cyp51A paralog. We created maximum likelihood trees to investigate the evolution of Cyp51 in fungi. Our results suggest Cyp51 is present in all fungi with 3 paralogs emerging in Pezizomycotina, including Cyp51C which appears to have diverged from the progenitor of the Cyp51A and Cyp51B groups.
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Affiliation(s)
| | - Brandon Mangum
- Department of Plant Biology, University of Georgia, Athens, GA 30606, USA
| | - Marin Brewer
- Department of Plant Pathology, University of Georgia, Athens, GA 30606, USA
| | - Michelle Momany
- Department of Plant Biology, University of Georgia, Athens, GA 30606, USA
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Brown A, Mead ME, Steenwyk JL, Goldman GH, Rokas A. Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:802494. [PMID: 36866034 PMCID: PMC9977105 DOI: 10.3389/ffunb.2022.802494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/09/2022] [Indexed: 11/13/2022]
Abstract
Invasive aspergillosis is a deadly fungal disease; more than 400,000 patients are infected worldwide each year and the mortality rate can be as high as 50-95%. Of the ~450 species in the genus Aspergillus only a few are known to be clinically relevant, with the major pathogen Aspergillus fumigatus being responsible for ~50% of all invasive mold infections. Genomic comparisons between A. fumigatus and other Aspergillus species have historically focused on protein-coding regions. However, most A. fumigatus genes, including those that modulate its virulence, are also present in other pathogenic and non-pathogenic closely related species. Our hypothesis is that differential gene regulation - mediated through the non-coding regions upstream of genes' first codon - contributes to A. fumigatus pathogenicity. To begin testing this, we compared non-coding regions upstream of the first codon of single-copy orthologous genes from the two A. fumigatus reference strains Af293 and A1163 and eight closely related Aspergillus section Fumigati species. We found that these non-coding regions showed extensive sequence variation and lack of homology across species. By examining the evolutionary rates of both protein-coding and non-coding regions in a subset of orthologous genes with highly conserved non-coding regions across the phylogeny, we identified 418 genes, including 25 genes known to modulate A. fumigatus virulence, whose non-coding regions exhibit a different rate of evolution in A. fumigatus. Examination of sequence alignments of these non-coding regions revealed numerous instances of insertions, deletions, and other types of mutations of at least a few nucleotides in A. fumigatus compared to its close relatives. These results show that closely related Aspergillus species that vary greatly in their pathogenicity exhibit extensive non-coding sequence variation and identify numerous changes in non-coding regions of A. fumigatus genes known to contribute to virulence.
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Affiliation(s)
- Alec Brown
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Matthew E. Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
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Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus. mBio 2022; 13:e0151922. [PMID: 35766381 PMCID: PMC9426589 DOI: 10.1128/mbio.01519-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aspergillus fumigatus is both an environmental saprobe and an opportunistic human fungal pathogen. Knowledge of genomic variation across A. fumigatus isolates is essential for understanding the evolution of pathogenicity, virulence, and resistance to antifungal drugs. Here, we investigated 206 A. fumigatus isolates (133 clinical and 73 environmental isolates), aiming to identify genes with variable presence across isolates and test whether this variation was related to the clinical or environmental origin of isolates. The PanOrtho genome of A. fumigatus consists of 13,085 ortholog groups, of which 7,773 (59.4%) are shared by all isolates (core groups) and 5,312 (40.6%) vary in their gene presence across isolates (accessory groups plus singletons). Despite differences in the distribution of orthologs across all isolates, no significant differences were observed among clinical versus environmental isolates when phylogeny was accounted for. Orthologs that differ in their distribution across isolates tend to occur at low frequency and/or be restricted to specific isolates; thus, the degree of genomic conservation between orthologs of A. fumigatus is high. These results suggest that differences in the distribution of orthologs within A. fumigatus cannot be associated with the clinical or environmental origin of isolates. IMPORTANCE Aspergillus fumigatus is a cosmopolitan species of fungus responsible for thousands of cases of invasive disease annually. Clinical and environmental isolates of A. fumigatus exhibit extensive phenotypic differences, including differences related to virulence and antifungal drug resistance. A comprehensive survey of the genomic diversity present in A. fumigatus and its relationship to the clinical or environmental origin of isolates can contribute to the prediction of the mechanisms of evolution and infection of the species. Our results suggest that there is no significant variation in ortholog distribution between clinical and environmental isolates when accounting for evolutionary history. The work supports the hypothesis that environmental and clinical isolates of A. fumigatus do not differ in their gene contents.
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Using genomics to understand the mechanisms of virulence and drug resistance in fungal pathogens. Biochem Soc Trans 2022; 50:1259-1268. [PMID: 35713390 PMCID: PMC9246328 DOI: 10.1042/bst20211123] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 02/06/2023]
Abstract
Fungal pathogens pose an increasingly worrying threat to human health, food security and ecosystem diversity. To tackle fungal infections and improve current diagnostic and therapeutic tools it is necessary to understand virulence and antifungal drug resistance mechanisms in diverse species. Recent advances in genomics approaches have provided a suitable framework to understand these phenotypes, which ultimately depend on genetically encoded determinants. In this work, we review how the study of genome sequences has been key to ascertain the bases of virulence and drug resistance traits. We focus on the contribution of comparative genomics, population genomics and directed evolution studies. In addition, we discuss how different types of genomic mutations (small or structural variants) contribute to intraspecific differences in virulence or drug resistance. Finally, we review current challenges in the field and anticipate future directions to solve them. In summary, this work provides a short overview of how genomics can be used to understand virulence and drug resistance in fungal pathogens.
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Rokas A. Evolution of the human pathogenic lifestyle in fungi. Nat Microbiol 2022; 7:607-619. [PMID: 35508719 PMCID: PMC9097544 DOI: 10.1038/s41564-022-01112-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/25/2022] [Indexed: 02/07/2023]
Abstract
Fungal pathogens cause more than a billion human infections every year, resulting in more than 1.6 million deaths annually. Understanding the natural history and evolutionary ecology of fungi is helping us understand how disease-relevant traits have repeatedly evolved. Different types and mechanisms of genetic variation have contributed to the evolution of fungal pathogenicity and specific genetic differences distinguish pathogens from non-pathogens. Insights into the traits, genetic elements, and genetic and ecological mechanisms that contribute to the evolution of fungal pathogenicity are crucial for developing strategies to both predict emergence of fungal pathogens and develop drugs to combat them.
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Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
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Nargesi S, Jafarzadeh J, Najafzadeh MJ, Nouripour-Sisakht S, Haghani I, Abastabar M, Ilkit M, Hedayati MT. Molecular identification and antifungal susceptibility of clinically relevant and cryptic species of Aspergillus sections Flavi and Nigri. J Med Microbiol 2022; 71. [PMID: 35451946 DOI: 10.1099/jmm.0.001480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Introduction. Aspergillus sections Flavi and Nigri comprise clinically relevant and cryptic species that differ significantly in drug susceptibility, meaning that effective treatment depends on correct species identification.Hypothesis/Gap Statement. There are no comprehensive data for molecular identification and antifungal susceptibility testing (AFST) of clinically relevant and cryptic species of Aspergillus sections Flavi and Nigri as the main agents of invasive and non-invasive aspergillosis in Iran. We aimed to perform molecular identification and AFST of 213 clinical Aspergillus isolates belonging to sections Flavi and Nigri. Molecular identification of isolates was performed using sequencing of the β-tubulin gene and in vitro AFST was conducted according to the Clinical and Laboratory Standards Institute (CLSI) M38-A3 guidelines.Results. The most common isolates in sections Flavi and Nigri were Aspergillus flavus (110/113, 97.3 %) and Aspergillus tubingensis (49/100, 49.0 %), respectively. A total of 62/213 (29.1 %) isolates belonging to cryptic species were identified; among them, A. tubingensis was the most prevalent (49/62, 79.0%). Aspergillus flavus and A. niger isolates that responded to the minimum inhibitory concentrations (MICs) of itraconazole above the epidemiological cutoff values were the most frequently detected: 8/110 (7.3 %) and 3/41 (7.3 %), respectively. In section Flavi, Aspergillus alliaceus responded to amphotericin B at a high MIC (>16 µg mL-1) and in section Nigri, one of the three Aspergillus luchuensis/awamori isolates responded to itraconazole at an MIC >16 µg ml-1. Interestingly, for all Aspergillus welwitschiae isolates, the MIC50 and MIC90 of itraconazole were both 16 µg ml-1.Conclusion. A considerable presence of A. flavus and A. niger isolates showing non-wild-type responses to azoles in clinical cases of aspergillosis indicates the importance of classifying clinical Aspergillus isolates at the species level and performing antifungal susceptibility testing on the isolates, which would ensure appropriate treatment.
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Affiliation(s)
- Sanaz Nargesi
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Invasive Fungi Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Jalal Jafarzadeh
- Department of Medical Parasitology and Mycology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 9199-91766, Iran
| | | | - Iman Haghani
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Invasive Fungi Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Abastabar
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Invasive Fungi Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Mohammad Taghi Hedayati
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Invasive Fungi Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
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Li Q, Kong D, Wang Y, Dou Z, Huang W, Hu B, Dong F, Jiang H, Lv Q, Zheng Y, Ren Y, Liu G, Liu P, Jiang Y. Characterization of a rare clinical isolate of A. spinulosporus following a central nervous system infection. Microbes Infect 2022; 24:104973. [DOI: 10.1016/j.micinf.2022.104973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/08/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
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15
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Tateno M, Umeyama T, Inukai T, Takatsuka S, Hoshino Y, Yamagoe S, Yamagata Murayama S, Ishino K, Miyazaki Y. Examination of Cyp51A-Mediated Azole Resistance in Aspergillus lentulus Using CRISPR/Cas9 Genome Editing. Med Mycol J 2022; 63:27-35. [PMID: 35173102 DOI: 10.3314/mmj.21-00024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aspergillus lentulus was first reported in 2005 as a cryptic species of Aspergillus fumigatus, and since then, its resistance to azole drugs and the high mortality rate of infected individuals have emerged as problems. Although it has been reported that P450 14-α sterol demethylase (Cyp51) is involved in azole resistance in A. lentulus, the specific resistance mechanism has not been elucidated. In this study, we successfully introduced the entire A. fumigatus cyp51A gene into the cyp51A locus in A. lentulus using the CRISPR/Cas9 genome-editing system. The A. lentulus strains harboring A. fumigatus cyp51A showed reduced minimum inhibitory concentrations for itraconazole and voriconazole compared with those of the parent strain. This finding suggests that Cyp51A is involved in azole resistance in A. lentulus and may contribute to the elucidation of the mechanism of resistance to azole drugs via Cyp51A and to the development of new antifungal drugs. In addition, our successful application of the CRISPR/Cas9 system to A. lentulus opens the door to examination of other gene functions in this fungus.
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Affiliation(s)
- Madoka Tateno
- Division of Infection Control Sciences, Department of Clinical Pharmacy, School of Pharmacy, Showa University.,Department of Fungal Infection, National Institute of Infectious Diseases
| | - Takashi Umeyama
- Department of Fungal Infection, National Institute of Infectious Diseases
| | - Tatsuya Inukai
- Department of Fungal Infection, National Institute of Infectious Diseases.,Department of Microbiology, Tokyo Medical University
| | - Shogo Takatsuka
- Department of Fungal Infection, National Institute of Infectious Diseases
| | - Yasutaka Hoshino
- Department of Fungal Infection, National Institute of Infectious Diseases
| | - Satoshi Yamagoe
- Department of Fungal Infection, National Institute of Infectious Diseases
| | | | - Keiko Ishino
- Division of Infection Control Sciences, Department of Clinical Pharmacy, School of Pharmacy, Showa University
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Colabardini AC, Wang F, Dong Z, Pardeshi L, Rocha MC, Costa JH, dos Reis TF, Brown A, Jaber QZ, Fridman M, Fill T, Rokas A, Malavazi I, Wong KH, Goldman GH. Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin. Genetics 2022; 220:iyab183. [PMID: 34718550 PMCID: PMC8733440 DOI: 10.1093/genetics/iyab183] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/07/2021] [Indexed: 01/11/2023] Open
Abstract
Aspergillus fumigatus is the main causative agent of invasive pulmonary aspergillosis (IPA), a severe disease that affects immunosuppressed patients worldwide. The fungistatic drug caspofungin (CSP) is the second line of therapy against IPA but has increasingly been used against clinical strains that are resistant to azoles, the first line antifungal therapy. In high concentrations, CSP induces a tolerance phenotype with partial reestablishment of fungal growth called CSP paradoxical effect (CPE), resulting from a change in the composition of the cell wall. An increasing number of studies has shown that different isolates of A. fumigatus exhibit phenotypic heterogeneity, including heterogeneity in their CPE response. To gain insights into the underlying molecular mechanisms of CPE response heterogeneity, we analyzed the transcriptomes of two A. fumigatus reference strains, Af293 and CEA17, exposed to low and high CSP concentrations. We found that there is a core transcriptional response that involves genes related to cell wall remodeling processes, mitochondrial function, transmembrane transport, and amino acid and ergosterol metabolism, and a variable response related to secondary metabolite (SM) biosynthesis and iron homeostasis. Specifically, we show here that the overexpression of a SM pathway that works as an iron chelator extinguishes the CPE in both backgrounds, whereas iron depletion is detrimental for the CPE in Af293 but not in CEA17. We next investigated the function of the transcription factor CrzA, whose deletion was previously shown to result in heterogeneity in the CPE response of the Af293 and CEA17 strains. We found that CrzA constitutively binds to and modulates the expression of several genes related to processes involved in CSP tolerance and that crzA deletion differentially impacts the SM production and growth of Af293 and CEA17. As opposed to the ΔcrzACEA17 mutant, the ΔcrzAAf293 mutant fails to activate cell wall remodeling genes upon CSP exposure, which most likely severely affects its macrostructure and extinguishes its CPE. This study describes how heterogeneity in the response to an antifungal agent between A. fumigatus strains stems from heterogeneity in the function of a transcription factor and its downstream target genes.
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Affiliation(s)
- Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Fang Wang
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Zhiqiang Dong
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Lakhansing Pardeshi
- Faculty of Health Sciences, University of Macau, Macau 999078, China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau, 999078, China
| | - Marina Campos Rocha
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos CEP 13565-905, Brazil
| | - Jonas Henrique Costa
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo CEP 13083-970, Brazil
| | - Thaila Fernanda dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
| | - Alec Brown
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Qais Z Jaber
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Taicia Fill
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo CEP 13083-970, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos CEP 13565-905, Brazil
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau 999078, China
- Faculty of Health Sciences, Institute of Translational Medicine, University of Macau, Macau 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
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Colabardini AC, Wang F, Miao Z, Pardeshi L, Valero C, de Castro PA, Akiyama DY, Tan K, Nora LC, Silva-Rocha R, Marcet-Houben M, Gabaldón T, Fill T, Wong KH, Goldman GH. Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus. PLoS Genet 2022; 18:e1010001. [PMID: 35007279 PMCID: PMC8782537 DOI: 10.1371/journal.pgen.1010001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 01/21/2022] [Accepted: 12/17/2021] [Indexed: 12/21/2022] Open
Abstract
Invasive Pulmonary Aspergillosis, which is caused by the filamentous fungus Aspergillus fumigatus, is a life-threatening infection for immunosuppressed patients. Chromatin structure regulation is important for genome stability maintenance and has the potential to drive genome rearrangements and affect virulence and pathogenesis of pathogens. Here, we performed the first A. fumigatus global chromatin profiling of two histone modifications, H3K4me3 and H3K9me3, focusing on the two most investigated A. fumigatus clinical isolates, Af293 and CEA17. In eukaryotes, H3K4me3 is associated with active transcription, while H3K9me3 often marks silent genes, DNA repeats, and transposons. We found that H3K4me3 deposition is similar between the two isolates, while H3K9me3 is more variable and does not always represent transcriptional silencing. Our work uncovered striking differences in the number, locations, and expression of transposable elements between Af293 and CEA17, and the differences are correlated with H3K9me3 modifications and higher genomic variations among strains of Af293 background. Moreover, we further showed that the Af293 strains from different laboratories actually differ in their genome contents and found a frequently lost region in chromosome VIII. For one such Af293 variant, we identified the chromosomal changes and demonstrated their impacts on its secondary metabolites production, growth and virulence. Overall, our findings not only emphasize the influence of genome heterogeneity on A. fumigatus fitness, but also caution about unnoticed chromosomal variations among common laboratory strains.
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Affiliation(s)
- Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Fang Wang
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Intensive Care Unit, Biomedical Research Center, Shenzhen Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhengqiang Miao
- Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Lakhansing Pardeshi
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Clara Valero
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Daniel Yuri Akiyama
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Luisa Czamanski Nora
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafael Silva-Rocha
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Taicia Fill
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR of China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR of China
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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Bader O. Phylogenetic Distribution of csp1 Types in Aspergillus fumigatus and Their Correlates to Azole Antifungal Drug Resistance. Microbiol Spectr 2021; 9:e0121421. [PMID: 34787484 PMCID: PMC8597649 DOI: 10.1128/spectrum.01214-21] [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: 09/01/2021] [Accepted: 09/22/2021] [Indexed: 11/20/2022] Open
Abstract
In Aspergillus fumigatus, the repetitive region of the csp1 gene is one of the most frequently used loci for intraspecies typing of this human pathogenic mold. Using PCR amplification and Sanger sequencing of only a single marker, csp1 typing is readily available to most laboratories and highly reproducible. Here, I evaluate the usefulness of the csp1 marker for resistance detection and epidemiologic stratification among A. fumigatus isolates. After resolving nomenclature conflicts from published studies and adding novel csp1 types, the number of known types now adds up to 38. Their distribution mostly correlates with A. fumigatus population structure, and they are also meaningful for narrowly defined cases of azole resistance phenotypes. Isolates carrying the pandemic resistance allele TR34/L98H show signs of interclade crossing of strains with t02 or t04A, into the t11 clade. Furthermore, absolute differences in voriconazole MIC values between t02/t04B versus t11 TR34/L98H isolates indicate that the genetic background of resistance mutations may have a pivotal role in cross-resistance phenotypes and, thus, clinical outcome and environmental selection. Despite the general genetic similarity of isolates with identical csp1 types, outcrossing into other clades is also observed. The csp1 type alone, therefore, does not sufficiently discriminate genetic clades to be used as the sole marker in epidemiologic studies. IMPORTANCE Aspergillus fumigatus is a ubiquitously distributed saprophytic mold and a leading cause of invasive aspergillosis in human hosts. Pandemic azole-resistant strains have emerged on a global scale, which are thought to be propagated through use of azole-based fungicides in agriculture. To perform epidemiologic studies, genetic typing of large cohorts is key. Here, I evaluate the usefulness of the frequently used csp1 marker for resistance detection and epidemiologic stratification among A. fumigatus isolates. The phylogenetic distribution of csp1 types mostly correlates with A. fumigatus population structure and is also meaningful for narrowly defined cases of azole resistance phenotypes. Nevertheless, outcrossing of csp1 into other clades is also observed. The csp1 type alone, therefore, does not sufficiently discriminate genetic clades and should not be used as the sole marker in epidemiologic studies.
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Affiliation(s)
- Oliver Bader
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
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Watanabe K, Yaguchi T, Hirose D. Ubiquitous Distribution of Azole-Resistant Aspergillus fumigatus- Related Species in Outdoor Environments in Japan. Med Mycol J 2021; 62:71-78. [PMID: 34853253 DOI: 10.3314/mmj.21-00014] [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: 11/05/2022]
Abstract
Aspergillus fumigatus-related species are responsible for causing aspergillosis, which is a fatal infectious disease. Recently, there has been a series of reports of A. fumigatus-related species that are resistant to azole drugs used in clinical practice for the treatment of fungal infections. Some of these species have been isolated from outdoor environments. Testing the drug susceptibility of the strains from outdoor environments, therefore, is important. In this study, we isolated and cultured 72 strains of A. fumigatus-related species from the outdoor environment in Japan. The isolates identified via morphological observation and molecular phylogenetic analysis were Aspergillus felis, Aspergillus lentulus, Aspergillus pseudoviridinutans, Aspergillus udagawae, and Aspergillus wyomingensis. The results of the drug susceptibility testing revealed that A. felis (6 of 14 strains) and A. pseudoviridinutans (13 of 17 strains) were resistant to itraconazole (ITCZ), with 4 mg/L or higher minimum inhibitory concentrations (MICs). The voriconazole (VRCZ)-resistant strains with 4 mg/L or higher MICs were A. felis (14 of 14), A. lentulus (4 of 4), A. pseudoviridinutans (15 of 17), A. udagawae (23 of 34), A. wyomingensis (1 of 3), and A. pseudoviridinutans (1 of 3). Among them, A. felis (1 of 14) and A. pseudoviridinutans (7 of 17) demonstrated 8 mg/L or higher MICs for ITCZ and VRCZ. These results indicate that A. fumigatus-related species resistant to ITCZ and VRCZ are widely distributed in outdoor environments in Japan.
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Barber AE, Sae-Ong T, Kang K, Seelbinder B, Li J, Walther G, Panagiotou G, Kurzai O. Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection. Nat Microbiol 2021; 6:1526-1536. [PMID: 34819642 DOI: 10.1038/s41564-021-00993-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 10/08/2021] [Indexed: 12/25/2022]
Abstract
Aspergillus fumigatus is an environmental saprobe and opportunistic human fungal pathogen. Despite an estimated annual occurrence of more than 300,000 cases of invasive disease worldwide, a comprehensive survey of the genomic diversity present in A. fumigatus-including the relationship between clinical and environmental isolates and how this genetic diversity contributes to virulence and antifungal drug resistance-has been lacking. In this study we define the pan-genome of A. fumigatus using a collection of 300 globally sampled genomes (83 clinical and 217 environmental isolates). We found that 7,563 of the 10,907 unique orthogroups (69%) are core and present in all isolates and the remaining 3,344 show presence/absence of variation, representing 16-22% of the genome of each isolate. Using this large genomic dataset of environmental and clinical samples, we found an enrichment for clinical isolates in a genetic cluster whose genomes also contain more accessory genes, including genes coding for transmembrane transporters and proteins with iron-binding activity, and genes involved in both carbohydrate and amino-acid metabolism. Finally, we leverage the power of genome-wide association studies to identify genomic variation associated with clinical isolates and triazole resistance as well as characterize genetic variation in known virulence factors. This characterization of the genomic diversity of A. fumigatus allows us to move away from a single reference genome that does not necessarily represent the species as a whole and better understand its pathogenic versatility, ultimately leading to better management of these infections.
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Affiliation(s)
- Amelia E Barber
- Research Group Fungal Septomics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.,Junior Research Group Fungal Informatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Tongta Sae-Ong
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Kang Kang
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Bastian Seelbinder
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.,School of Data Science, City University of Hong Kong, Hong Kong, China
| | - Grit Walther
- National Reference Center for Invasive Fungal Infections (NRZMyk), Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Gianni Panagiotou
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany. .,Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China.
| | - Oliver Kurzai
- Research Group Fungal Septomics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany. .,National Reference Center for Invasive Fungal Infections (NRZMyk), Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany. .,Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany.
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Abstract
Azoles are the most commonly used clinical antifungal therapy and also play an important role in control of plant pathogens. Intrinsic resistance to the azole class of fungicides, which target lanosterol demethylase (CYP51), is observed in many fungal species; however, the mechanisms underpinning this phenomenon are unknown. In this study, 5 azole-resistant Penicillium isolates from patients attending the UK National Aspergillosis Centre that could not be morphologically identified to species level were analyzed by genome sequencing. The genomes and CYP51 paralogue structure from these isolates were compared with those of 46 representative fungal isolates to identify to species level and examine possible mechanisms of drug resistance. Analysis of CYP51 paralogues showed that azole-resistant isolates from this study (n = 2) and from public databases (n = 6) contained a new CYP51 paralogue, CYP51D, which was associated with azole resistance in 6/8 cases and never occurred in azole-sensitive species (46/46 tested). Furthermore, one isolate from this study and an azole-resistant Aspergillus fumigatiaffinis isolate were shown to encode a CYP51A paralogue, CYP51A2. Introduction of CYP51A2 to the closely related but azole-sensitive Aspergillus fumigatus resulted in azole resistance. The identification of novel CYP51A and CYP51D paralogues in resistant fungi and the observation that resistance to azoles can be conferred by introducing a CYP51A paralogue from a resistant species into an azole-sensitive species are a potentially important new azole resistance mechanism.
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22
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dos Santos RAC, Mead ME, Steenwyk JL, Rivero-Menéndez O, Alastruey-Izquierdo A, Goldman GH, Rokas A. Examining Signatures of Natural Selection in Antifungal Resistance Genes Across Aspergillus Fungi. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:723051. [PMID: 37744093 PMCID: PMC10512362 DOI: 10.3389/ffunb.2021.723051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/16/2021] [Indexed: 09/26/2023]
Abstract
Certain Aspergillus fungi cause aspergillosis, a set of diseases that typically affect immunocompromised individuals. Most cases of aspergillosis are caused by Aspergillus fumigatus, which infects millions of people annually. Some closely related so-called cryptic species, such as Aspergillus lentulus, can also cause aspergillosis, albeit at lower frequencies, and they are also clinically relevant. Few antifungal drugs are currently available for treating aspergillosis and there is increasing worldwide concern about the presence of antifungal drug resistance in Aspergillus species. Furthermore, isolates from both A. fumigatus and other Aspergillus pathogens exhibit substantial heterogeneity in their antifungal drug resistance profiles. To gain insights into the evolution of antifungal drug resistance genes in Aspergillus, we investigated signatures of positive selection in 41 genes known to be involved in drug resistance across 42 susceptible and resistant isolates from 12 Aspergillus section Fumigati species. Using codon-based site models of sequence evolution, we identified ten genes that contain 43 sites with signatures of ancient positive selection across our set of species. None of the sites that have experienced positive selection overlap with sites previously reported to be involved in drug resistance. These results identify sites that likely experienced ancient positive selection in Aspergillus genes involved in resistance to antifungal drugs and suggest that historical selective pressures on these genes likely differ from any current selective pressures imposed by antifungal drugs.
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Affiliation(s)
- Renato Augusto Corrêa dos Santos
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Matthew E. Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Olga Rivero-Menéndez
- Medical Mycology Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Alastruey-Izquierdo
- Medical Mycology Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Gustavo Henrique Goldman
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
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23
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Steenwyk JL, Mead ME, de Castro PA, Valero C, Damasio A, dos Santos RAC, Labella AL, Li Y, Knowles SL, Raja HA, Oberlies NH, Zhou X, Cornely OA, Fuchs F, Koehler P, Goldman GH, Rokas A. Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatus. Microbiol Spectr 2021; 9:e0001021. [PMID: 34106569 PMCID: PMC8552514 DOI: 10.1128/spectrum.00010-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 02/06/2023] Open
Abstract
The ongoing global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for coronavirus disease 2019 (COVID-19), first described in Wuhan, China. A subset of COVID-19 patients has been reported to have acquired secondary infections by microbial pathogens, such as opportunistic fungal pathogens from the genus Aspergillus. To gain insight into COVID-19-associated pulmonary aspergillosis (CAPA), we analyzed the genomes and characterized the phenotypic profiles of four CAPA isolates of Aspergillus fumigatus obtained from patients treated in the area of North Rhine-Westphalia, Germany. By examining the mutational spectrum of single nucleotide polymorphisms, insertion-deletion polymorphisms, and copy number variants among 206 genes known to modulate A. fumigatus virulence, we found that CAPA isolate genomes do not exhibit significant differences from the genome of the Af293 reference strain. By examining a number of factors, including virulence in an invertebrate moth model, growth in the presence of osmotic, cell wall, and oxidative stressors, secondary metabolite biosynthesis, and the MIC of antifungal drugs, we found that CAPA isolates were generally, but not always, similar to A. fumigatus reference strains Af293 and CEA17. Notably, CAPA isolate D had more putative loss-of-function mutations in genes known to increase virulence when deleted. Moreover, CAPA isolate D was significantly more virulent than the other three CAPA isolates and the A. fumigatus reference strains Af293 and CEA17, but similarly virulent to two other clinical strains of A. fumigatus. These findings expand our understanding of the genomic and phenotypic characteristics of isolates that cause CAPA. IMPORTANCE The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has already killed millions of people. COVID-19 patient outcome can be further complicated by secondary infections, such as COVID-19-associated pulmonary aspergillosis (CAPA). CAPA is caused by Aspergillus fungal pathogens, but there is little information about the genomic and phenotypic characteristics of CAPA isolates. We conducted genome sequencing and extensive phenotyping of four CAPA isolates of Aspergillus fumigatus from Germany. We found that CAPA isolates were often, but not always, similar to other reference strains of A. fumigatus across 206 genetic determinants of infection-relevant phenotypes, including virulence. For example, CAPA isolate D was more virulent than other CAPA isolates and reference strains in an invertebrate model of fungal disease, but similarly virulent to two other clinical strains. These results expand our understanding of COVID-19-associated pulmonary aspergillosis.
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Affiliation(s)
- Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Matthew E. Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Clara Valero
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - André Damasio
- Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas-SP, Brazil
| | - Renato A. C. dos Santos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Abigail L. Labella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Sonja L. Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Oliver A. Cornely
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Cologne, Germany
- University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- ZKS Köln, Clinical Trials Centre Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn‐Cologne, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Frieder Fuchs
- Faculty of Medicine, Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Philipp Koehler
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Cologne, Germany
- University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
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24
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Arastehfar A, Carvalho A, Houbraken J, Lombardi L, Garcia-Rubio R, Jenks J, Rivero-Menendez O, Aljohani R, Jacobsen I, Berman J, Osherov N, Hedayati M, Ilkit M, Armstrong-James D, Gabaldón T, Meletiadis J, Kostrzewa M, Pan W, Lass-Flörl C, Perlin D, Hoenigl M. Aspergillus fumigatus and aspergillosis: From basics to clinics. Stud Mycol 2021; 100:100115. [PMID: 34035866 PMCID: PMC8131930 DOI: 10.1016/j.simyco.2021.100115] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The airborne fungus Aspergillus fumigatus poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employed to treat aspergillosis. The global emergence of azole-resistant A. fumigatus isolates in clinic and environment, however, notoriously limits the therapeutic options of mould-active antifungals and potentially can be attributed to a mortality rate reaching up to 100 %. Although specific mutations in CYP 51A are the main cause of azole resistance, there is a new wave of azole-resistant isolates with wild-type CYP 51A genotype challenging the efficacy of the current diagnostic tools. Therefore, applications of whole-genome sequencing are increasingly gaining popularity to overcome such challenges. Prominent echinocandin tolerance, as well as liver and kidney toxicity posed by amphotericin B, necessitate a continuous quest for novel antifungal drugs to combat emerging azole-resistant A. fumigatus isolates. Animal models and the tools used for genetic engineering require further refinement to facilitate a better understanding about the resistance mechanisms, virulence, and immune reactions orchestrated against A. fumigatus. This review paper comprehensively discusses the current clinical challenges caused by A. fumigatus and provides insights on how to address them.
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Affiliation(s)
- A. Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - A. Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - L. Lombardi
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - R. Garcia-Rubio
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - J.D. Jenks
- Department of Medicine, University of California San Diego, San Diego, CA, 92103, USA
- Clinical and Translational Fungal-Working Group, University of California San Diego, La Jolla, CA, 92093, USA
| | - O. Rivero-Menendez
- Medical Mycology Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, 28222, Spain
| | - R. Aljohani
- Department of Infectious Diseases, Imperial College London, London, UK
| | - I.D. Jacobsen
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - J. Berman
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
| | - N. Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, 69978, Israel
| | - M.T. Hedayati
- Invasive Fungi Research Center/Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - M. Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey
| | | | - T. Gabaldón
- Life Sciences Programme, Supercomputing Center (BSC-CNS), Jordi Girona, Barcelona, 08034, Spain
- Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - J. Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - W. Pan
- Medical Mycology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - C. Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - D.S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - M. Hoenigl
- Department of Medicine, University of California San Diego, San Diego, CA, 92103, USA
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, 8036, Graz, Austria
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
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25
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Detection of azole resistance in Aspergillus fumigatus complex isolates using MALDI-TOF mass spectrometry. Clin Microbiol Infect 2021; 28:260-266. [PMID: 34147673 DOI: 10.1016/j.cmi.2021.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 01/24/2023]
Abstract
OBJECTIVES The main goal of this study was to accurately detect azole resistance in species of the Aspergillus fumigatus complex by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). METHODS Identification of isolates (n = 868) was done with MALDI-TOF MS using both commercial and in-house libraries. To determine azole susceptibility, the EUCAST E.Def. 9.3.2 method was applied as the reference standard. Identification of resistant isolates was confirmed by DNA sequence analysis. Protein spectra obtained by MALDI-TOF MS were analysed to differentiate species within the A. fumigatus complex and to detect azole-resistant A. fumigatus sensu stricto isolates. RESULTS Correct discrimination of A. fumigatus sensu stricto from cryptic species was accomplished in 100% of the cases applying principal component analysis (PCA) to protein spectra generated by MALDI-TOF MS. Furthermore, a specific peak (4586 m/z) was found to be present only in cryptic species. The application of partial least squares (PLS) discriminant analysis allowed 98.43% (±0.038) discrimination between susceptible and azole-resistant A. fumigatus sensu stricto isolates. Finally, based on PLS and SVM, A. fumigatus sensu stricto isolates with different cyp51A gene mutations were correctly clustered in 91.5% of the cases. CONCLUSIONS MALDI-TOF MS combined with peak analysis is a novel tool that allows the differentiation of A. fumigatus sensu stricto from other species within the A. fumigatus complex, as well as the detection of azole-resistant A. fumigatus sensu stricto. Although further studies are still needed, the results reported here show the great potential of MALDI-TOF and machine learning for the rapid detection of azole-resistant Aspergillus fumigatus isolates from clinical origins.
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Emergence of Triazole Resistance in Aspergillus spp. in Latin America. CURRENT FUNGAL INFECTION REPORTS 2021; 15:93-103. [PMID: 34025901 PMCID: PMC8132279 DOI: 10.1007/s12281-021-00418-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 11/26/2022]
Abstract
Purpose of Review Azole resistance in Aspergillus spp. is becoming a public health problem worldwide. However, data about this subject is lacking in Latin American countries. This review focuses in the epidemiology and molecular mechanisms of azole resistance in Aspergillus spp. emphasizing in Latin America. Data on Aspergillus fumigatus stands out because it is the most prevalent Aspergillus spp. pathogen. Recent Findings Azole resistance in Aspergillus spp. emergence was linked with intensive use of these antifungals both in the clinical setting and in the environment (as pesticides). Reports on azole-resistant A. fumigatus strains are being constantly published in different countries. Molecular mechanisms of resistance mainly involve substitution in the azole target (CYP51A) and/or overexpression of this gene. However, several other non-CYP51A-related mechanisms were described. Moreover, intrinsically resistant cryptic Aspergillus species are starting to be reported as human pathogens. Summary After a comprehensive literature review, it is clear that azole resistance in Aspergillus spp. is emerging in Latin America and perhaps it is underestimated. All the main molecular mechanisms of azole resistance were described in patients and/or environmental samples. Moreover, one of the molecular mechanisms was described only in South America. Cryptic intrinsic azole-resistant species are also described.
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Mead ME, Steenwyk JL, Silva LP, de Castro PA, Saeed N, Hillmann F, Goldman GH, Rokas A. An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi. Genetics 2021; 218:6263860. [PMID: 33944921 DOI: 10.1093/genetics/iyab066] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/20/2021] [Indexed: 11/12/2022] Open
Abstract
Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus Aspergillus. Roughly 70% of infections are caused by Aspergillus fumigatus, with the rest stemming from approximately a dozen other Aspergillus species. Several of these pathogens are closely related to A. fumigatus and belong in the same taxonomic section, section Fumigati. Pathogenic species are frequently most closely related to nonpathogenic ones, suggesting Aspergillus pathogenicity evolved multiple times independently. To understand the repeated evolution of Aspergillus pathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in section Fumigati, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and nonpathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified over 1700 genes whose evolutionary rate differed between pathogens and nonpathogens and dozens of genes whose rates differed between specific pathogens and the rest of the taxa. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and nonpathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity in Aspergillus involved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.
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Affiliation(s)
- Matthew E Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Lilian P Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Patrícia A de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Nauman Saeed
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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28
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Naicker SD, Magobo RE, Maphanga TG, Firacative C, van Schalkwyk E, Monroy-Nieto J, Bowers J, Engelthaler DM, Shuping L, Meyer W, Govender NP. Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005-2009. J Fungi (Basel) 2021; 7:jof7050338. [PMID: 33925754 PMCID: PMC8146981 DOI: 10.3390/jof7050338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/04/2023] Open
Abstract
In South Africa, Cryptococcus neoformans is the most common cause of adult meningitis. We performed multi locus sequence typing and fluconazole susceptibility testing of clinical C. neoformans isolates collected from 251 South African patients with cryptococcosis through national surveillance from 2005 to 2009. We examined the association between clinical characteristics of patients and genotype, and the effect of genotype on in-hospital mortality. We performed whole genome phylogenetic analysis of fifteen C. neoformans isolates with the molecular type VNB and tested their virulence in a Galleria mellonella model. Most isolates had the molecular type VNI (206/251, 82%), followed by VNII (25/251, 10%), VNB (15/251, 6%), and VNIV (5/251, 2%); 67 sequence types were identified. There were no differences in fluconazole minimum inhibitory concentration (MIC) values among molecular types and the majority of strains had low MIC values (MIC50 of 1 µg/mL and MIC90 of 4 µg/mL). Males were almost twice as likely of being infected with a non-VNI genotype (adjusted odds ratio [OR]: 1.65, 95% confidence interval [CI]: 0.25–10.99; p = 0.61). Compared to patients infected with a VNI genotype, those with a non-VNI genotype had a 50% reduced adjusted odds of dying in hospital (95% CI: 0.03–7.57; p = 0.62). However, for both these analyses, our estimates had wide confidence intervals spanning 1 with large p-values. Fifteen VNB strains were not as virulent in a G. mellonella larval model as the H99 reference strain. A majority of these VNB strains belonged to the VNBII clade and were very closely related by phylogenetic analysis.
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Affiliation(s)
- Serisha D. Naicker
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa
- Correspondence: ; Tel.: +27-11-555-0491
| | - Rindidzani E. Magobo
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
| | - Tsidiso G. Maphanga
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
| | - Carolina Firacative
- Studies in Translational Microbiology and Emerging Diseases (MICROS) Research Group, School of Medicine and Health Sciences, Universidad del Rosario, 111611 Bogota, Colombia;
| | - Erika van Schalkwyk
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
| | - Juan Monroy-Nieto
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; (J.M.-N.); (J.B.); (D.M.E.)
| | - Jolene Bowers
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; (J.M.-N.); (J.B.); (D.M.E.)
| | - David M. Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; (J.M.-N.); (J.B.); (D.M.E.)
| | - Liliwe Shuping
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia;
- Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW 2006, Australia
- Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Research and Educational Network, Westmead Hospital, Western Sydney Local Health District, Westmead, NSW 2145, Australia
| | - Nelesh P. Govender
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town 7701, South Africa
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Takahashi H, Umemura M, Ninomiya A, Kusuya Y, Shimizu M, Urayama SI, Watanabe A, Kamei K, Yaguchi T, Hagiwara D. Interspecies Genomic Variation and Transcriptional Activeness of Secondary Metabolism-Related Genes in Aspergillus Section Fumigati. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:656751. [PMID: 37744138 PMCID: PMC10512231 DOI: 10.3389/ffunb.2021.656751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/23/2021] [Indexed: 09/26/2023]
Abstract
Filamentous fungi produce various bioactive compounds that are biosynthesized by sets of proteins encoded in biosynthesis gene clusters (BGCs). For an unknown reason, many BGCs are transcriptionally silent in laboratory conditions, which has hampered the discovery of novel fungal compounds. The transcriptional reactiveness of fungal secondary metabolism is not fully understood. To gain the comprehensive view, we conducted comparative genomic and transcriptomic analyses of nine closely-related species of Aspergillus section Fumigati (A. fumigatus, A. fumigatiaffinis, A. novofumigatus, A. thermomutatus, A. viridinutans, A. pseudoviridinutans, A. lentulus, A. udagawae, and Neosartorya fischeri). For expanding our knowledge, we newly sequenced genomes of A. viridinutans and A. pseudoviridinutans, and reassembled and reannotated the previously released genomes of A. lentulus and A. udagawae. Between 34 and 84 secondary metabolite (SM) backbone genes were identified in the genomes of these nine respective species, with 8.7-51.2% being unique to the species. A total of 247 SM backbone gene types were identified in the nine fungi. Ten BGCs are shared by all nine species. Transcriptomic analysis using A. fumigatus, A. lentulus, A. udagawae, A. viridinutans, and N. fischeri was conducted to compare expression levels of all SM backbone genes in four different culture conditions; 32-83% of SM backbone genes in these species were not expressed in the tested conditions, which reconfirmed that large part of fungal SM genes are hard to be expressed. The species-unique SM genes of the five species were expressed with lower frequency (18.8% in total) than the SM genes that are conserved in all five species (56%). These results suggest that the expression tendency of BGCs is correlated with their interspecies distribution pattern. Our findings increase understanding of the evolutionary processes associated with the regulation of fungal secondary metabolism.
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Affiliation(s)
- Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
- Molecular Chirality Research Center, Chiba University, Chiba, Japan
- Plant Molecular Science Center, Chiba University, Chiba, Japan
| | - Maiko Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Akihiro Ninomiya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoko Kusuya
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Masaaki Shimizu
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Syun-ichi Urayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Akira Watanabe
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Katsuhiko Kamei
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, Chiba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
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Gu X, Hua YH, Zhang YD, Bao DI, Lv J, Hu HF. The Pathogenesis of Aspergillus fumigatus, Host Defense Mechanisms, and the Development of AFMP4 Antigen as a Vaccine. Pol J Microbiol 2021; 70:3-11. [PMID: 33815522 PMCID: PMC8008755 DOI: 10.33073/pjm-2021-003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Aspergillus fumigatus is one of the ubiquitous fungi with airborne conidia, which accounts for most aspergillosis cases. In immunocompetent hosts, the inhaled conidia are rapidly eliminated. However, immunocompromised or immunodeficient hosts are particularly vulnerable to most Aspergillus infections and invasive aspergillosis (IA), with mortality from 50% to 95%. Despite the improvement of antifungal drugs over the last few decades, the therapeutic effect for IA patients is still limited and does not provide significant survival benefits. The drawbacks of antifungal drugs such as side effects, antifungal drug resistance, and the high cost of antifungal drugs highlight the importance of finding novel therapeutic and preventive approaches to fight against IA. In this article, we systemically addressed the pathogenic mechanisms, defense mechanisms against A. fumigatus, the immune response, molecular aspects of host evasion, and vaccines' current development against aspergillosis, particularly those based on AFMP4 protein, which might be a promising antigen for the development of anti-A. fumigatus vaccines.
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Affiliation(s)
- Xiang Gu
- College of Law and Political Science, Nanjing University of Information Science and Technology, Nanjing, China.,The University of Hong Kong Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Yan-Hong Hua
- The University of Hong Kong Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Yang-Dong Zhang
- The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - D I Bao
- The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Jin Lv
- The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Hong-Fang Hu
- The PLA Rocket Force Characteristic Medical Center, Beijing, China
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Airway bacterial and fungal microbiome in chronic obstructive pulmonary disease. MEDICINE IN MICROECOLOGY 2021. [DOI: 10.1016/j.medmic.2021.100035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Aspergillus fumigatus and Its Allergenic Ribotoxin Asp f I: Old Enemies but New Opportunities for Urine-Based Detection of Invasive Pulmonary Aspergillosis Using Lateral-Flow Technology. J Fungi (Basel) 2020; 7:jof7010019. [PMID: 33396482 PMCID: PMC7823411 DOI: 10.3390/jof7010019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/17/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022] Open
Abstract
Invasive pulmonary aspergillosis (IPA) caused by Aspergillus fumigatus is a life-threatening lung disease of immunocompromised patients. Diagnosis currently relies on non-specific chest CT, culture of the fungus from invasive lung biopsy, and detection of the cell wall carbohydrate galactomannan (GM) in serum or in BAL fluids recovered during invasive bronchoscopy. Urine provides an ideal bodily fluid for the non-invasive detection of pathogen biomarkers, with current urine-based immunodiagnostics for IPA focused on GM. Surrogate protein biomarkers might serve to improve disease detection. Here, we report the development of a monoclonal antibody (mAb), PD7, which is specific to A. fumigatus and related species in the section Fumigati, and which binds to its 18 kDa ribotoxin Asp f I. Using PD7, we show that the protein is secreted during hyphal development, and so represents an ideal candidate for detecting invasive growth. We have developed a lateral-flow device (Afu-LFD®) incorporating the mAb which has a limit of detection of ~15 ng Asp f I/mL urine. Preliminary evidence of the test’s diagnostic potential is demonstrated with urine from a patient with acute lymphoid leukaemia with probable IPA. The Afu-LFD® therefore provides a potential novel opportunity for non-invasive urine-based detection of IPA caused by A. fumigatus.
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Steenwyk JL, Mead ME, de Castro PA, Valero C, Damasio A, dos Santos RAC, Labella AL, Li Y, Knowles SL, Raja HA, Oberlies NH, Zhou X, Cornely OA, Fuchs F, Koehler P, Goldman GH, Rokas A. Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.06.371971. [PMID: 33173866 PMCID: PMC7654854 DOI: 10.1101/2020.11.06.371971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ongoing global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) first described from Wuhan, China. A subset of COVID-19 patients has been reported to have acquired secondary infections by microbial pathogens, such as fungal opportunistic pathogens from the genus Aspergillus . To gain insight into COVID-19 associated pulmonary aspergillosis (CAPA), we analyzed the genomes and characterized the phenotypic profiles of four CAPA isolates of Aspergillus fumigatus obtained from patients treated in the area of North Rhine-Westphalia, Germany. By examining the mutational spectrum of single nucleotide polymorphisms, insertion-deletion polymorphisms, and copy number variants among 206 genes known to modulate A. fumigatus virulence, we found that CAPA isolate genomes do not exhibit major differences from the genome of the Af293 reference strain. By examining virulence in an invertebrate moth model, growth in the presence of osmotic, cell wall, and oxidative stressors, and the minimum inhibitory concentration of antifungal drugs, we found that CAPA isolates were generally, but not always, similar to A. fumigatus reference strains Af293 and CEA17. Notably, CAPA isolate D had more putative loss of function mutations in genes known to increase virulence when deleted (e.g., in the FLEA gene, which encodes a lectin recognized by macrophages). Moreover, CAPA isolate D was significantly more virulent than the other three CAPA isolates and the A. fumigatus reference strains tested. These findings expand our understanding of the genomic and phenotypic characteristics of isolates that cause CAPA.
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Affiliation(s)
- Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Matthew E. Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Clara Valero
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - André Damasio
- Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas-SP, Brazil
| | - Renato A. C. dos Santos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Abigail L. Labella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Sonja L. Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina 27402
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina 27402
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina 27402
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Oliver A. Cornely
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Cologne, Germany
- University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- ZKS Köln, Clinical Trials Centre Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn Cologne, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Frieder Fuchs
- Faculty of Medicine, Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Philipp Koehler
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Cologne, Germany
- University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
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Steenwyk JL, Mead ME, Knowles SL, Raja HA, Roberts CD, Bader O, Houbraken J, Goldman GH, Oberlies NH, Rokas A. Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species. Genetics 2020; 216:481-497. [PMID: 32817009 PMCID: PMC7536862 DOI: 10.1534/genetics.120.303549] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/01/2020] [Indexed: 02/07/2023] Open
Abstract
Aspergillus fumigatus is a major human pathogen. In contrast, Aspergillus fischeri and the recently described Aspergillus oerlinghausenensis, the two species most closely related to A. fumigatus, are not known to be pathogenic. Some of the genetic determinants of virulence (or "cards of virulence") that A. fumigatus possesses are secondary metabolites that impair the host immune system, protect from host immune cell attacks, or acquire key nutrients. To examine whether secondary metabolism-associated cards of virulence vary between these species, we conducted extensive genomic and secondary metabolite profiling analyses of multiple A. fumigatus, one A. oerlinghausenensis, and multiple A. fischeri strains. We identified two cards of virulence (gliotoxin and fumitremorgin) shared by all three species and three cards of virulence (trypacidin, pseurotin, and fumagillin) that are variable. For example, we found that all species and strains examined biosynthesized gliotoxin, which is known to contribute to virulence, consistent with the conservation of the gliotoxin biosynthetic gene cluster (BGC) across genomes. For other secondary metabolites, such as fumitremorgin, a modulator of host biology, we found that all species produced the metabolite but that there was strain heterogeneity in its production within species. Finally, species differed in their biosynthesis of fumagillin and pseurotin, both contributors to host tissue damage during invasive aspergillosis. A. fumigatus biosynthesized fumagillin and pseurotin, while A. oerlinghausenensis biosynthesized fumagillin and A. fischeri biosynthesized neither. These biochemical differences were reflected in sequence divergence of the intertwined fumagillin/pseurotin BGCs across genomes. These results delineate the similarities and differences in secondary metabolism-associated cards of virulence between a major fungal pathogen and its nonpathogenic closest relatives, shedding light onto the genetic and phenotypic changes associated with the evolution of fungal pathogenicity.
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Affiliation(s)
- Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Matthew E Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Sonja L Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina 27402
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina 27402
| | - Christopher D Roberts
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina 27402
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075, Germany
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-900 Brazil
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, North Carolina 27402
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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