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Gibbons JG, D’Avino P, Zhao S, Cox GW, Rinker DC, Fortwendel JR, Latge JP. Comparative Genomics Reveals a Single Nucleotide Deletion in pksP That Results in White-Spore Phenotype in Natural Variants of Aspergillus fumigatus. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:897954. [PMID: 37746219 PMCID: PMC10512363 DOI: 10.3389/ffunb.2022.897954] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/03/2022] [Indexed: 09/26/2023]
Abstract
Aspergillus fumigatus is a potentially deadly opportunistic human pathogen. A. fumigatus has evolved a variety of mechanisms to evade detection by the immune system. For example, the conidium surface is covered in a layer of 1,8-dihydroxynaphthalene (DHN) melanin which masks the antigen macrophages use for recognition. DHN melanin also protects conidia from ultraviolet radiation and gives A. fumigatus conidia their characteristic green-grayish color. Here, we conducted genomic analysis of two closely related white-spore natural variants of A. fumigatus in comparison to two closely related green-spore isolates to identify a genetic basis of the white-spore phenotype. Illumina whole-genome resequencing data of the four isolates was used to identify variants that were shared in the white-spore isolates and different from both the green-spore isolates and the Af293 reference genome (which is also a green-spore isolate). We identified 4,279 single nucleotide variants and 1,785 insertion/deletions fitting this pattern. Among these, we identified 64 variants predicted to be high impact, loss-of-function mutations. One of these variants is a single nucleotide deletion that results in a frameshift in pksP (Afu2g17600), the core biosynthetic gene in the DHN melanin encoding gene cluster. The frameshift mutation in the white-spore isolates leads to a truncated protein in which a phosphopantetheine attachment site (PP-binding domain) is interrupted and an additional PP-binding domain and a thioesterase domain are omitted. Growth rate analysis of white-spore and green-spore isolates at 37°C and 48°C revealed that white-spore isolates are thermosensitive. Growth rate of A. fumigatus Af293 and a pksP null mutant in the Af293 background suggests pksP is not directly involved in the thermosensitivity phenotype. Further, our study identified a mutation in a gene (Afu4g04740) associated with thermal sensitivity in yeasts which could also be responsible for the thermosensitivity of the white-spore mutants. Overall, we used comparative genomics to identify the mutation and protein alterations responsible for the white-spore phenotype of environmental isolates of A. fumigatus.
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Affiliation(s)
- John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
- Organismic & Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
| | - Paolo D’Avino
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
| | - Shu Zhao
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
| | - Grace W. Cox
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - David C. Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Jarrod R. Fortwendel
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center, Memphis, TN, United States
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El-Kamand S, Steiner M, Ramirez C, Halliday C, Chen SCA, Papanicolaou A, Morton CO. Assessing Differences between Clinical Isolates of Aspergillus fumigatus from Cases of Proven Invasive Aspergillosis and Colonizing Isolates with Respect to Phenotype (Virulence in Tenebrio molitor Larvae) and Genotype. Pathogens 2022; 11:pathogens11040428. [PMID: 35456102 PMCID: PMC9029132 DOI: 10.3390/pathogens11040428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/26/2022] [Accepted: 03/29/2022] [Indexed: 02/01/2023] Open
Abstract
The fungus Aspergillus fumigatus, the cause of invasive aspergillosis (IA), is a serious risk to transplant patients and those with respiratory diseases. Host immune suppression is considered the most important factor for the development of IA. Less is known about the importance of fungal virulence in the development of IA including the significance of variation between isolates. In this study, isolates of A. fumigatus from cases diagnosed as having proven IA or colonisation (no evidence of IA) were compared in assays to measure isolate virulence. These assays included the measurement of radial growth and protease production on agar, sensitivity to UV light and oxidative stressors, and virulence in Tenebrio molitor (mealworm) larvae. These assays did not reveal obvious differences in virulence between the two groups of isolates; this provided the impetus to conduct genomic analysis. Whole genome sequencing and analysis did not allow grouping into coloniser or IA isolates. However, focused analysis of single nucleotide polymorphisms revealed variation in three putative genes: AFUA_5G09420 (ccg-8), AFUA_4G00330, and AFUA_4G00350. These are known to be responsive to azole exposure, and ccg-8 deletion leads to azole hypersensitivity in other fungi. A. fumigatus virulence is challenging, but the findings of this study indicate that further research into the response to oxidative stress and azole exposure are required to understand the development of IA.
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Affiliation(s)
- Sam El-Kamand
- Western Sydney University, School of Science, Campbelltown Campus, Campbelltown, NSW 2560, Australia; (S.E.-K.); (M.S.); (C.R.)
| | - Martina Steiner
- Western Sydney University, School of Science, Campbelltown Campus, Campbelltown, NSW 2560, Australia; (S.E.-K.); (M.S.); (C.R.)
| | - Carl Ramirez
- Western Sydney University, School of Science, Campbelltown Campus, Campbelltown, NSW 2560, Australia; (S.E.-K.); (M.S.); (C.R.)
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (C.H.); (S.C.-A.C.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (C.H.); (S.C.-A.C.)
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW 2145, Australia
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, NSW 2753, Australia
- Correspondence: (A.P.); (C.O.M.); Tel.: +61-2-4570-1385 (A.P.); +61-2-4620-3446 (C.O.M.)
| | - Charles Oliver Morton
- Western Sydney University, School of Science, Campbelltown Campus, Campbelltown, NSW 2560, Australia; (S.E.-K.); (M.S.); (C.R.)
- Correspondence: (A.P.); (C.O.M.); Tel.: +61-2-4570-1385 (A.P.); +61-2-4620-3446 (C.O.M.)
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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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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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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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Durieux MF, Melloul É, Jemel S, Roisin L, Dardé ML, Guillot J, Dannaoui É, Botterel F. Galleria mellonella as a screening tool to study virulence factors of Aspergillus fumigatus. Virulence 2021; 12:818-834. [PMID: 33682618 PMCID: PMC7946008 DOI: 10.1080/21505594.2021.1893945] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The invertebrate Galleria mellonella has increasingly and widely been used in the last few years to study complex host–microbe interactions. Aspergillus fumigatus is one of the most pathogenic fungi causing life-threatening diseases in humans and animals. Galleria mellonella larvae has been proven as a reliable model for the analysis of pathogenesis and virulence factors, enable to screen a large number of A. fumigatus strains. This review describes the different uses of G. mellonella to study A. fumigatus and provides a comparison of the different protocols to trace fungal pathogenicity. The review also includes a summary of the diverse mutants tested in G. mellonella, and their respective contribution to A. fumigatus virulence. Previous investigations indicated that G. mellonella should be considered as an interesting tool even though a mammalian model may be required to complete and verify initial data.
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Affiliation(s)
- Marie-Fleur Durieux
- Laboratoire de Parasitologie - Mycologie, CHU de Limoges, Limoges, France.,EA 7380 Dynamic, Université Paris Est Créteil, EnvA, USC ANSES, Créteil, France
| | - Élise Melloul
- EA 7380 Dynamic, Université Paris Est Créteil, EnvA, USC ANSES, Créteil, France
| | - Sana Jemel
- EA 7380 Dynamic, Université Paris Est Créteil, EnvA, USC ANSES, Créteil, France
| | - Lolita Roisin
- EA 7380 Dynamic, Université Paris Est Créteil, EnvA, USC ANSES, Créteil, France
| | - Marie-Laure Dardé
- Laboratoire de Parasitologie - Mycologie, CHU de Limoges, Limoges, France
| | - Jacques Guillot
- EA 7380 Dynamic, Université Paris Est Créteil, EnvA, USC ANSES, Créteil, France.,École Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - Éric Dannaoui
- EA 7380 Dynamic, Université Paris Est Créteil, EnvA, USC ANSES, Créteil, France.,Unité de Parasitologie-mycologie, Service de Microbiologie, Université Paris Descartes, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Françoise Botterel
- EA 7380 Dynamic, Université Paris Est Créteil, EnvA, USC ANSES, Créteil, France.,Unité de Mycologie, Département de Prévention, Diagnostic Et Traitement Des Infections, Groupe Hospitalier Henri Mondor - Albert Chenevier, APHP, France
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Virulence traits within a community of the fungal entomopathogen Beauveria: Associations with abundance and distribution. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100992] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Lackner M, Obermair J, Naschberger V, Raschbichler LM, Kandelbauer C, Pallua J, Metzlaff J, Furxer S, Lass-Flörl C, Binder U. Cryptic species of Aspergillus section Terrei display essential physiological features to cause infection and are similar in their virulence potential in Galleria mellonella. Virulence 2020; 10:542-554. [PMID: 31169442 PMCID: PMC6592363 DOI: 10.1080/21505594.2019.1614382] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aspergillus species account for the majority of invasive mold infections in immunocompromised patients. Most commonly, members of the Aspergillus section Fumigati are isolated from clinical material, followed by isolates belonging to section Terrei. The section Terrei contains 16 accepted species. Six species were found to be of clinical relevance and studied for differences in growth adaptability and virulence potential. Therefore, a set of 73 isolates (22 A. terreus s.s., 8 A. alabamensis, 27 A. citrinoterreus, 2 A. floccosus, 13 A. hortai, and 1 A. neoafricanus) was studied to determine differences in (a) germination kinetics, (b) temperature tolerance, (c) oxygen stress tolerance (1% O2), and (d) a combination of the latter two. Virulence potential of phialidic (PC) and accessory conidia (AC) was studied in G. mellonella larvae, using survival as read out. Further, the formation of AC was evaluated in larval tissue. All isolates were able to grow at elevated temperature and hypoxia, with highest growth and germination rates at 37°C. A. terreus s.s., A. citrinoterreus, and A. hortai exhibited highest growth rates. Virulence potential in larvae was inoculum and temperature dependent. All species except A. floccosus formed AC and germination kinetics of AC was variable. Significantly higher virulence potential of AC was found for one A. hortai isolate. AC could be detected in larval tissue 96 h post infection. Based on these findings, cryptic species of section Terrei are well adapted to the host environment and have similar potential to cause infections.
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Affiliation(s)
- Michaela Lackner
- a Division of Hygiene and Medical Microbiology , Medical University Innsbruck , Austria
| | - Judith Obermair
- a Division of Hygiene and Medical Microbiology , Medical University Innsbruck , Austria
| | - Verena Naschberger
- a Division of Hygiene and Medical Microbiology , Medical University Innsbruck , Austria
| | | | - Carmen Kandelbauer
- a Division of Hygiene and Medical Microbiology , Medical University Innsbruck , Austria
| | - Johannes Pallua
- b Department of Pathology , Medical University Innsbruck , Austria
| | - Julia Metzlaff
- a Division of Hygiene and Medical Microbiology , Medical University Innsbruck , Austria
| | - Sibylle Furxer
- a Division of Hygiene and Medical Microbiology , Medical University Innsbruck , Austria
| | - Cornelia Lass-Flörl
- a Division of Hygiene and Medical Microbiology , Medical University Innsbruck , Austria
| | - Ulrike Binder
- a Division of Hygiene and Medical Microbiology , Medical University Innsbruck , Austria
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Loeffert ST, Melloul E, Gustin MP, Hénaff L, Guillot C, Dupont D, Wallon M, Cassier P, Dananché C, Bénet T, Botterel F, Guillot J, Vanhems P. Investigation of the Relationships Between Clinical and Environmental Isolates of Aspergillus fumigatus by Multiple-locus Variable Number Tandem Repeat Analysis During Major Demolition Work in a French Hospital. Clin Infect Dis 2020; 68:321-329. [PMID: 30247539 DOI: 10.1093/cid/ciy498] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 09/17/2018] [Indexed: 01/28/2023] Open
Abstract
Background Genotyping is needed to explore the link between clinical cases from colonization of invasive aspergillosis (IA) and major building construction. Attempts to correlate Aspergillus fumigatus strains from clinical infection or colonization with those found in the environment remain controversial due to the lack of a large prospective study. Our aim in this study was to compare the genetic diversity of clinical and environmental A. fumigatus isolates during a demolition period. Methods Fungal contamination was monitored daily for 11 months in 2015. Environmental surveillance was undertaken indoors and outdoors at 8 locations with automatic agar samplers. IA infection cases were investigated according to European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group criteria. Isolates were identified by amplification and sequencing of the β- tubulin gene. They were genotyped by multiple-locus variable number tandem repeat analysis (MLVA). The phylogenetic relationships between isolates were assessed by generating a minimum spanning tree. Results Based on 3885 samples, 394 A. fumigatus isolates (383 environmental and 11 clinical) were identified and genotyped using MLVA. Clinical isolates were collected from patients diagnosed as having probable IA (n = 2), possible IA (n = 1), or bronchial colonization (n = 6). MLVA generated 234 genotypes. Seven clinical isolates shared genotypes identical to environmental isolates. Conclusions Among the diversity of genotypes described, similar genotypes were found in clinical and environmental isolates, indicating that A. fumigatus infection and colonization may originate from hospital environments.
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Affiliation(s)
- Sophie T Loeffert
- Equipe Epidémiologie et Santé Internationale, Laboratoire des Pathogènes Emergents-Fondation Mérieux, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon
| | - Elise Melloul
- EA 7380 Dynamyc, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est Créteil, Créteil
| | - Marie-Paule Gustin
- Département de Santé Publique, Institut des Sciences Pharmaceutiques et Biologiques-Faculté de Pharmacie, Université Claude Bernard Lyon 1
| | - Laetitia Hénaff
- Equipe Epidémiologie et Santé Internationale, Laboratoire des Pathogènes Emergents-Fondation Mérieux, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon
| | - Chloé Guillot
- EA 7380 Dynamyc, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est Créteil, Créteil
| | - Damien Dupont
- Institut de Parasitologie et de Mycologie Médicale, Hôpital de la Croix Rousse, Lyon
| | - Martine Wallon
- Institut de Parasitologie et de Mycologie Médicale, Hôpital de la Croix Rousse, Lyon
| | - Pierre Cassier
- Laboratoire de Biologie Sécurité Environnement, Groupement Hospitalier Centre, Hospices Civils de Lyon
| | - Cédric Dananché
- Equipe Epidémiologie et Santé Internationale, Laboratoire des Pathogènes Emergents-Fondation Mérieux, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon.,Unité d'Hygiène, Epidémiologie et Prévention, Groupement Hospitalier Centre, Hospices Civils de Lyon, France
| | - Thomas Bénet
- Unité d'Hygiène, Epidémiologie et Prévention, Groupement Hospitalier Centre, Hospices Civils de Lyon, France
| | - Françoise Botterel
- EA 7380 Dynamyc, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est Créteil, Créteil
| | - Jacques Guillot
- EA 7380 Dynamyc, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est Créteil, Créteil
| | - Philippe Vanhems
- Equipe Epidémiologie et Santé Internationale, Laboratoire des Pathogènes Emergents-Fondation Mérieux, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon.,Unité d'Hygiène, Epidémiologie et Prévention, Groupement Hospitalier Centre, Hospices Civils de Lyon, France
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10
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Puértolas-Balint F, Rossen JWA, Oliveira Dos Santos C, Chlebowicz MMA, Raangs EC, van Putten ML, Sola-Campoy PJ, Han L, Schmidt M, García-Cobos S. Revealing the Virulence Potential of Clinical and Environmental Aspergillus fumigatus Isolates Using Whole-Genome Sequencing. Front Microbiol 2019; 10:1970. [PMID: 31551947 PMCID: PMC6737835 DOI: 10.3389/fmicb.2019.01970] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/12/2019] [Indexed: 01/09/2023] Open
Abstract
Aspergillus fumigatus is considered a common causative agent of human fungal infections. A restricted number of virulence factors have been described, and none of them lead to a differentiation in the virulence level among different strains. Variations in the virulence phenotype depending on the isolate origin, measured as survival percentage in animal infection models, have been previously reported. In this study, we analyzed the whole-genome sequence of A. fumigatus isolates from clinical and environmental origins to determine their virulence genetic content. The sample included four isolates sequenced at the University Medical Center Groningen (UMCG), three clinical (two of them isolated from the same patient) and the experimental strain B5233, and the draft genomes of one reference strain, two environmental and two clinical isolates obtained from a public database. The fungal genomes were screened for the presence of virulence-related genes (VRGs) using an in-house database of 244 genes related to thermotolerance, resistance to immune responses, cell wall formation, nutrient uptake, signaling and regulation, and production of toxins and secondary metabolites and allergens. In addition, we performed a variant calling analysis to compare the isolates sequenced at the UMCG and investigated their genetic relatedness using the TRESP (Tandem Repeats located within Exons of Surface Protein coding genes) genotyping method. We neither observed a difference in the virulence genetic content between the clinical isolates causing an invasive infection and a colonizing clinical isolate nor between isolates from the clinical and environmental origin. The four novel A. fumigatus sequences had a different TRESP genotype and a total number of genetic variants ranging from 48,590 to 68,352. In addition, a comparative genomics analysis showed the presence of single nucleotide polymorphisms in VRGs and repetitive genetic elements located next to VRG groups, which could influence the regulation of these genes. In conclusion, our genomic analysis revealed a high genetic diversity between environmental and clinical A. fumigatus isolates, as well as between clinical isolates from the same patient, indicating an infection with a mixed-population in the latter case. However, all isolates had a similar virulence genetic content, demonstrating their pathogenic potential at least at the genomic level.
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Affiliation(s)
- Fabiola Puértolas-Balint
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands.,University of Groningen, Department of Molecular Pharmacology, Groningen, Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Claudy Oliveira Dos Santos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Monika M A Chlebowicz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Erwin C Raangs
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Maarten L van Putten
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
| | - Pedro J Sola-Campoy
- Reference and Research Laboratory on Antimicrobial Resistance and Healthcare Infections, National Microbiology Centre, Institute of Health Carlos III, Madrid, Spain
| | - Li Han
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Martina Schmidt
- University of Groningen, Department of Molecular Pharmacology, Groningen, Netherlands.,University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, Netherlands
| | - Silvia García-Cobos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, Netherlands
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11
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Zhao S, Gibbons JG. A population genomic characterization of copy number variation in the opportunistic fungal pathogen Aspergillus fumigatus. PLoS One 2018; 13:e0201611. [PMID: 30071059 PMCID: PMC6072042 DOI: 10.1371/journal.pone.0201611] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/18/2018] [Indexed: 12/19/2022] Open
Abstract
Aspergillus fumigatus is a potentially deadly opportunistic fungal pathogen. Molecular studies have shaped our understanding of the genes, proteins, and molecules that contribute to A. fumigatus pathogenicity, but few studies have characterized genome-wide patterns of genetic variation at the population level. Of A. fumigatus genomic studies to-date, most focus mainly on single nucleotide polymorphisms and large structural variants, while overlooking the contribution of copy number variation (CNV). CNV is a class of small structural variation defined as loci that vary in their number of copies between individuals due to duplication, gain, or deletion. CNV can influence phenotype, including fungal virulence. In the present study, we characterized the population genomic patterns of CNV in a diverse collection of 71 A. fumigatus isolates using publicly available sequencing data. We used genome-wide single nucleotide polymorphisms to infer the population structure of these isolates and identified three populations consisting of at least 8 isolates. We then computationally predicted genome-wide CNV profiles for each isolate and conducted analyses at the species-, population-, and individual levels. Our results suggest that CNV contributes to genetic variation in A. fumigatus, with ~10% of the genome being CN variable. Our analysis indicates that CNV is non-randomly distributed across the A. fumigatus genome, and is overrepresented in subtelomeric regions. Analysis of gene ontology categories in genes that overlapped CN variants revealed an enrichment of genes related to transposable element and secondary metabolism functions. We further identified 72 loci containing 33 genes that showed divergent copy number profiles between the three A. fumigatus populations. Many of these genes encode proteins that interact with the cell surface or are involved in pathogenicity. Our results suggest that CNV is an important source of genetic variation that could account for some of the phenotypic differences between A. fumigatus populations and isolates.
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Affiliation(s)
- Shu Zhao
- Biology Department, Clark University, Worcester, Massachusetts, United States of America
| | - John G. Gibbons
- Biology Department, Clark University, Worcester, Massachusetts, United States of America
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12
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Abstract
Aspergillus fumigatus is a ubiquitous environmental mold and the leading cause of diverse human diseases ranging from allergenic bronchopulmonary aspergillosis (ABPA) to invasive pulmonary aspergillosis (IPA). Experimental investigations of the biology and virulence of this opportunistic pathogen have historically used a few type strains; however, it is increasingly observed with this fungus that heterogeneity among isolates potentially confounds the use of these reference isolates. Illustrating this point, Kowalski et al. (mBio 7:e01515-16, 2016, https://doi.org/10.1128/mBio.01515-16) demonstrated that variation in 16 environmental and clinical isolates of A. fumigatus correlated virulence with fitness in low oxygen, whereas Fuller et al. (mBio 7:e01517-16, 2016, https://doi.org/10.1128/mBio.01517-16) showed wide variation in light responses at a physiological and protein functionality level in 15 A. fumigatus isolates. In both studies, two commonly used type strains, Af293 and CEA10, displayed significant differences in physiological responses to abiotic stimuli and virulence in a murine model of IPA.
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13
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Characterization of Aspergillus fumigatus Isolates from Air and Surfaces of the International Space Station. mSphere 2016; 1:mSphere00227-16. [PMID: 27830189 PMCID: PMC5082629 DOI: 10.1128/msphere.00227-16] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/01/2016] [Indexed: 01/02/2023] Open
Abstract
One mission of the Microbial Observatory Experiments on the International Space Station (ISS) is to examine the traits and diversity of fungal isolates to gain a better understanding of how fungi may adapt to microgravity environments and how this may affect interactions with humans in a closed habitat. Here, we report an initial characterization of two isolates, ISSFT-021 and IF1SW-F4, of Aspergillus fumigatus collected from the ISS and a comparison to the experimentally established clinical isolates Af293 and CEA10. Whole-genome sequencing of ISSFT-021 and IF1SW-F4 showed 54,960 and 52,129 single nucleotide polymorphisms, respectively, compared to Af293, which is consistent with observed genetic heterogeneity among sequenced A. fumigatus isolates from diverse clinical and environmental sources. Assessment of in vitro growth characteristics, secondary metabolite production, and susceptibility to chemical stresses revealed no outstanding differences between ISS and clinical strains that would suggest special adaptation to life aboard the ISS. Virulence assessment in a neutrophil-deficient larval zebrafish model of invasive aspergillosis revealed that both ISSFT-021 and IF1SW-F4 were significantly more lethal than Af293 and CEA10. Taken together, these genomic, in vitro, and in vivo analyses of two A. fumigatus strains isolated from the ISS provide a benchmark for future investigations of these strains and for continuing research on specific microbial isolates from manned space environments. IMPORTANCE As durations of manned space missions increase, it is imperative to understand the long-term consequence of microbial exposure on human health in a closed human habitat. To date, studies aimed at bacterial and fungal contamination of space vessels have highlighted species compositions biased toward hardy, persistent organisms capable of withstanding harsh conditions. In the current study, we assessed traits of two independent Aspergillus fumigatus strains isolated from the International Space Station. Ubiquitously found in terrestrial soil and atmospheric environments, A. fumigatus is a significant opportunistic fungal threat to human health, particularly among the immunocompromised. Using two well-known clinical isolates of A. fumigatus as comparators, we found that both ISS isolates exhibited normal in vitro growth and chemical stress tolerance yet caused higher lethality in a vertebrate model of invasive disease. These findings substantiate the need for additional studies of physical traits and biological activities of microbes adapted to microgravity and other extreme extraterrestrial conditions.
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14
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Heterogeneity among Isolates Reveals that Fitness in Low Oxygen Correlates with Aspergillus fumigatus Virulence. mBio 2016; 7:mBio.01515-16. [PMID: 27651366 PMCID: PMC5040115 DOI: 10.1128/mbio.01515-16] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Previous work has shown that environmental and clinical isolates of Aspergillus fumigatus represent a diverse population that occupies a variety of niches, has extensive genetic diversity, and exhibits virulence heterogeneity in a number of animal models of invasive pulmonary aspergillosis (IPA). However, mechanisms explaining differences in virulence among A. fumigatus isolates remain enigmatic. Here, we report a significant difference in virulence of two common lab strains, CEA10 and AF293, in the murine triamcinolone immunosuppression model of IPA, in which we previously identified severe low oxygen microenvironments surrounding fungal lesions. Therefore, we hypothesize that the ability to thrive within these lesions of low oxygen promotes virulence of A. fumigatus in this model. To test this hypothesis, we performed in vitro fitness and in vivo virulence analyses in the triamcinolone murine model of IPA with 14 environmental and clinical isolates of A. fumigatus Among these isolates, we observed a strong correlation between fitness in low oxygen in vitro and virulence. In further support of our hypothesis, experimental evolution of AF293, a strain that exhibits reduced fitness in low oxygen and reduced virulence in the triamcinolone model of IPA, results in a strain (EVOL20) that has increased hypoxia fitness and a corresponding increase in virulence. Thus, the ability to thrive in low oxygen correlates with virulence of A. fumigatus isolates in the context of steroid-mediated murine immunosuppression. IMPORTANCE Aspergillus fumigatus occupies multiple environmental niches, likely contributing to the genotypic and phenotypic heterogeneity among isolates. Despite reports of virulence heterogeneity, pathogenesis studies often utilize a single strain for the identification and characterization of virulence and immunity factors. Here, we describe significant variation between A. fumigatus isolates in hypoxia fitness and virulence, highlighting the advantage of including multiple strains in future studies. We also illustrate that hypoxia fitness correlates strongly with increased virulence exclusively in the nonleukopenic murine triamcinolone immunosuppression model of IPA. Through an experimental evolution experiment, we observe that chronic hypoxia exposure results in increased virulence of A. fumigatus We describe here the first observation of a model-specific virulence phenotype correlative with in vitro fitness in hypoxia and pave the way for identification of hypoxia-mediated mechanisms of virulence in the fungal pathogen A. fumigatus.
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15
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Caffrey AK, Obar JJ. Alarmin(g) the innate immune system to invasive fungal infections. Curr Opin Microbiol 2016; 32:135-143. [PMID: 27351354 DOI: 10.1016/j.mib.2016.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/04/2016] [Accepted: 06/07/2016] [Indexed: 11/24/2022]
Abstract
Fungi encounter numerous stresses in a mammalian host, including the immune system, which they must adapt to in order to grow and cause disease. The host immune system tunes its response to the threat level posed by the invading pathogen. We discuss recent findings on how interleukin (IL)-1 signaling is central to tuning the immune response to the virulence potential of invasive fungi, as well as other pathogens. Moreover, we discuss fungal factors that may drive tissue invasion and destruction that regulate IL-1 cytokine release. Moving forward understanding the mechanisms of fungal adaption to the host, together with understanding how the host innate immune system recognizes invading fungal pathogens will increase our therapeutic options for treatment of invasive fungal infections.
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Affiliation(s)
- Alayna K Caffrey
- Montana State University, Department of Microbiology & Immunology, Bozeman, MT 59718, United States; Geisel School of Medicine at Dartmouth, Department of Microbiology & Immunology, Lebanon, NH 03756, United States
| | - Joshua J Obar
- Geisel School of Medicine at Dartmouth, Department of Microbiology & Immunology, Lebanon, NH 03756, United States.
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16
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Galleria mellonella: An invertebrate model to study pathogenicity in correctly defined fungal species. Fungal Biol 2016; 120:288-95. [DOI: 10.1016/j.funbio.2015.06.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 11/18/2022]
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17
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Melloul E, Thierry S, Durand B, Cordonnier N, Desoubeaux G, Chandenier J, Bostvironnois C, Botterel F, Chermette R, Guillot J, Arné P. Assessment of Aspergillus fumigatus burden in lungs of intratracheally-challenged turkeys (Meleagris gallopavo) by quantitative PCR, galactomannan enzyme immunoassay, and quantitative culture. Comp Immunol Microbiol Infect Dis 2014; 37:271-9. [DOI: 10.1016/j.cimid.2014.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/04/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
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