1
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Miguel CB, Vilela GP, Almeida LM, Moreira MA, Silva GP, Miguel-Neto J, Martins-de-Abreu MC, Agostinho F, Lazo-Chica JE, Cardoso MS, Soares SDC, Góes-Neto A, Rodrigues WF. Adaptative Divergence of Cryptococcus neoformans: Phenetic and Metabolomic Profiles Reveal Distinct Pathways of Virulence and Resistance in Clinical vs. Environmental Isolates. J Fungi (Basel) 2025; 11:215. [PMID: 40137253 PMCID: PMC11943092 DOI: 10.3390/jof11030215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Revised: 02/26/2025] [Accepted: 02/27/2025] [Indexed: 03/27/2025] Open
Abstract
Cryptococcus neoformans is a life-threatening fungal pathogen that primarily affects immunocompromised individuals. While antiretroviral therapy has reduced incidence in developed nations, fluconazole-resistant strains and virulent environmental isolates continue to pose challenges, especially because they have many mechanisms of adaptability, supporting their survival. This study explores the phenetic and metabolomic adaptations of C. neoformans in clinical and environmental contexts to understand the factors influencing pathogenicity and resistance. METHODS An in silico observational study was conducted with 16 C. neoformans isolates (6 clinical, 9 environmental, and 1 reference) from the NCBI database. Molecular phenetic analysis used MEGA version 11.0.13 and focused on efflux pump protein sequences. Molecular phenetic relationships were assessed via the UPGMA clustering method with 1000 bootstrap replicates. The enzymatic profiling of glycolytic pathways was conducted with dbCAN, and metabolomic pathway enrichment analysis was performed in MetaboAnalyst 6.0 using the KEGG pathway database. RESULTS Molecular phenetic analysis revealed distinct clustering patterns among isolates, reflecting adaptations associated with clinical and environmental niches. Clinical isolates demonstrated enriched sulfur metabolism and glutathione pathways, likely adaptations to oxidative stress in host environments, while environmental isolates favored methane and glyoxylate pathways, suggesting adaptations for survival in carbon-rich environments. CONCLUSION Significant phenetic and metabolomic distinctions between isolates reveal adaptive strategies for enhancing virulence and antifungal resistance, highlighting potential therapeutic targets.
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Affiliation(s)
- Camila Botelho Miguel
- Multidisciplinary Laboratory of Scientific Evidence, University Center of Mineiros (Unifimes), Mineiros 75833-130, GO, Brazil; (C.B.M.); (G.P.V.); (L.M.A.); (M.A.M.); (G.P.S.); (J.M.-N.); (M.C.M.-d.-A.)
- Postgraduate Program in Tropical Medicine and Infectious Diseases, Federal University of the Triângulo Mineiro—UFTM, Uberaba 38025-180, MG, Brazil;
| | - Geovana Pina Vilela
- Multidisciplinary Laboratory of Scientific Evidence, University Center of Mineiros (Unifimes), Mineiros 75833-130, GO, Brazil; (C.B.M.); (G.P.V.); (L.M.A.); (M.A.M.); (G.P.S.); (J.M.-N.); (M.C.M.-d.-A.)
| | - Lara Mamede Almeida
- Multidisciplinary Laboratory of Scientific Evidence, University Center of Mineiros (Unifimes), Mineiros 75833-130, GO, Brazil; (C.B.M.); (G.P.V.); (L.M.A.); (M.A.M.); (G.P.S.); (J.M.-N.); (M.C.M.-d.-A.)
| | - Mariane Andrade Moreira
- Multidisciplinary Laboratory of Scientific Evidence, University Center of Mineiros (Unifimes), Mineiros 75833-130, GO, Brazil; (C.B.M.); (G.P.V.); (L.M.A.); (M.A.M.); (G.P.S.); (J.M.-N.); (M.C.M.-d.-A.)
| | - Glicélia Pereira Silva
- Multidisciplinary Laboratory of Scientific Evidence, University Center of Mineiros (Unifimes), Mineiros 75833-130, GO, Brazil; (C.B.M.); (G.P.V.); (L.M.A.); (M.A.M.); (G.P.S.); (J.M.-N.); (M.C.M.-d.-A.)
| | - Jamil Miguel-Neto
- Multidisciplinary Laboratory of Scientific Evidence, University Center of Mineiros (Unifimes), Mineiros 75833-130, GO, Brazil; (C.B.M.); (G.P.V.); (L.M.A.); (M.A.M.); (G.P.S.); (J.M.-N.); (M.C.M.-d.-A.)
| | - Melissa Carvalho Martins-de-Abreu
- Multidisciplinary Laboratory of Scientific Evidence, University Center of Mineiros (Unifimes), Mineiros 75833-130, GO, Brazil; (C.B.M.); (G.P.V.); (L.M.A.); (M.A.M.); (G.P.S.); (J.M.-N.); (M.C.M.-d.-A.)
| | - Ferdinando Agostinho
- Faculty of Physiotherapy, University of Rio Verde, UniRv, Rio Verde 75901-970, GO, Brazil;
| | - Javier Emilio Lazo-Chica
- Laboratory of Cell Biology, Department of Structural Biology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba 38061-500, MG, Brazil;
| | - Mariana Santos Cardoso
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (M.S.C.); (A.G.-N.)
| | - Siomar de Castro Soares
- Postgraduate Program in Tropical Medicine and Infectious Diseases, Federal University of the Triângulo Mineiro—UFTM, Uberaba 38025-180, MG, Brazil;
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (M.S.C.); (A.G.-N.)
| | - Wellington Francisco Rodrigues
- Multidisciplinary Laboratory of Scientific Evidence, University Center of Mineiros (Unifimes), Mineiros 75833-130, GO, Brazil; (C.B.M.); (G.P.V.); (L.M.A.); (M.A.M.); (G.P.S.); (J.M.-N.); (M.C.M.-d.-A.)
- Postgraduate Program in Tropical Medicine and Infectious Diseases, Federal University of the Triângulo Mineiro—UFTM, Uberaba 38025-180, MG, Brazil;
- Laboratory of Cell Biology, Department of Structural Biology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba 38061-500, MG, Brazil;
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (M.S.C.); (A.G.-N.)
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2
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Jimenez IA, Stempinski PR, Dragotakes Q, Greengo SD, Sanchez Ramirez L, Casadevall A. The buoyancy of cryptococcal cells and its implications for transport and persistence of Cryptococcus in aqueous environments. mSphere 2024; 9:e0084824. [PMID: 39601568 DOI: 10.1128/msphere.00848-24] [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: 10/08/2024] [Accepted: 11/05/2024] [Indexed: 11/29/2024] Open
Abstract
Cryptococcus is a genus of saprophytic fungi with global distribution. Two species complexes, Cryptococcus neoformans and Cryptococcus gattii, pose health risks to humans and animals. Cryptococcal infections result from inhalation of aerosolized spores and/or desiccated yeasts from terrestrial reservoirs such as soil and trees. More recently, C. gattii has been implicated in infections in marine mammals, suggesting that inhalation of cells from the air-water interface is also an important, yet understudied, mode of respiratory exposure. Based on historical records and epidemiological factors, water transport has been hypothesized to play a role in the spread of C. gattii from tropical to temperate environments. However, the dynamics of fungal persistence and transport in water have not been fully studied. The size of the cryptococcal capsule was previously shown to reduce cell density and increase buoyancy. Here, we demonstrate that cell buoyancy is also impacted by the salinity of the solution in which cells are suspended, with the formation of a halocline significantly slowing the rate of settling and resulting in persistence of C. neoformans within 1 cm of the water surface for over 60 min and C. gattii for 4-6 h. During the culture of three strains of C. gattii in yeast peptone dextrose media, we also identified aggregates of extracellular polysaccharide with complex structures, which we hypothesize from rafts that entrap cells and augment buoyancy. These findings illustrate new mechanisms by which cryptococcal cells may persist in aquatic environments, with important implications for aqueous transport and pathogen exposure. IMPORTANCE Cryptococcosis is a major fungal disease leading to morbidity and mortality worldwide. Cryptococcus neoformans is a major fungal species of public health concern, causing opportunistic systemic infections in immunocompromised patients. Cryptococcus gattii was traditionally a pathogenic fungus confined primarily to tropical regions, but in the 1990s, it emerged in the temperate climates of British Columbia, Canada and the Pacific Northwest of the United States. Outbreaks in these areas also led to the first host record of cryptococcosis in free-ranging cetaceans. C. gattii is particularly concerning as an emerging fungal pathogen due to its capacity to cause clinical disease in immunocompetent patients, its recent spread to a new ecological niche, and its higher resistance to antifungal therapies. Our research defines fungal characteristics that influence the transport of cryptococci through water and persistence of fungal cells near the water surface, improving our understanding of potential mechanisms for cryptococcal environmental transport.
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Affiliation(s)
- Isabel A Jimenez
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Piotr R Stempinski
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Quigly Dragotakes
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Seth D Greengo
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lia Sanchez Ramirez
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
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3
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Hallas-Møller M, Burow M, Henrissat B, Johansen KS. Cryptococcus neoformans: plant-microbe interactions and ecology. Trends Microbiol 2024; 32:984-995. [PMID: 38519353 DOI: 10.1016/j.tim.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
While the opportunistic human pathogens Cryptococcus neoformans and Cryptococcus gattii are often isolated from plants and plant-related material, evidence suggests that these Cryptococcus species do not directly infect plants. Studies find that plants are important for Cryptococcus mating and dispersal. However, these studies have not provided enough detail about how plants and these fungi interact, especially in ways that could show the fungi are capable of causing disease. This review synthesizes recent findings from studies utilizing different plant models associated with the ecology of C. neoformans and C. gattii. Unanswered questions about their environmental role are highlighted. Overall, current research indicates that Cryptococcus utilizes plants as a substrate rather than harming them, arguing against Cryptococcus as a genuine plant pathogen. We hypothesize that plants represent reservoirs that aid dispersal, not hosts vulnerable to infection.
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Affiliation(s)
- Magnus Hallas-Møller
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Meike Burow
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kgs, Lyngby, Denmark
| | - Katja Salomon Johansen
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark.
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4
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Després PC, Shapiro RS, Cuomo CA. New approaches to tackle a rising problem: Large-scale methods to study antifungal resistance. PLoS Pathog 2024; 20:e1012478. [PMID: 39236046 PMCID: PMC11376582 DOI: 10.1371/journal.ppat.1012478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024] Open
Affiliation(s)
- Philippe C Després
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, United States of America
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, United States of America
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5
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Stempinski PR, Greengo SD, Casadevall A. Growth on Douglas fir media facilitates Cryptococcus virulence factor production and enhances fungal survival against environmental and immune stressors. Med Mycol 2024; 62:myae068. [PMID: 38982313 DOI: 10.1093/mmy/myae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/27/2024] [Accepted: 07/08/2024] [Indexed: 07/11/2024] Open
Abstract
The yeasts Cryptococcus neoformans and Cryptococcus gattii are fungal pathogens that can be isolated from the environment, including the surfaces of many plants. Cryptococcus gattii caused an outbreak on Vancouver Island, British Columbia beginning in 1999 that has since spread to the Pacific Northwest of the United States. Coastal Douglas fir (Pseudotsuga menziesii) is an important lumber species and a major component of the ecosystems in this area. Previous research has explored Cryptococcus survival and mating on Douglas fir plants and plant-derived material, but no studies have been done on the production of cryptococcal virulence factors by cells grown on those media. Here, we investigated the effects of growth on Douglas fir-derived media on the production of the polysaccharide capsule and melanin, two of the most important cryptococcal virulence factors. We found that while the capsule was mostly unchanged by growth in Douglas fir media compared to cells grown in defined minimal media, Cryptococcus spp. can use substrates present in Douglas fir to synthesize functional and protective melanin. These results suggest mechanisms by which Cryptococcus species may survive in the environment and emphasize the need to explore how association with Douglas fir trees could affect its epidemiology for human cryptococcosis.
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Affiliation(s)
- Piotr R Stempinski
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland 21205, USA
| | - Seth D Greengo
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland 21205, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland 21205, USA
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6
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de Holanda Fonseca DL, Silva DMWD, de Albuquerque Maranhão FC. Molecular characterization of clinical and environmental isolates from the Cryptococcus neoformans/C. Gattii species complexes of Maceió, Alagoas, Brazil. Braz J Microbiol 2024; 55:1369-1380. [PMID: 38619732 PMCID: PMC11153433 DOI: 10.1007/s42770-024-01313-1] [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: 07/03/2023] [Accepted: 03/21/2024] [Indexed: 04/16/2024] Open
Abstract
Cryptococcosis is one of the major life-threatening opportunistic/systemic fungal diseases of worldwide occurrence, which can be asymptomatic or establish pneumonia and meningoencephalitis mainly in immunosuppressed patients, caused by the Cryptococcus neoformans and C. gattii species complexes. Acquisition is by inhaling fungal propagules from avian droppings, tree hollows and decaying wood, and the association of the molecular types with geographic origin, virulence and antifungal resistance have epidemiological importance. Since data on cryptococcosis in Alagoas are limited, we sought to determine the molecular types of etiological agents collected from clinical and environmental sources. We evaluated 21 isolates previously collected from cerebrospinal fluid and from environment sources (pigeon droppings and tree hollows) in Maceió-Alagoas (Brazil). Restriction fragment length polymorphism of URA5 gene was performed to characterize among the eight standard molecular types (VNI-VNIV and VGI-VGIV). Among isolates, 66.67% (14) were assigned to C. neoformans VNI - 12 of them (12/14) recovered from liquor and 2 from a tree hollow (2/14). One isolate from pigeon droppings (4.76%) corresponded to C. neoformans VNIV, while five strains from tree hollows and one from pigeon droppings (6, 28.57%) to C. gattii VGII. VNI-type was present in clinical and environmental samples and most C. neoformans infections were observed in HIV-positive patients, while types VNIV and VGII were prevalent in environmental sources in Alagoas. This is the first molecular characterization of Cryptococcus spp. in Alagoas, our study provides additional information on the ecoepidemiology of Cryptococcus spp. in Brazil, contributing to a closer view of the endemic species.
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Affiliation(s)
| | - Denise Maria Wanderlei da Silva
- Institute of Biological and Health Sciences, Sector of Microbiology, Laboratory of Clinical Microbiology, Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Fernanda Cristina de Albuquerque Maranhão
- Institute of Biological and Health Sciences, Sector of Microbiology, Laboratory of Clinical Microbiology, Federal University of Alagoas, Av. Lourival de Melo Mota, S/N, Tabuleiro do Martins, Maceió, 57072-900, Alagoas, Brazil.
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7
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Jimenez IA, Stempinski PR, Dragotakes Q, Greengo SD, Ramirez LS, Casadevall A. The buoyancy of cryptococcal cells and its implications for transport and persistence of Cryptococcus in aqueous environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.595024. [PMID: 38826196 PMCID: PMC11142132 DOI: 10.1101/2024.05.20.595024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Cryptococcus is a genus of saprophytic fungi with global distribution. Two species complexes, C. neoformans and C. gattii, pose health risks to humans and animals. Cryptococcal infections result from inhalation of aerosolized spores and/or desiccated yeasts from terrestrial reservoirs such as soil, trees, and avian guano. More recently, C. gattii has been implicated in infections in marine mammals, suggesting that inhalation of liquid droplets or aerosols from the air-water interface is also an important, yet understudied, mode of respiratory exposure. Water transport has also been suggested to play a role in the spread of C. gattii from tropical to temperate environments. However, the dynamics of fungal survival, persistence, and transport via water have not been fully studied. The size of the cryptococcal capsule was previously shown to reduce cell density and increase buoyancy. Here, we demonstrate that cell buoyancy is also impacted by the salinity of the media in which cells are suspended, with formation of a halocline interface significantly slowing the rate of settling of cryptococcal cells through water, resulting in persistence of C. neoformans within 1 cm of the air-water interface for over 60 min and C. gattii for 4-6 h. Our data also showed that during culture in yeast peptone dextrose media (YPD), polysaccharide accumulating in the supernatant formed a raft that augmented buoyancy and further slowed settling of cryptococcal cells. These findings illustrate new mechanisms by which cryptococcal cells may persist in aquatic environments, with important implications for aqueous transport and pathogen exposure.
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Affiliation(s)
- Isabel A. Jimenez
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Piotr R. Stempinski
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Quigly Dragotakes
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Seth D. Greengo
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lia Sanchez Ramirez
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
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8
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Cohen DG, Wingert RA. Caught red feathered: infection from cockatoo to human and mice reveals genetic plasticity of Cryptococcus neoformans during mammalian passage. Tissue Barriers 2024:2309717. [PMID: 38282267 DOI: 10.1080/21688370.2024.2309717] [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: 12/15/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
The fungus Cryptococcus neoformans is pervasive in our environment and causes the infectious disease cryptococcosis in humans, most commonly in immunocompromised patients. In addition to corroborating the avian origins of a case of cryptococcosis in an immunocompromised patient in 2000, a fascinating recent report has now characterized the genetic and phenotypic changes that occur in this C. neoformans during passage in mammalian hosts. Interestingly, mouse-passaged isolates showed differences in virulence factors ranging from capsule size, melanization, nonlytic macrophage exocytosis, and amoeba predation resistance as compared to the patient strain. Taken together, these results provide new insights about the relationship between mutations acquired during an infection and changes in virulence.
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Affiliation(s)
- Dorrian G Cohen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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9
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Hilbert ZA, Bednarek JM, Schwiesow MJW, Chung KY, Moreau CT, Brown JCS, Elde NC. Distinct pathways of adaptive evolution in Cryptococcus neoformans reveal a mutation in adenylyl cyclase with trade-offs for pathogenicity. Curr Biol 2023; 33:4136-4149.e9. [PMID: 37708888 PMCID: PMC10592076 DOI: 10.1016/j.cub.2023.08.054] [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: 04/06/2023] [Revised: 07/13/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
Pathogenic fungi populate a wide range of environments and infect a diversity of host species. Despite this substantial biological flexibility, the impact of interactions between fungi and their hosts on the evolution of pathogenicity remains unclear. We studied how repeated interactions between the fungus Cryptococcus neoformans and relevant environmental and mammalian host cells-amoeba and mouse macrophages-shape the evolution of this model fungal pathogen. First, using a collection of clinical and environmental isolates of C. neoformans, we characterized a range of survival phenotypes for these strains when exposed to host cells of different species. We then performed serial passages of an environmentally isolated C. neoformans strain through either amoeba or macrophages for ∼75 generations to observe how these interactions select for improved replication within hosts. In one adapted population, we identified a single point mutation in the adenylyl cyclase gene, CAC1, that swept to fixation and confers a strong competitive advantage for growth inside macrophages. Strikingly, this growth advantage in macrophages is inversely correlated with disease severity during mouse infections, suggesting that adaptation to specific host niches can markedly reduce the pathogenicity of these fungi. These results raise intriguing questions about the influence of cyclic AMP (cAMP) signaling on pathogenicity and highlight the role of seemingly small adaptive changes in promoting fundamental shifts in the intracellular behavior and virulence of these important human pathogens.
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Affiliation(s)
- Zoë A Hilbert
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Joseph M Bednarek
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Mara J W Schwiesow
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Krystal Y Chung
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Christian T Moreau
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Jessica C S Brown
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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10
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Sephton-Clark P, Nguyen T, Hoa NT, Ashton P, van Doorn HR, Ly VT, Le T, Cuomo CA. Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam. Genetics 2023; 224:iyad100. [PMID: 37226893 PMCID: PMC10411598 DOI: 10.1093/genetics/iyad100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 03/29/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
Talaromycosis, a severe and invasive fungal infection caused by Talaromyces marneffei, is difficult to treat and impacts those living in endemic regions of Southeast Asia, India, and China. While 30% of infections result in mortality, our understanding of the genetic basis of pathogenesis for this fungus is limited. To address this, we apply population genomics and genome-wide association study approaches to a cohort of 336 T. marneffei isolates collected from patients who enrolled in the Itraconazole vs Amphotericin B for Talaromycosis trial in Vietnam. We find that isolates from northern and southern Vietnam form two distinct geographical clades, with isolates from southern Vietnam associated with increased disease severity. Leveraging longitudinal isolates, we identify multiple instances of disease relapse linked to unrelated strains, highlighting the potential for multistrain infections. In more frequent cases of persistent talaromycosis caused by the same strain, we identify variants arising over the course of patient infections that impact genes predicted to function in the regulation of gene expression and secondary metabolite production. By combining genetic variant data with patient metadata for all 336 isolates, we identify pathogen variants significantly associated with multiple clinical phenotypes. In addition, we identify genes and genomic regions under selection across both clades, highlighting loci undergoing rapid evolution, potentially in response to external pressures. With this combination of approaches, we identify links between pathogen genetics and patient outcomes and identify genomic regions that are altered during T. marneffei infection, providing an initial view of how pathogen genetics affects disease outcomes.
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Affiliation(s)
- Poppy Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thu Nguyen
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Oxford University, Ho Chi Minh City 749000, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX37LG, UK
- Microbiology department and Biological Research Center, Pham Ngoc Thach University of Medicine, Ho Chi Minh City 740500, Vietnam
| | - Philip Ashton
- Veterinary and Ecological Sciences, Institute of Infection, University of Liverpool, Liverpool CH647TE, UK
| | - H Rogier van Doorn
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX37LG, UK
- Oxford University Clinical Research Unit, Oxford University, Hanoi 113000, Vietnam
| | - Vo Trieu Ly
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX37LG, UK
- Department of Medicine and Pharmacy, Hospital for Tropical Diseases, Ho Chi Minh City 749000, Vietnam
| | - Thuy Le
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC 27710, USA
- Tropical Medicine Research Center for Talaromycosis, Pham Ngoc Thach University of Medicine, Ho Chi Minh City 740500, Vietnam
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Sephton-Clark P, Nguyen T, Hoa NT, Ashton P, van Doorn HR, Ly VT, Le T, Cuomo CA. Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534926. [PMID: 37034632 PMCID: PMC10081260 DOI: 10.1101/2023.03.30.534926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Talaromycosis, a severe and invasive fungal infection caused by Talaromyces marneffei , is difficult to treat and impacts those living in endemic regions of southeast Asia, India, and China. While 30% of infections result in mortality, our understanding of the genetic basis of pathogenesis for this fungus is limited. To address this, we apply population genomics and genome wide association study approaches to a cohort of 336 T. marneffei isolates collected from patients who enrolled in the Itraconazole versus Amphotericin B for Talaromycosis (IVAP) trial in Vietnam. We find that isolates from northern and southern Vietnam form two distinct geographical clades, with isolates from southern Vietnam associated with increased disease severity. Leveraging longitudinal isolates, we identify multiple instances of disease relapse linked to unrelated strains, highlighting the potential for multi-strain infections. In more frequent cases of persistent talaromycosis caused by the same strain, we identify variants arising over the course of patient infections that impact genes predicted to function in the regulation of gene expression and secondary metabolite production. By combining genetic variant data with patient metadata for all 336 isolates, we identify pathogen variants significantly associated with multiple clinical phenotypes. In addition, we identify genes and genomic regions under selection across both clades, highlighting loci undergoing rapid evolution, potentially in response to external pressures. With this combination of approaches, we identify links between pathogen genetics and patient outcomes and identify genomic regions that are altered during T. marneffei infection, providing an initial view of how pathogen genetics affects disease outcomes.
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Affiliation(s)
- Poppy Sephton-Clark
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 02142
| | - Thu Nguyen
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, North Carolina, USA 27710
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom OX37LG
- Microbiology department and Biological Research Center, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Philip Ashton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK CH647TE
| | - H. Rogier van Doorn
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom OX37LG
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Vo Trieu Ly
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom OX37LG
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Thuy Le
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, North Carolina, USA 27710
- Tropical Medicine Research Center for Talaromycosis, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Christina A. Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 02142
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