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Coelho MA, David-Palma M, Shea T, Bowers K, McGinley-Smith S, Mohammad AW, Gnirke A, Yurkov AM, Nowrousian M, Sun S, Cuomo CA, Heitman J. Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis. PLoS Biol 2024; 22:e3002682. [PMID: 38843310 PMCID: PMC11185503 DOI: 10.1371/journal.pbio.3002682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 06/18/2024] [Accepted: 05/17/2024] [Indexed: 06/19/2024] Open
Abstract
In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5, or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes showed reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Overall, our findings advance our understanding of genetic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Katharine Bowers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sage McGinley-Smith
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Arman W. Mohammad
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Andrey M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
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2
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Alves MJ, Cruz KS, Alves GSB, Grisolia ME, Menescal VVF, do Nascimento IS, Menescal LSF, Pinheiro SB, da Silva FA, Trilles L, de Souza JVB, Lazera MDS, Jackisch-Matsuura AB. Antifungal susceptibility and multilocus sequence typing (MLST) of Cryptococcus neoformans complex from HIV-associated cryptococcal meningitis patients in Manaus, Amazonas, Brazil. Braz J Microbiol 2024:10.1007/s42770-024-01378-y. [PMID: 38755408 DOI: 10.1007/s42770-024-01378-y] [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: 02/16/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Cryptococcus neoformans is primarily responsible for cases of cryptococcal meningitis in individuals with HIV/AIDS. This study evaluated the susceptibility of C. neoformans obtained from individuals with cryptococcal meningitis associated with HIV/AIDS in Manaus, Amazonas, Brazil, against the action of the antifungals amphotericin B, flucytosine, fluconazole, itraconazole and posaconazole and analyzed it using Multilocus Sequence Typing (MLST) in order to identify the Sequence Types (STs). We analyzed 30 isolates of C. neoformans, from 24 HIV/AIDS patients diagnosed with cryptococcosis from 2017 to 2019 in a reference hospital, in addition to 3 environmental isolates: 1 isolate obtained in the home of a patient and 2 isolates obtained from neighboring homes of patients. 86.6% (n = 26/30) of the clinical isolates were identified as C. neoformans VNI ST93, 6.6% (n = 2/30) as C. neoformans VNI ST5, 3.3% (n = 1/30) as C. neoformans VNI ST32 and 3.3% (n = 1/30) as C. neoformans VNB ST232. The environmental isolates were identified as C. neoformans VNI ST93 (n = 3/3). 96.6% (n = 29/30) isolates were sensitive to amphotericin B, though there was variation in the MIC. 60% (n = 18/30) presented a MIC above the proposed epidemiological cutoff values for one or more antifungals. All environmental isolates were sensitive to the tested antifungals. The MLST showed that there is an important relationship between C. neoformans VNI ST93 and individuals with HIV/AIDS, including in the environmental isolates analyzed. C. neoformans VNB ST232 was observed for the first time in Amazonas. Amphotericin B was proven to be the best drug, but fluconazole and posaconazole also showed relevant action.
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Affiliation(s)
- Marla Jalene Alves
- Laboratório de Diversidade Microbiana da Amazônia com importância para a Saúde, Instituto Leônidas e Maria Deane - FIOCRUZ, Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Convenio ILMD/IOC - FIOCRUZ, Manaus, Amazonas, Brazil
| | - Katia Santana Cruz
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Laboratório de Micologia Médica, Manaus, Amazonas, Brazil
| | - Gleica Soyan Barbosa Alves
- Instituto de Ciências Exatas e Tecnologia, Universidade Federal do Amazonas - UFAM, Itacoatiara, Amazonas, Brazil
| | - Maria Eduarda Grisolia
- Laboratório de Diversidade Microbiana da Amazônia com importância para a Saúde, Instituto Leônidas e Maria Deane - FIOCRUZ, Manaus, Amazonas, Brazil
| | - Victoria Violeta Fernandes Menescal
- Laboratório de Diversidade Microbiana da Amazônia com importância para a Saúde, Instituto Leônidas e Maria Deane - FIOCRUZ, Manaus, Amazonas, Brazil
| | - Izabella Sadalla do Nascimento
- Laboratório de Diversidade Microbiana da Amazônia com importância para a Saúde, Instituto Leônidas e Maria Deane - FIOCRUZ, Manaus, Amazonas, Brazil
| | | | - Silviane Bezerra Pinheiro
- Laboratório de Micologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
- Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Felipe Almeida da Silva
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Luciana Trilles
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Marcia Dos Santos Lazera
- Programa de Pós-Graduação em Medicina Tropical, Convenio ILMD/IOC - FIOCRUZ, Manaus, Amazonas, Brazil
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ani Beatriz Jackisch-Matsuura
- Laboratório de Diversidade Microbiana da Amazônia com importância para a Saúde, Instituto Leônidas e Maria Deane - FIOCRUZ, Manaus, Amazonas, Brazil.
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Coelho MA, David-Palma M, Shea T, Bowers K, McGinley-Smith S, Mohammad AW, Gnirke A, Yurkov AM, Nowrousian M, Sun S, Cuomo CA, Heitman J. Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.27.573464. [PMID: 38234769 PMCID: PMC10793447 DOI: 10.1101/2023.12.27.573464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
A large-scale comparative genomic analysis was conducted for the global human fungal pathogens within the Cryptococcus genus, compared to non-pathogenic Cryptococcus species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species of both genera, resulting in a dataset encompassing virtually all of their known diversity. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at pre-adaptive pathogenic potential, our analysis found evidence in pathogenic Cryptococcus species of specific examples of gene gain (via horizontal gene transfer) and gene loss, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the two genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5 or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes, underwent chromosome reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Taken together, our findings advance our understanding of genomic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Katharine Bowers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrey M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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4
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Abstract
Cryptococcosis is a disease caused by the pathogenic fungi Cryptococcus neoformans and Cryptococcus gattii, both environmental fungi that cause severe pneumonia and may even lead to cryptococcal meningoencephalitis. Although C. neoformans affects more fragile individuals, such as immunocompromised hosts through opportunistic infections, C. gattii causes a serious indiscriminate primary infection in immunocompetent individuals. Typically seen in tropical and subtropical environments, C. gattii has increased its endemic area over recent years, largely due to climatic factors that favor contagion in warmer climates. It is important to point out that not only C. gattii, but the Cryptococcus species complex produces a polysaccharidic capsule with immunomodulatory properties, enabling the pathogenic species of Cryptococccus to subvert the host immune response during the establishment of cryptococcosis, facilitating its dissemination in the infected organism. C. gattii causes a more severe and difficult-to-treat infection, with few antifungals eliciting an effective response during chronic treatment. Much of the immunopathology of this cryptococcosis is still poorly understood, with most studies focusing on cryptococcosis caused by the species C. neoformans. C. gattii became more important in the epidemiological scenario with the outbreaks in the Pacific Northwest of the United States, which resulted in phylogenetic studies of the virulent variant responsible for the severe infection in the region. Since then, the study of cryptococcosis caused by C. gattii has helped researchers understand the immunopathological aspects of different variants of this pathogen.
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Naicker SD, Firacative C, van Schalkwyk E, Maphanga TG, Monroy-Nieto J, Bowers JR, Engelthaler DM, Meyer W, Govender NP. Molecular type distribution and fluconazole susceptibility of clinical Cryptococcus gattii isolates from South African laboratory-based surveillance, 2005–2013. PLoS Negl Trop Dis 2022; 16:e0010448. [PMID: 35767529 PMCID: PMC9242473 DOI: 10.1371/journal.pntd.0010448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Abstract
As is the case globally, Cryptococcus gattii is a less frequent cause of cryptococcosis than Cryptococcus neoformans in South Africa. We performed multilocus sequence typing (MLST) and fluconazole susceptibility testing of 146 isolates randomly selected from 750 South African patients with C. gattii disease identified through enhanced laboratory surveillance, 2005 to 2013. The dominant molecular type was VGIV (101/146, 70%), followed by VGI (40/146, 27%), VGII (3/146, 2%) and VGIII (2/146, 1%). Among the 146 C. gattii isolates, 99 different sequence types (STs) were identified, with ST294 (14/146, 10%) and ST155 (10/146, 7%) being most commonly observed. The fluconazole MIC50 and MIC90 values of 105 (of 146) randomly selected C. gattii isolates were 4 μg/ml and 16 μg/ml, respectively. VGIV isolates had a lower MIC50 value compared to non-VGIV isolates, but these values were within one double-dilution of each other. HIV-seropositive patients had a ten-fold increased adjusted odds of a VGIV infection compared to HIV-seronegative patients, though with small numbers (99/136; 73% vs. 2/10; 20%), the confidence interval (CI) was wide (95% CI: 1.93–55.31, p = 0.006). Whole genome phylogeny of 98 isolates of South Africa’s most prevalent molecular type, VGIV, identified that this molecular type is highly diverse, with two interesting clusters of ten and six closely related isolates being identified, respectively. One of these clusters consisted only of patients from the Mpumalanga Province in South Africa, suggesting a similar environmental source. This study contributed new insights into the global population structure of this important human pathogen. Cryptococcus is the most common cause of meningitis among adults in South Africa. Most human disease is caused by the members of two species complexes within the genus, Cryptococcus neoformans and Cryptococcus gattii. The environmental range of these species complexes, both found in soil, overlaps in southern Africa though C. gattii is a less common human pathogen. C. gattii is divided into six molecular types: VGI, VGII, VGIII, VGIV, VGV and VGVI. In earlier molecular epidemiology studies including relatively few isolates, most southern African isolates were confirmed as molecular type VGIV. We aimed to determine the molecular diversity of C. gattii in South Africa by genotyping patient isolates obtained through laboratory surveillance, 2005–2013. We confirmed that VGIV was the dominant molecular type and that HIV-seropositive patients were more likely to be infected with VGIV compared to those HIV-seronegative. Analysis of the genomes of South African VGIV isolates revealed that they spanned the whole VGIV clade and confirmed that most isolates did not cluster specifically. However, we observed two interesting clusters of closely related isolates, consisting of patients from three neighbouring provinces in South Africa, suggesting a similar environmental source. Further studies of clinical and environmental African C. gattii isolates are needed to gain a better understanding of this pathogen.
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Affiliation(s)
- Serisha D. Naicker
- National Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Carolina Firacative
- Studies in Translational Microbiology and Emerging Diseases (MICROS) Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Erika van Schalkwyk
- National Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Tsidiso G. Maphanga
- National Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Juan Monroy-Nieto
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Jolene R. Bowers
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - David M. Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Research and Educational Network, Westmead Hospital, Western Sydney Local Health District, Westmead, New South Wales, Australia
- Curtin Medical School, Curtin University, Perth, Australia
| | - Nelesh P. Govender
- National Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Medical Research Council Centre for Medical Mycology, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
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Central Nervous System Cryptococcosis due to Cryptococcus gattii in the Tropics. CURRENT TROPICAL MEDICINE REPORTS 2022; 9:1-7. [PMID: 35378784 PMCID: PMC8967080 DOI: 10.1007/s40475-022-00253-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 10/27/2022]
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7
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Genetic and Phenotypic Diversities in Experimental Populations of Diploid Inter-Lineage Hybrids in the Human Pathogenic Cryptococcus. Microorganisms 2021; 9:microorganisms9081579. [PMID: 34442658 PMCID: PMC8398696 DOI: 10.3390/microorganisms9081579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/18/2021] [Accepted: 07/22/2021] [Indexed: 11/29/2022] Open
Abstract
To better understand the potential factors contributing to genome instability and phenotypic diversity, we conducted mutation accumulation (MA) experiments for 120 days for 7 diploid cryptococcal hybrids under fluconazole (10 MA lines each) and non-fluconazole conditions (10 MA lines each). The genomic DNA content, loss of heterozygosity (LOH) rate, growth ability, and fluconazole susceptibility were determined for all 140 evolved cultures. Compared to that of their ancestral clones, the evolved clones showed: (i) genomic DNA content changes ranging from ~22% less to ~27% more, and (ii) reduced, similar, and increased phenotypic values for each tested trait, with most evolved clones displaying increased growth at 40 °C and increased fluconazole resistance. Aside from the ancestral multi-locus genotypes (MLGs) and heterozygosity patterns (MHPs), 77 unique MLGs and 70 unique MPHs were identified among the 140 evolved cultures at day 120. The average LOH rates of the MA lines in the absence and presence of fluconazole were similar at 1.27 × 10−4 and 1.38 × 10−4 LOH events per MA line per mitotic division, respectively. While LOH rates varied among MA lines from different ancestors, there was no apparent correlation between the genetic divergence of the parental haploid genomes within ancestral clones and LOH rates. Together, our results suggest that hybrids between diverse lineages of the human pathogenic Cryptococcus can generate significant genotypic and phenotypic diversities during asexual reproduction.
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Danesi P, Falcaro C, Schmertmann LJ, de Miranda LHM, Krockenberger M, Malik R. Cryptococcus in Wildlife and Free-Living Mammals. J Fungi (Basel) 2021; 7:jof7010029. [PMID: 33419125 PMCID: PMC7825559 DOI: 10.3390/jof7010029] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/22/2020] [Accepted: 01/01/2021] [Indexed: 12/21/2022] Open
Abstract
Cryptococcosis is typically a sporadic disease that affects a broad range of animal species globally. Disease is a consequence of infection with members of the Cryptococcus neoformans or Cryptococcus gattii species complexes. Although cryptococcosis in many domestic animals has been relatively well-characterized, free-living wildlife animal species are often neglected in the literature outside of occasional case reports. This review summarizes the clinical presentation, pathological findings and potential underlying causes of cryptococcosis in various other animals, including terrestrial wildlife species and marine mammals. The evaluation of the available literature supports the hypothesis that anatomy (particularly of the respiratory tract), behavior and environmental exposures of animals play vital roles in the outcome of host–pathogen–environment interactions resulting in different clinical scenarios. Key examples range from koalas, which exhibit primarily C. gattii species complex disease presumably due to their behavior and environmental exposure to eucalypts, to cetaceans, which show predominantly pulmonary lesions due to their unique respiratory anatomy. Understanding the factors at play in each clinical scenario is a powerful investigative tool, as wildlife species may act as disease sentinels.
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Affiliation(s)
- Patrizia Danesi
- Laboratory of Parasitology, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padua, Italy;
- Correspondence:
| | - Christian Falcaro
- Laboratory of Parasitology, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padua, Italy;
| | - Laura J. Schmertmann
- Veterinary Pathology Diagnostic Services, Sydney School of Veterinary Science, The University of Sydney, Sydney 2006, Australia; (L.J.S.); (L.H.M.d.M.); (M.K.)
| | - Luisa Helena Monteiro de Miranda
- Veterinary Pathology Diagnostic Services, Sydney School of Veterinary Science, The University of Sydney, Sydney 2006, Australia; (L.J.S.); (L.H.M.d.M.); (M.K.)
| | - Mark Krockenberger
- Veterinary Pathology Diagnostic Services, Sydney School of Veterinary Science, The University of Sydney, Sydney 2006, Australia; (L.J.S.); (L.H.M.d.M.); (M.K.)
| | - Richard Malik
- Centre for Veterinary Education, The University of Sydney, Sydney 2006, Australia;
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Hao S, Han K, Meng L, Huang X, Cao W, Shi C, Zhang M, Wang Y, Liu Q, Zhang Y, Sun H, Seim I, Xu X, Liu X, Fan G. African Arowana Genome Provides Insights on Ancient Teleost Evolution. iScience 2020; 23:101662. [PMID: 33134892 PMCID: PMC7586111 DOI: 10.1016/j.isci.2020.101662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/27/2020] [Accepted: 10/07/2020] [Indexed: 12/11/2022] Open
Abstract
Osteoglossiformes is a basal clade of teleost, evolving since the Jurassic period. The genomes of Osteoglossiformes species would shed light on the evolution and adaptation of teleost. Here, we established a chromosome-level genome of African arowana. Together with the genomes of pirarucu and Asian arowana, we found that they diverged at ∼106.1 million years ago (MYA) and ∼59.2 MYA, respectively, which are coincident with continental separation. Interestingly, we identified a dynamic genome evolution characterized by a fast evolutionary rate and a high pseudogenization rate in African arowana and pirarucu. Additionally, more transposable elements were found in Asian arowana which confer more gene duplications. Moreover, we found the contraction of olfactory receptor and the expansion of UGT in African arowana might be related to its transformation from carnivore to be omnivore. Taken together, we provided valuable genomic resource of Osteoglossidae and revealed the correlation of biogeography and teleost evolution. An evolutionary model of Osteoglossidae along the continental drift is provided A faster evolving rate of African arowana than Asian arowana is revealed The gene duplications of Asian arowana are related to more class I TE insertions A mechanism of African arowana’s feeding habits transition is proposed.
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Affiliation(s)
- Shijie Hao
- BGI Education Center, University of Chinese Academic of Sciences, Shenzhen 518083, China.,BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China
| | - Kai Han
- BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China
| | - Lingfeng Meng
- BGI Education Center, University of Chinese Academic of Sciences, Shenzhen 518083, China.,BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China
| | | | - Wei Cao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chengcheng Shi
- BGI Education Center, University of Chinese Academic of Sciences, Shenzhen 518083, China.,BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China
| | - Mengqi Zhang
- BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China
| | - Yilin Wang
- BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China
| | - Qun Liu
- BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China
| | - Yaolei Zhang
- BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Haixi Sun
- BGI-Shenzhen, Shenzhen 518083, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China.,School of Biology and Environmental Science, Queensland University of Technology, Brisbane 4102, QLD, Australia
| | - Xun Xu
- BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Xin Liu
- BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Guangyi Fan
- BGI-Qingqao, BGI-Shenzhen, Qingdao, 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
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10
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Hybridization Facilitates Adaptive Evolution in Two Major Fungal Pathogens. Genes (Basel) 2020; 11:genes11010101. [PMID: 31963231 PMCID: PMC7017293 DOI: 10.3390/genes11010101] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/02/2020] [Accepted: 01/14/2020] [Indexed: 01/13/2023] Open
Abstract
Hybridization is increasingly recognized as an important force impacting adaptation and evolution in many lineages of fungi. During hybridization, divergent genomes and alleles are brought together into the same cell, potentiating adaptation by increasing genomic plasticity. Here, we review hybridization in fungi by focusing on two fungal pathogens of animals. Hybridization is common between the basidiomycete yeast species Cryptococcus neoformans × Cryptococcus deneoformans, and hybrid genotypes are frequently found in both environmental and clinical settings. The two species show 10-15% nucleotide divergence at the genome level, and their hybrids are highly heterozygous. Though largely sterile and unable to mate, these hybrids can propagate asexually and generate diverse genotypes by nondisjunction, aberrant meiosis, mitotic recombination, and gene conversion. Under stress conditions, the rate of such genetic changes can increase, leading to rapid adaptation. Conversely, in hybrids formed between lineages of the chytridiomycete frog pathogen Batrachochytrium dendrobatidis (Bd), the parental genotypes are considerably less diverged (0.2% divergent). Bd hybrids are formed from crosses between lineages that rarely undergo sex. A common theme in both species is that hybrids show genome plasticity via aneuploidy or loss of heterozygosity and leverage these mechanisms as a rapid way to generate genotypic/phenotypic diversity. Some hybrids show greater fitness and survival in both virulence and virulence-associated phenotypes than parental lineages under certain conditions. These studies showcase how experimentation in model species such as Cryptococcus can be a powerful tool in elucidating the genotypic and phenotypic consequences of hybridization.
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11
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Chrissian C, Camacho E, Fu MS, Prados-Rosales R, Chatterjee S, Cordero RJB, Lodge JK, Casadevall A, Stark RE. Melanin deposition in two Cryptococcus species depends on cell-wall composition and flexibility. J Biol Chem 2020; 295:1815-1828. [PMID: 31896575 DOI: 10.1074/jbc.ra119.011949] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/31/2019] [Indexed: 12/14/2022] Open
Abstract
Cryptococcus neoformans and Cryptococcus gattii are two species complexes in the large fungal genus Cryptococcus and are responsible for potentially lethal disseminated infections. These two complexes share several phenotypic traits, such as production of the protective compound melanin. In C. neoformans, the pigment associates with key cellular constituents that are essential for melanin deposition within the cell wall. Consequently, melanization is modulated by changes in cell-wall composition or ultrastructure. However, whether similar factors influence melanization in C. gattii is unknown. Herein, we used transmission EM, biochemical assays, and solid-state NMR spectroscopy of representative isolates and "leaky melanin" mutant strains from each species complex to examine the compositional and structural factors governing cell-wall pigment deposition in C. neoformans and C. gattii. The principal findings were the following. 1) C. gattii R265 had an exceptionally high chitosan content compared with C. neoformans H99; a rich chitosan composition promoted homogeneous melanin distribution throughout the cell wall but did not increase the propensity of pigment deposition. 2) Strains from both species manifesting the leaky melanin phenotype had reduced chitosan content, which was compensated for by the production of lipids and other nonpolysaccharide constituents that depended on the species or mutation. 3) Changes in the relative rigidity of cell-wall chitin were associated with aberrant pigment retention, implicating cell-wall flexibility as an independent variable in cryptococcal melanin assembly. Overall, our results indicate that cell-wall composition and molecular architecture are critical factors for the anchoring and arrangement of melanin pigments in both C. neoformans and C. gattii species complexes.
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Affiliation(s)
- Christine Chrissian
- Department of Chemistry and Biochemistry, City College of New York and CUNY Institute for Macromolecular Assemblies, New York, New York 10031; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016
| | - Emma Camacho
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Man Shun Fu
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Rafael Prados-Rosales
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York 10033; Department of Preventive Medicine and Public Health and Microbiology, Autonoma University of Madrid, 28049 Madrid, Spain
| | - Subhasish Chatterjee
- Department of Chemistry and Biochemistry, City College of New York and CUNY Institute for Macromolecular Assemblies, New York, New York 10031
| | - Radames J B Cordero
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Jennifer K Lodge
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Ruth E Stark
- Department of Chemistry and Biochemistry, City College of New York and CUNY Institute for Macromolecular Assemblies, New York, New York 10031; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016; Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016.
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12
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Sun S, Coelho MA, David-Palma M, Priest SJ, Heitman J. The Evolution of Sexual Reproduction and the Mating-Type Locus: Links to Pathogenesis of Cryptococcus Human Pathogenic Fungi. Annu Rev Genet 2019; 53:417-444. [PMID: 31537103 PMCID: PMC7025156 DOI: 10.1146/annurev-genet-120116-024755] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cryptococcus species utilize a variety of sexual reproduction mechanisms, which generate genetic diversity, purge deleterious mutations, and contribute to their ability to occupy myriad environmental niches and exhibit a range of pathogenic potential. The bisexual and unisexual cycles of pathogenic Cryptococcus species are stimulated by properties associated with their environmental niches and proceed through well-characterized signaling pathways and corresponding morphological changes. Genes governing mating are encoded by the mating-type (MAT) loci and influence pathogenesis, population dynamics, and lineage divergence in Cryptococcus. MAT has undergone significant evolutionary changes within the Cryptococcus genus, including transition from the ancestral tetrapolar state in nonpathogenic species to a bipolar mating system in pathogenic species, as well as several internal reconfigurations. Owing to the variety of established sexual reproduction mechanisms and the robust characterization of the evolution of mating and MAT in this genus, Cryptococcus species provide key insights into the evolution of sexual reproduction.
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Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| | - Shelby J Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
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13
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Sun S, Coelho MA, Heitman J, Nowrousian M. Convergent evolution of linked mating-type loci in basidiomycete fungi. PLoS Genet 2019; 15:e1008365. [PMID: 31490920 PMCID: PMC6730849 DOI: 10.1371/journal.pgen.1008365] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Sexual development is a key evolutionary innovation of eukaryotes. In many species, mating involves interaction between compatible mating partners that can undergo cell and nuclear fusion and subsequent steps of development including meiosis. Mating compatibility in fungi is governed by the mating type (MAT) loci. In basidiomycetes, the ancestral state is hypothesized to be tetrapolar, with two genetically unlinked MAT loci containing homeodomain transcription factor genes (HD locus) and pheromone and pheromone receptor genes (P/R locus), respectively. Alleles at both loci must differ between mating partners for completion of sexual development. However, there are also basidiomycetes with bipolar mating systems, which can arise through genomic linkage of the HD and P/R loci. In the order Tremellales, bipolarity is found only in the pathogenic Cryptococcus species. Here, we describe the analysis of MAT loci from 24 species of the Trichosporonales, a sister order to the Tremellales. In all of the species analyzed, the MAT loci are fused and a single HD gene is present in each mating type, similar to the organization in the pathogenic Cryptococci. However, the HD and P/R allele combinations in the Trichosporonales are different from those in the pathogenic Cryptococci. This and the existence of tetrapolar species in the Tremellales suggest that fusion of the HD and P/R loci occurred independently in the Trichosporonales and pathogenic Cryptococci, supporting the hypothesis of convergent evolution towards fused MAT regions, similar to previous findings in other fungal groups. Unlike the fused MAT loci in several other basidiomycete lineages though, the gene content and gene order within the fused MAT loci are highly conserved in the Trichosporonales, and there is no apparent suppression of recombination extending from the MAT loci to adjacent chromosomal regions, suggesting different mechanisms for the evolution of physically linked MAT loci in these groups.
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Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
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14
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El Helou G, Hellinger W. Cryptococcus
neoformans
pericarditis in a lung transplant recipient: Case report, literature review and pearls. Transpl Infect Dis 2019; 21:e13137. [DOI: 10.1111/tid.13137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/13/2019] [Accepted: 06/26/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Guy El Helou
- Division of Infectious Disease and global health, Department of Medicine University of Florida Health Gainesville Florida
| | - Walter Hellinger
- Division of Infectious Disease, Department of internal medicine Mayo Clinic Jacksonville Florida
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15
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Ponzio V, Chen Y, Rodrigues AM, Tenor JL, Toffaletti DL, Medina-Pestana JO, Colombo AL, Perfect JR. Genotypic diversity and clinical outcome of cryptococcosis in renal transplant recipients in Brazil. Emerg Microbes Infect 2019; 8:119-129. [PMID: 30866766 PMCID: PMC6455115 DOI: 10.1080/22221751.2018.1562849] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genotypic diversity and fluconazole susceptibility of 82 Cryptococcus neoformans and Cryptococcus gattii isolates from 60 renal transplant recipients in Brazil were characterized. Clinical characteristics of the patients and prognostic factors were analysed. Seventy-two (87.8%) isolates were C. neoformans and 10 (12.2%) were C. gattii. VNI was the most common molecular type (40 cases; 66.7%), followed by VNII (9 cases; 15%), VGII (6 cases; 10%), VNB (4 cases; 6.7%) and VNI/II (1 case; 1.7%). The isolates showed a high genetic diversity in the haplotype network and six new sequence types were described, most of them for VNB. There was a bias towards skin involvement in the non-VNI population (P = .012). VGII isolates exhibited higher fluconazole minimum inhibitory concentrations compared to C. neoformans isolates (P = 0.008). The 30-day mortality rate was 38.3%, and it was significantly associated with fungemia and absence of headache. Patients infected with VGII had a high mortality rate at 90 days (66.7%). A variety of molecular types produce disease in renal transplant recipients in Brazil and highlighted by VGII and VNB. We report the clinical appearance and impact of the molecular type, fluconazole susceptibility of the isolates, and clinical characteristics on patient outcome in this population.
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Affiliation(s)
- Vinicius Ponzio
- a Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina , Universidade Federal de São Paulo (UNIFESP) , São Paulo , Brazil
| | - Yuan Chen
- b Division of Infectious Disease, Department of Medicine , Duke University School of Medicine , Durham , NC , USA
| | - Anderson Messias Rodrigues
- c Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology and Parasitology , Universidade Federal de São Paulo (UNIFESP) , São Paulo , Brazil
| | - Jennifer L Tenor
- b Division of Infectious Disease, Department of Medicine , Duke University School of Medicine , Durham , NC , USA
| | - Dena L Toffaletti
- b Division of Infectious Disease, Department of Medicine , Duke University School of Medicine , Durham , NC , USA
| | - José Osmar Medina-Pestana
- d Hospital do Rim Oswaldo Ramos Foundation, Discipline of Nephrology , Universidade Federal de São Paulo (UNIFESP) , São Paulo , Brazil
| | - Arnaldo Lopes Colombo
- a Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina , Universidade Federal de São Paulo (UNIFESP) , São Paulo , Brazil
| | - John R Perfect
- b Division of Infectious Disease, Department of Medicine , Duke University School of Medicine , Durham , NC , USA
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16
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Lockhart SR, Roe CC, Engelthaler DM. Timing the Origin of Cryptococcus gattii sensu stricto, Southeastern United States. Emerg Infect Dis 2019; 24:2095-2097. [PMID: 30334716 PMCID: PMC6200013 DOI: 10.3201/eid2411.180975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We conducted molecular clock analysis of whole-genome sequences from a set of autochthonous isolates of Cryptococcus gattii sensu stricto from the southeastern United States. Our analysis indicates that C. gattii arrived in the southeastern United States approximately 9,000–19,000 years ago, long before its arrival in the Pacific Northwest.
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17
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Abstract
Diagnosing fungal infections poses a number of unique problems, including a decline in expertise needed for identifying fungi, and a reduced number of instruments and assays specific for fungal identification compared to that of bacteria and viruses.These problems are exacerbated by the fact that patients with fungal infections are often immunosuppressed, which predisposes to infections from both commonly and rarely seen fungi. In this review, we discuss current and future molecular technologies used for fungal identification, and some of the problems associated with development and implementation of these technologies in today’s clinical microbiology laboratories. Diagnosing fungal infections poses a number of unique problems. In this Review, Wickes and Wiederhold discuss molecular technologies used for fungal identification, and the problems associated with their development and implementation in today’s clinical microbiology laboratories.
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18
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Camacho E, Casadevall A. Cryptococcal Traits Mediating Adherence to Biotic and Abiotic Surfaces. J Fungi (Basel) 2018; 4:jof4030088. [PMID: 30060601 PMCID: PMC6162697 DOI: 10.3390/jof4030088] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 07/25/2018] [Accepted: 07/27/2018] [Indexed: 01/22/2023] Open
Abstract
Several species in the genus Cryptococcus are facultative intracellular pathogens capable of causing disease associated with high mortality and morbidity in humans. These fungi interact with other organisms in the soil, and these interactions may contribute to the development of adaptation mechanisms that function in virulence by promoting fungal survival in animal hosts. Fungal adhesion molecules, also known as adhesins, have been classically considered as cell-surface or secreted proteins that play critical roles in microbial pathogenesis or in biofilm formation as structural components. Pathogenic Cryptococcus spp. differ from other pathogenic yeasts in having a polysaccharide capsule that covers the cell wall surface and precludes interactions of those structures with host cell receptors. Hence, pathogenic Cryptococcus spp. use unconventional tools for surface attachment. In this essay, we review the unique traits and mechanisms favoring adhesion of Cryptococcus spp. to biotic and abiotic surfaces. Knowledge of the traits that mediate adherence could be exploited in the development of therapeutic, biomedical, and/or industrial products.
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Affiliation(s)
- Emma Camacho
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, 615 N Wolfe St Room E5132, Baltimore, MD 21205, USA.
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, 615 N Wolfe St Room E5132, Baltimore, MD 21205, USA.
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19
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Freij JB, Fu MS, De Leon Rodriguez CM, Dziedzic A, Jedlicka AE, Dragotakes Q, Rossi DCP, Jung EH, Coelho C, Casadevall A. Conservation of Intracellular Pathogenic Strategy among Distantly Related Cryptococcal Species. Infect Immun 2018; 86:e00946-17. [PMID: 29712729 PMCID: PMC6013651 DOI: 10.1128/iai.00946-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/02/2018] [Indexed: 01/22/2023] Open
Abstract
The genus Cryptococcus includes several species pathogenic for humans. Until recently, the two major pathogenic species were recognized to be Cryptococcus neoformans and Cryptococcus gattii We compared the interaction of murine macrophages with three C. gattii species complex strains (WM179, R265, and WM161, representing molecular types VGI, VGIIa, and VGIII, respectively) and one C. neoformans species complex strain (H99, molecular type VNI) to ascertain similarities and differences in the yeast intracellular pathogenic strategy. The parameters analyzed included nonlytic exocytosis frequency, phagolysosomal pH, intracellular capsular growth, phagolysosomal membrane permeabilization, and macrophage transcriptional response, assessed using time-lapse microscopy, fluorescence microscopy, flow cytometry, and gene expression microarray analysis. The most striking result was that the intracellular pathogenic strategies of C. neoformans and C. gattii species complex strains were qualitatively similar, despite the species having separated an estimated 100 million years ago. Macrophages exhibited a leaky phagolysosomal membrane phenotype and nonlytic exocytosis when infected with either C. gattii or C. neoformans Conservation of the intracellular strategy among species that separated long ago suggests that it is ancient and possibly maintained by similar selection pressures through eons.
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Affiliation(s)
- Joudeh B Freij
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Man Shun Fu
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Amanda Dziedzic
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Anne E Jedlicka
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Quigly Dragotakes
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Diego C P Rossi
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Eric H Jung
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Albert Einstein School of Medicine, Department of Microbiology and Immunology, New York, New York, USA
| | - Carolina Coelho
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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20
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Nnadi EN, Enweani IB, Ayanbimpe GM. Infection of Chick Chorioallantoic Membrane (CAM) as a Model for the Pathogenesis of Cryptococcus gattii. Med Mycol J 2018; 59:E25-E30. [PMID: 29848908 DOI: 10.3314/mmj.17-00018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Emmanuel Nnaemeka Nnadi
- Department of Microbiology, Faculty of Natural and Applied Sciences, Plateau State University
| | - Ifeoma Bessie Enweani
- Department of Medical Laboratory Science, Faculty of health sciences and Technology, Nnamdi Azikiwe University
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21
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de S Araújo GR, Souza WD, Frases S. The hidden pathogenic potential of environmental fungi. Future Microbiol 2017; 12:1533-1540. [PMID: 29168657 DOI: 10.2217/fmb-2017-0124] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Invasive fungal infections are a growing threat to immunocompromised patients, highlighting the importance of monitoring fungal pathogens. Global warming (including climatic oscillations) may select for environmental species that have acquired thermotolerance, a key step toward pathogenesis to humans. Also, important virulence factors have developed in environmental fungi, because they are essential for yeast survival in the environment. Thus, fungi traditionally regarded as nonpathogenic to humans have virulence factors similar to those of their pathogenic relatives. Here, we highlight the emergence of saprophytic environmental fungi - including species of Cryptococcus, Aspergillus, Penicillium, Candida and Scedosporium - as new human pathogens. Emerging pathogens are, in some cases, resistant to the available antifungals, potentiating the threat of novel fungal diseases.
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Affiliation(s)
- Glauber R de S Araújo
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Susana Frases
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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22
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Ecoepidemiology of Cryptococcus gattii in Developing Countries. J Fungi (Basel) 2017; 3:jof3040062. [PMID: 29371578 PMCID: PMC5753164 DOI: 10.3390/jof3040062] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 01/06/2023] Open
Abstract
Cryptococcosis is a systemic infection caused by species of the encapsulated yeast Cryptococcus. The disease may occur in immunocompromised and immunocompetent hosts and is acquired by the inhalation of infectious propagules present in the environment. Cryptococcus is distributed in a plethora of ecological niches, such as soil, pigeon droppings, and tree hollows, and each year new reservoirs are discovered, which helps researchers to better understand the epidemiology of the disease. In this review, we describe the ecoepidemiology of the C. gattii species complex focusing on clinical cases and ecological reservoirs in developing countries from different continents. We also discuss some important aspects related to the antifungal susceptibility of different species within the C. gattii species complex and bring new insights on the revised Cryptococcus taxonomy.
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23
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Hagen F, Lumbsch HT, Arsic Arsenijevic V, Badali H, Bertout S, Billmyre RB, Bragulat MR, Cabañes FJ, Carbia M, Chakrabarti A, Chaturvedi S, Chaturvedi V, Chen M, Chowdhary A, Colom MF, Cornely OA, Crous PW, Cuétara MS, Diaz MR, Espinel-Ingroff A, Fakhim H, Falk R, Fang W, Herkert PF, Ferrer Rodríguez C, Fraser JA, Gené J, Guarro J, Idnurm A, Illnait-Zaragozi MT, Khan Z, Khayhan K, Kolecka A, Kurtzman CP, Lagrou K, Liao W, Linares C, Meis JF, Nielsen K, Nyazika TK, Pan W, Pekmezovic M, Polacheck I, Posteraro B, de Queiroz Telles F, Romeo O, Sánchez M, Sampaio A, Sanguinetti M, Sriburee P, Sugita T, Taj-Aldeen SJ, Takashima M, Taylor JW, Theelen B, Tomazin R, Verweij PE, Wahyuningsih R, Wang P, Boekhout T. Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus. mSphere 2017; 2:e00238-17. [PMID: 28875175 PMCID: PMC5577652 DOI: 10.1128/msphere.00238-17] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoformans were raised to species level, and the same was done for five genotypes within C. gattii. In a recent perspective (K. J. Kwon-Chung et al., mSphere 2:e00357-16, 2017, https://doi.org/10.1128/mSphere.00357-16), it was argued that this taxonomic proposal was premature and without consensus in the community. Although the authors of the perspective recognized the existence of genetic diversity, they preferred the use of the informal nomenclature "C. neoformans species complex" and "C. gattii species complex." Here we highlight the advantage of recognizing these seven species, as ignoring these species will impede deciphering further biologically and clinically relevant differences between them, which may in turn delay future clinical advances.
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Affiliation(s)
- Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | | | | | - Hamid Badali
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Sebastien Bertout
- Unité Mixte Internationale Recherches Translationnelles sur l’Infection à VIH et les Maladies Infectieuses, Laboratoire de Parasitologie et Mycologie Médicale, UFR Pharmacie, Université Montpellier, Montpellier, France
| | - R. Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - M. Rosa Bragulat
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - F. Javier Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Mauricio Carbia
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Min Chen
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | | | - Oliver A. Cornely
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
- Center for Clinical Trials, University Hospital Cologne, Cologne, Germany
| | - Pedro W. Crous
- Phytopathology Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Maria S. Cuétara
- Department of Microbiology, Hospital Severo Ochoa, Madrid, Spain
| | - Mara R. Diaz
- University of Miami, NSF NIEHS Oceans and Human Health Center, Miami, Florida, USA
- Rosentiel School of Marine and Atmospheric Science, Division of Marine Biology and Fisheries, University of Miami, Miami, Florida, USA
| | | | - Hamed Fakhim
- Department of Medical Parasitology and Mycology/Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Rama Falk
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
- Department of Fisheries and Aquaculture, Ministry of Agriculture and Rural Development, Nir-David, Israel
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Patricia F. Herkert
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Postgraduate Program in Microbiology, Parasitology and Pathology, Biological Sciences, Department of Basic Pathology, Federal University of Parana, Curitiba, Brazil
| | | | - James A. Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Josepa Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Josep Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Alexander Idnurm
- School of BioSciences, BioSciences 2, University of Melbourne, Melbourne, Australia
| | | | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, Thailand
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Kolecka
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Cletus P. Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Katrien Lagrou
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Carlos Linares
- Medical School, Universidad Miguel Hernández, Alicante, Spain
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tinashe K. Nyazika
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
- Malawi-Liverpool-Wellcome Trust, College of Medicine, University of Malawi, Blantyre, Malawi
- School of Tropical Medicine, Liverpool, United Kingdom
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | | | - Itzhack Polacheck
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Flavio de Queiroz Telles
- Department of Communitarian Health, Hospital de Clínicas, Federal University of Parana, Curitiba, Brazil
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- IRCCS Centro Neurolesi Bonino-Pulejo, Messina, Italy
| | - Manuel Sánchez
- Medical School, Universidad Miguel Hernández, Alicante, Spain
| | - Ana Sampaio
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro (UTAD), Quinta dos Prados, Vila Real, Portugal
| | - Maurizio Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Pojana Sriburee
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, Noshio, Kiyose, Tokyo, Japan
| | - Saad J. Taj-Aldeen
- Mycology Unit, Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, Japan
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Bart Theelen
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Rok Tomazin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Paul E. Verweij
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Retno Wahyuningsih
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Parasitology, School of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Ping Wang
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
- Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Teun Boekhout
- Institute of Biodiversity and Ecosystems Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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Reply to Engelthaler and Meyer, “Furthering the Continental Drift Speciation Hypothesis in the Pathogenic
Cryptococcus
Species Complexes”. mSphere 2017. [PMID: 28635996 PMCID: PMC5471351 DOI: 10.1128/msphere.00242-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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