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Sepúlveda VE, Goldman WE, Matute DR. Genotypic diversity, virulence, and molecular genetic tools in Histoplasma. Microbiol Mol Biol Rev 2024; 88:e0007623. [PMID: 38819148 DOI: 10.1128/mmbr.00076-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
Abstract
SUMMARYHistoplasmosis is arguably the most common fungal respiratory infection worldwide, with hundreds of thousands of new infections occurring annually in the United States alone. The infection can progress in the lung or disseminate to visceral organs and can be difficult to treat with antifungal drugs. Histoplasma, the causative agent of the disease, is a pathogenic fungus that causes life-threatening lung infections and is globally distributed. The fungus has the ability to germinate from conidia into either hyphal (mold) or yeast form, depending on the environmental temperature. This transition also regulates virulence. Histoplasma and histoplasmosis have been classified as being of emergent importance, and in 2022, the World Health Organization included Histoplasma as 1 of the 19 most concerning human fungal pathogens. In this review, we synthesize the current understanding of the ecological niche, evolutionary history, and virulence strategies of Histoplasma. We also describe general patterns of the symptomatology and epidemiology of histoplasmosis. We underscore areas where research is sorely needed and highlight research avenues that have been productive.
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Affiliation(s)
- Victoria E Sepúlveda
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William E Goldman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel R Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Sepúlveda VE, Rader JA, Li JJ, Goldman WE, Matute DR. Phenotypic characterization of cryptic species in the fungal pathogen Histoplasma. mSphere 2024; 9:e0000924. [PMID: 38771035 DOI: 10.1128/msphere.00009-24] [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: 01/04/2024] [Accepted: 04/11/2024] [Indexed: 05/22/2024] Open
Abstract
Histoplasmosis is an endemic mycosis that often presents as a respiratory infection in immunocompromised patients. Hundreds of thousands of new infections are reported annually around the world. The etiological agent of the disease, Histoplasma, is a dimorphic fungus commonly found in the soil where it grows as mycelia. Humans can become infected by Histoplasma through inhalation of its spores (conidia) or mycelial particles. The fungi transition into the yeast phase in the lungs at 37°C. Once in the lungs, yeast cells reside and proliferate inside alveolar macrophages. Genomic work has revealed that Histoplasma is composed of at least five cryptic phylogenetic species that differ genetically. Three of those lineages have received new names. Here, we evaluated multiple phenotypic characteristics (colony morphology, secreted proteolytic activity, yeast size, and growth rate) of strains from five of the phylogenetic species of Histoplasma to identify phenotypic traits that differentiate between these species: Histoplasma capsulatum sensu stricto, Histoplasma ohiense, Histoplasma mississippiense, Histoplasma suramericanum, and an African lineage. We report diagnostic traits for three species. The other two species can be identified by a combination of traits. Our results suggest that (i) there are significant phenotypic differences among the cryptic species of Histoplasma and (ii) those differences can be used to positively distinguish those species in a clinical setting and for further study of the evolution of this fungal pathogen.IMPORTANCEIdentifying species boundaries is a critical component of evolutionary biology. Genome sequencing and the use of molecular markers have advanced our understanding of the evolutionary history of fungal pathogens, including Histoplasma, and have allowed for the identification of new species. This is especially important in organisms where morphological characteristics have not been detected. In this study, we revised the taxonomic status of the four named species of the genus Histoplasma, H. capsulatum sensu stricto (ss), H. ohiense, H. mississippiense, and H. suramericanum, and propose the use of species-specific phenotypic traits to aid their identification when genome sequencing is not available. These results have implications not only for evolutionary study of Histoplasma but also for clinicians, as the Histoplasma species could determine the outcome of disease and treatment needed.
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Affiliation(s)
- Victoria E Sepúlveda
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan A Rader
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jingbaoyi Janet Li
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William E Goldman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel R Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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3
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Gandhi P, Hebert B, Yun A, Bradley J, Moldoveanu B. Histoplasmosis around the world: A global perspective on the presentation, virulence factors, and treatment of histoplasmosis. Am J Med Sci 2024:S0002-9629(24)01283-7. [PMID: 38885929 DOI: 10.1016/j.amjms.2024.06.011] [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: 10/31/2023] [Revised: 04/29/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
Histoplasmosis is a systemic infection caused by an endemic dimorphic fungus, Histoplasma capsulatum. Though prevalent in the eastern United States of America, near the Ohio and Mississippi River Valleys, the evidence underlying the global prevalence of histoplasmosis, especially in immunocompromised populations, is underappreciated. This article highlights the global epidemiology, risk factors, microbiology and pathophysiological characteristics, pulmonary and extrapulmonary manifestations, prevention measures, radiographic patterns, diagnostic techniques, and antifungal treatment approaches for Histoplasma capsulatum.
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Affiliation(s)
- Pooja Gandhi
- Division of General Internal Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Brandon Hebert
- Division of General Internal Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Angelica Yun
- Division of General Internal Medicine, University of Louisville, Louisville, Kentucky, USA
| | - James Bradley
- Division of Pulmonary, Critical Care Medicine, and Sleep Disorders, University of Louisville, Louisville, Kentucky, USA.
| | - Bogdan Moldoveanu
- Division of Pulmonary, Critical Care Medicine, and Sleep Disorders, University of Louisville, Louisville, Kentucky, USA
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de Souza Rabello VB, de Melo Teixeira M, Meyer W, Irinyi L, Xavier MO, Poester VR, Pereira Brunelli JG, Almeida-Silva F, Bernardes-Engemann AR, Ferreira Gremião ID, Dos Santos Angelo DF, Clementino IJ, Almeida-Paes R, Zancopé-Oliveira RM. Multi-locus sequencing typing reveals geographically related intraspecies variability of Sporothrix brasiliensis. Fungal Genet Biol 2024; 170:103845. [PMID: 38040325 DOI: 10.1016/j.fgb.2023.103845] [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: 09/28/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023]
Abstract
Sporotrichosis is a subcutaneous mycosis caused by pathogenic Sporothrix species. Among them, Sporothrix brasiliensis is the main species associated with endemic regions in South America, especially Brazil. It is highly virulent and can be spread through zoonotic transmission. Molecular epidemiological surveys are needed to determine the extent of genetic variation, to investigate outbreaks, and to identify genotypes associated with antifungal resistance and susceptibility. This study investigated the sequence variation of different constitutive genes and established a novel multilocus sequence typing (MLST) scheme for S. brasiliensis. Specific primers were designed for 16 genes using Primer-BLAST software based on the genome sequences of three S. brasiliensis strains (ATCC MYA-4823, A001 and A005). Ninety-one human, animal, and environmental S. brasiliensis isolates from different Brazilian geographic regions (South, Southeast, Midwest and Northeast) andtwo isolates from Paraguay were sequenced. The loci that presented the highest nucleotide diversity (π) were selected for the MLST scheme. Among the 16 studied genetic loci, four presented increased π value and were able to distinguish all S. brasiliensis isolates into seven distinct haplotypes. The PCR conditions were standardized for four loci. Some of the obtained haplotypes were associated with the geographic origin of the strains. This study presents an important advance in the understanding of this important agent of sporotrichosis in Brazil. It significantly increased the discriminatory power for genotyping of S. brasiliensis isolates, and enabled new contributions to the epidemiological studies of this human and animal pathogen in Brazil and in other countries.
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Affiliation(s)
- Vanessa Brito de Souza Rabello
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas (INI), Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil.
| | - Marcus de Melo Teixeira
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília (UnB), Brasília, DF, Brazil
| | - Wieland Meyer
- Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands; Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, Sydney Infectious Diseases Institute, University of Sydney, Westmead Hospital, Research and Education Network, Westmead Institute for Medical Research, Sydney, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, Sydney Infectious Diseases Institute, University of Sydney, Westmead Hospital, Research and Education Network, Westmead Institute for Medical Research, Sydney, Australia
| | - Melissa Orzechowski Xavier
- Laboratório de Micologia e Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande (FAMED-FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Vanice Rodrigues Poester
- Laboratório de Micologia e Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande (FAMED-FURG), Rio Grande, Rio Grande do Sul, Brazil
| | | | - Fernando Almeida-Silva
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas (INI), Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Andrea Reis Bernardes-Engemann
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas (INI), Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Isabella Dib Ferreira Gremião
- Laboratório de Pesquisa Clínica em Dermatozoonoses em Animais Domésticos, Instituto Nacional de Infectologia Evandro Chagas (INI), Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Inácio José Clementino
- Departamento de Medicina Veterinária, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Rodrigo Almeida-Paes
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas (INI), Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Rosely Maria Zancopé-Oliveira
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas (INI), Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
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Sepúlveda VE, Rader JA, Li J(J, Goldman WE, Matute DR. Phenotypic characterization of cryptic species in the fungal pathogen Histoplasma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574719. [PMID: 38260643 PMCID: PMC10802462 DOI: 10.1101/2024.01.08.574719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Histoplasmosis is an endemic mycosis that often presents as a respiratory infection in immunocompromised patients. Hundreds of thousands of new infections are reported annually around the world. The etiological agent of the disease, Histoplasma, is a dimorphic fungus commonly found in the soil where it grows as mycelia. Humans can become infected by Histoplasma through inhalation of its spores (conidia) or mycelial particles. The fungi transitions into the yeast phase in the lungs at 37°C. Once in the lungs, yeast cells reside and proliferate inside alveolar macrophages. We have previously described that Histoplasma is composed of at least five cryptic species that differ genetically, and assigned new names to the lineages. Here we evaluated multiple phenotypic characteristics of 12 strains from five phylogenetic species of Histoplasma to identify phenotypic traits that differentiate between these species: H. capsulatum sensu stricto, H. ohiense, H. mississippiense, H. suramericanum, and an African lineage. We report diagnostic traits for two species. The other three species can be identified by a combination of traits. Our results suggest that 1) there are significant phenotypic differences among the cryptic species of Histoplasma, and 2) that those differences can be used to positively distinguish those species in a clinical setting and for further study of the evolution of this fungal pathogen.
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Affiliation(s)
| | | | | | - William E. Goldman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | - Daniel R. Matute
- Department of Biology, University of North Carolina at Chapel Hill
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Borman AM, Johnson EM. Changes in fungal taxonomy: mycological rationale and clinical implications. Clin Microbiol Rev 2023; 36:e0009922. [PMID: 37930182 PMCID: PMC10732072 DOI: 10.1128/cmr.00099-22] [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: 05/22/2023] [Accepted: 07/13/2023] [Indexed: 11/07/2023] Open
Abstract
Numerous fungal species of medical importance have been recently subjected to and will likely continue to undergo nomenclatural changes as a result of the application of molecular approaches to fungal classification together with abandonment of dual nomenclature. Here, we summarize those changes affecting key groups of fungi of medical importance, explaining the mycological (taxonomic) rationale that underpinned the changes and the clinical relevance/importance (where such exists) of the key nomenclatural revisions. Potential mechanisms to mitigate unnecessary taxonomic instability are suggested, together with approaches to raise awareness of important changes to minimize potential clinical confusion.
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Affiliation(s)
- Andrew M. Borman
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
| | - Elizabeth M. Johnson
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
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Calvopiña M, Toro M, Bastidas-Caldes C, Vasco-Julio D, Muñoz G. A Fatal Case of Disseminated Histoplasmosis by Histoplasma capsulatum var. capsulatum Misdiagnosed as Visceral Leishmaniasis-Molecular Diagnosis and Identification. Pathogens 2023; 12:1112. [PMID: 37764920 PMCID: PMC10538155 DOI: 10.3390/pathogens12091112] [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: 07/11/2023] [Revised: 08/08/2023] [Accepted: 08/12/2023] [Indexed: 09/29/2023] Open
Abstract
Histoplasmosis is an endemic mycosis in the Americas. However, its diagnosis is challenging due to the complexity and limited availability of conventional laboratory techniques-antigen tests, culture, and staining. Microscopic preparations often confuse with other pathogens, such as Leishmania spp. The genus Histoplasma capsulatum comprises three varieties: var. capsulatum, var. duboissi, and var. farciminosum, which cannot be distinguished using conventional techniques. An infant from a tropical region of Ecuador was hospitalized for fever, bloody diarrhea, and anemia persisting for two months. Upon admission, he received antibiotics and immunosuppressants. Histopathological examination of the lymph nodes, intestines, and bone marrow aspirate reported the presence of Leishmania-like amastigotes, and treatment was initiated with meglumine antimoniate and conventional amphotericin B. However, subsequent analysis of samples using PCR and DNA sequencing identified H. capsulatum var. capsulatum but not Leishmania. Despite fluconazole and amphotericin B, the infant succumbed to the disease. The delay in clinical and laboratory diagnosis of histoplasmosis and the use of nonspecific and ineffective drugs such as fluconazole led to disease dissemination and, ultimately, death. Implementing molecular diagnosis and antigen tests in laboratories located in endemic regions and reference hospitals is crucial.
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Affiliation(s)
- Manuel Calvopiña
- One Health Research Group, Universidad de Las Américas (UDLA), Quito 170124, Ecuador;
| | - Marcelo Toro
- Hospital Pediátrico “Baca Ortiz”, Quito 170523, Ecuador; (M.T.); (G.M.)
| | | | - David Vasco-Julio
- Programa de Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca 62050, Mexico
| | - Greta Muñoz
- Hospital Pediátrico “Baca Ortiz”, Quito 170523, Ecuador; (M.T.); (G.M.)
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Cornell TR, Thomas LF, Cook EAJ, Pinchbeck G, Bettridge J, Gordon L, Kivali V, Kiyong’a A, Fèvre EM, Scantlebury CE. Evidence of Histoplasma capsulatum seropositivity and exploration of risk factors for exposure in Busia county, western Kenya: Analysis of the PAZ dataset. PLoS Negl Trop Dis 2023; 17:e0011295. [PMID: 37172015 PMCID: PMC10180684 DOI: 10.1371/journal.pntd.0011295] [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: 01/07/2023] [Accepted: 04/07/2023] [Indexed: 05/14/2023] Open
Abstract
BACKGROUND Despite recognition of histoplasmosis as a disease of national public health concern in Kenya, the burden of Histoplasma capsulatum in the general population remains unknown. This study examined the human seroprevalence of anti-Histoplasma antibody and explored associations between seropositivity and demographic and environmental variables, in Busia county, western Kenya. METHODOLOGY Biobanked serum samples and associated data, from a previous cross-sectional survey, were examined. Latex agglutination tests to detect the presence of anti-Histoplasma antibody were performed on serum samples from 670 survey respondents, representing 178 households within 102 sub-locations. Potential epidemiologic risk factors for H. capsulatum exposure were explored using multi-level multivariable logistic regression analysis with household and sub-location included as random effects. PRINCIPAL FINDINGS The apparent sample seroprevalence of anti-Histoplasma antibody was 15.5% (n = 104/670, 95% Confidence Interval (CI) 12.9-18.5%). A multivariable logistic regression model identified increased odds of H. capsulatum seropositivity in respondents reporting rats within the household within the previous 12 months (OR = 2.99 90% CI 1.04-8.55, p = 0.04). Compared to respondents aged 25-34 years, the odds of seropositivity were higher in respondents aged 15-24 years (OR = 2.70 90% CI 1.04-6.97, p = 0.04). CONCLUSIONS The seroprevalence result provides a baseline for sample size approximations for future epidemiologic studies of the burden of H. capsulatum exposure in Busia county. The final model explored theoretically plausible risk factors for H. capsulatum exposure in the region. A number of factors may contribute to the complex epidemiological picture impacting H. capsulatum exposure status at the human-animal-environment interface in western Kenya. Focussed H. capsulatum research is warranted to determine the contextual significance of identified associations, and in representative sample populations.
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Affiliation(s)
- Tessa Rose Cornell
- Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Lian Francesca Thomas
- Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | | | - Gina Pinchbeck
- Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Judy Bettridge
- Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Lauren Gordon
- Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Velma Kivali
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Alice Kiyong’a
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Eric Maurice Fèvre
- Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Claire Elizabeth Scantlebury
- Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
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Rana M, Yilmaz T, Cohen S, Beyhan S, Argun AA. A novel biosensor for ultrasensitive detection of fungal genes. Biosens Bioelectron 2023; 222:114986. [PMID: 36508932 PMCID: PMC10289176 DOI: 10.1016/j.bios.2022.114986] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/03/2022]
Abstract
Fungal infections are a rapidly increasing public health problem due to their high morbidity and mortality rates, especially in populations with compromised immune systems. Rapid and accurate diagnosis of these diseases is, therefore, necessary to improve the prognosis of afflicted patients. Unfortunately, current clinical chemistry practice relies on lengthy culturing methods that are insufficient to meet the fast turnaround requirements. Here we present a cost-effective and robust nucleic acid sensor that can identify the presence of histoplasmosis causing fungal genes, in whole blood or bronchoalveolar lavage (BAL) samples, far earlier than current methods. Our novel assay involves the hybridization of target gene sequences with immobilized nucleic acid probes, allowing direct, label-free detection of Hcp100, CBP1, and M antigen genes through electrochemical analysis. The resultant current is attributed to the presence of fungal targets in the sample solution. The assay provides ultra-sensitive detection of DNA molecules with a limit of detection (LOD) values down to 100 aM, sufficient to meet the clinical diagnostic need. In addition, the turnaround time for the sample to result is less than 90 min compared to the current clinical procedure's turnaround time of 3-4 weeks.
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Affiliation(s)
- Muhit Rana
- Giner Inc., 89 Rumford Avenue, Newton, MA, 02466, United States
| | - Tugba Yilmaz
- Giner Inc., 89 Rumford Avenue, Newton, MA, 02466, United States
| | - Shirli Cohen
- J. Craig Venter Institute (JCVI), 4120 Capricorn Lane La Jolla, CA, 92037, United States
| | - Sinem Beyhan
- J. Craig Venter Institute (JCVI), 4120 Capricorn Lane La Jolla, CA, 92037, United States; The University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA, 92093, United States
| | - Avni A Argun
- Giner Inc., 89 Rumford Avenue, Newton, MA, 02466, United States.
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Genetic Diversity of Human Fungal Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023. [DOI: 10.1007/s40588-023-00188-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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Santos AS, Borges Dos Anjos LR, Costa VAF, Freitas VAQ, Zara ALDSA, Costa CR, Neves BJ, Silva MDRR. In silico-chemogenomic repurposing of new chemical scaffolds for histoplasmosis treatment. J Mycol Med 2023; 33:101363. [PMID: 36842411 DOI: 10.1016/j.mycmed.2023.101363] [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: 09/27/2022] [Revised: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023]
Abstract
BACKGROUND Histoplasmosis is a systemic form of endemic mycosis to the American continent and may be lethal to people living with HIV/AIDS. The drugs available for treating histoplasmosis are limited, costly, and highly toxic. New drug development is time-consuming and costly; hence, drug repositioning is an advantageous strategy for discovering new therapeutic options. OBJECTIVE This study was conducted to identify drugs that can be repositioned for treating histoplasmosis in immunocompromised patients. METHODS Homologous proteins among Histoplasma capsulatum strains were selected and used to search for homologous targets in the DrugBank and Therapeutic Target Database. Essential genes were selected using Saccharomyces cerevisiae as a model, and functional regions of the therapeutic targets were analyzed. The antifungal activity of the selected drugs was verified, and homology modeling and molecular docking were performed to verify the interactions between the drugs with low inhibitory concentration values and their corresponding targets. RESULTS We selected 149 approved drugs with potential activity against histoplasmosis, among which eight were selected for evaluating their in vitro activity. For drugs with low minimum inhibitory concentration values, such as mebendazole, everolimus, butenafine, and bifonazole, molecular docking studies were performed. A chemogenomic framework revealed lanosterol 14-α-demethylase, squalene monooxygenase, serine/threonine-protein kinase mTOR, and the β-4B tubulin chain of H. capsulatum, respectively, as the protein targets of the drugs. CONCLUSIONS Our strategy can be used to identify promising antifungal targets, and drugs with repositioning potential for treating H. capsulatum.
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Affiliation(s)
- Andressa Santana Santos
- Institute of Tropical Pathology and Public Health (IPTSP), Federal University of Goiás, Goiânia, Brazil
| | | | | | | | | | - Carolina Rodrigues Costa
- Institute of Tropical Pathology and Public Health (IPTSP), Federal University of Goiás, Goiânia, Brazil
| | - Bruno Junior Neves
- Laboratory of Cheminformatics (LabChem), Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
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Wilmes D, Mayer U, Wohlsein P, Suntz M, Gerkrath J, Schulze C, Holst I, von Bomhard W, Rickerts V. Animal Histoplasmosis in Europe: Review of the Literature and Molecular Typing of the Etiological Agents. J Fungi (Basel) 2022; 8:jof8080833. [PMID: 36012821 PMCID: PMC9410202 DOI: 10.3390/jof8080833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Histoplasmosis has been previously diagnosed in animals from Europe. The aim of this study is to review the literature on these reports, to analyze cases diagnosed at our laboratory (2000–2022) and to improve molecular typing of Histoplasma capsulatum directly from tissue to study the molecular epidemiology of Histoplasma capsulatum causing animal infections in Europe. Including 15 cases studied in our laboratory, we identified 39 cases of animal histoplasmosis between 1968 and 2022. They were diagnosed mostly in superficial tissue biopsies from cats and badgers from Central Europe. Using phylogenetic analyses of six partial genes, we were able to classify eight of the etiological agents as belonging to a highly supported lineage within the Eurasian clade. This study confirms the occurrence of autochthonous histoplasmosis in animals in Central Europe and proposes the addition of new loci to the MLST scheme to study the molecular epidemiology of histoplasmosis using either formalin-fixed paraffin-embedded tissue and fresh or cadaveric biopsies.
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Affiliation(s)
- Dunja Wilmes
- Reference Laboratory for Cryptococcosis and Uncommon Invasive Fungal Infections, Division for Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, 13353 Berlin, Germany
- Correspondence:
| | - Ursula Mayer
- VetMed Labor GmbH–Division of IDEXX Laboratories, 70806 Kornwestheim, Germany
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hanover, Germany
| | - Michael Suntz
- State Institute for Chemical and Veterinary Analysis Freiburg, 79108 Freiburg, Germany
| | - Jasmin Gerkrath
- Reference Laboratory for Cryptococcosis and Uncommon Invasive Fungal Infections, Division for Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, 13353 Berlin, Germany
| | - Christoph Schulze
- Landeslabor Berlin-Brandenburg, Fb III-1 Pathologie, Bakteriologie, Fleischhygiene, 15236 Frankfurt (Oder), Germany
| | - Ina Holst
- Staatliches Tierärztliches Untersuchungsamt Aulendorf-Diagnostikzentrum, 88326 Aulendorf, Germany
| | | | - Volker Rickerts
- Reference Laboratory for Cryptococcosis and Uncommon Invasive Fungal Infections, Division for Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, 13353 Berlin, Germany
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Ameni G, Messele Kebede A, Zewude A, Girma Abdulla M, Asfaw R, Gobena MM, Kyalo M, Stomeo F, Gumi B, Sori T. Equine Histoplasmosis in Ethiopia: Phylogenetic Analysis by Sequencing of the Internal Transcribed Spacer Region of rRNA Genes. Front Cell Infect Microbiol 2022; 12:789157. [PMID: 35909976 PMCID: PMC9330904 DOI: 10.3389/fcimb.2022.789157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/23/2022] [Indexed: 11/22/2022] Open
Abstract
Equine histoplasmosis commonly known as epizootic lymphangitis (EL) is a neglected granulomatous disease of equine that is endemic to Ethiopia. It is caused by Histoplasma capsulatum variety farciminosum, a dimorphic fungus that is closely related to H. capsulatum variety capsulatum. The objective of this study was to undertake a phylogenetic analysis of H. capsulatum isolated from EL cases of horses in central Ethiopia and evaluate their relationship with H. capsulatum isolates in other countries and/or clades using the internal transcribed spacer (ITS) region of rRNA genes. Clinical and mycological examinations, DNA extraction, polymerase chain reaction (PCR), Sanger sequencing, and phylogenetic analysis were used for undertaking this study. Additionally, sequence data of Histoplasma isolates were retrieved from GenBank and included for a comprehensive phylogenetic analysis. A total of 390 horses were screened for EL and 97 were positive clinically while H. capsulatum was isolated from 60 horses and further confirmed with PCR, of which 54 were sequenced. BLAST analysis of these 54 isolates identified 29 H. capsulatum isolates and 14 isolates from other fungal genera while the remaining 11 samples were deemed insufficient for further downstream analysis. The phylogenetic analysis identified five clades, namely, African, Eurasian, North American 1 and 2, and Latin American A and B. The Ethiopian isolates were closely aggregated with isolates of the Latin American A and Eurasian clades, whereas being distantly related to isolates from North American 1 and 2 clades as well as Latin American B clade. This study highlights the possible origins and transmission routes of Histoplasmosis in Ethiopia.
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Affiliation(s)
- Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
- *Correspondence: Gobena Ameni, ;
| | | | - Aboma Zewude
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Musse Girma Abdulla
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Rahel Asfaw
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mesfin Mamo Gobena
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Debre Zeit, Ethiopia
| | - Martina Kyalo
- Capacity Building, Biosciences for Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Francesca Stomeo
- Capacity Building, Biosciences for Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Teshale Sori
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Debre Zeit, Ethiopia
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Considerations about the Geographic Distribution of Histoplasma Species. Appl Environ Microbiol 2022; 88:e0201021. [PMID: 35262368 DOI: 10.1128/aem.02010-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Histoplasmosis is a mycotic infection principally affecting pulmonary tissue; sometimes, histoplasmosis can progress into a systemic disease. This infection involves immunocompetent and immunosuppressed human and other mammalian hosts, depending on particular circumstances. Histoplasmosis infection has been documented worldwide. The infection is acquired by inhaling infective mycelial propagules of the dimorphic fungus Histoplasma capsulatum. New reports of clinical cases of histoplasmosis in extreme latitudes could be related to human social adaptations and climate changes in the world, which are creating new favorable environments for this fungus and for bats, its major natural reservoirs and dispersers. Histoplasma has been isolated from most continents, and it is considered a complex of cryptic species, consisting of various groups of isolates that differ genetically and correlate with a particular geographic distribution. Based on updated studies, Histoplasma taxonomy is adjusting to new genetic data. Here, we have suggested that Histoplasma has at least 14 phylogenetic species distributed worldwide and new genotypes that could be under deliberation. Histoplasma's geographic radiation began in South America millions of years ago when the continents were joined and the climate was favorable. For fungal spreading, the role of bats and some birds is crucial, although other natural factors could also participate.
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15
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Ocansey BK, Kosmidis C, Agyei M, Dorkenoo AM, Ayanlowo OO, Oladele RO, Darre T, Denning DW. Histoplasmosis in Africa: Current perspectives, knowledge gaps, and research priorities. PLoS Negl Trop Dis 2022; 16:e0010111. [PMID: 35202403 PMCID: PMC8870498 DOI: 10.1371/journal.pntd.0010111] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background Histoplasmosis is a chronic granulomatous disease caused by the thermally dimorphic fungus Histoplasma capsulatum. The 2 variants Histoplasma capsulatum var. capsulatum (Hcc) and Histoplasma capsulatum var. duboisii (Hcd) causes infection in humans and commonly termed classical or American histoplasmosis and African histoplasmosis, respectively. Histoplasma capsulatum var. farciminosum (Hcf) affects equines. In recent times, there have been heightened sensitization on fungal infections such as histoplasmosis in Africa, aimed at improving awareness among relevant stakeholders, particularly healthcare workers. This effort is expected to be paralleled with increased detection of both classical and African histoplasmosis, which has remained underdiagnosed over the years. In this narrative review, we describe the current perspectives of histoplasmosis in Africa, identify knowledge gaps, and suggest research priorities. Methods A PubMed, Google Scholar, and Africa Journal Online (AJOL) literature search was conducted for studies on histoplasmosis in Africa between 2000 and 2020. Histoplasmosis essays in medical mycology textbooks were also consulted. This narrative review was prepared from the data gathered. Findings In the past 2 decades, histoplasmosis in general has seen a relative increase in case detection in some Africa countries, probably attributable to the gradually increasing medical mycology advocacy efforts in Africa. Histoplasmosis cases are dominated by African histoplasmosis mostly in Western and Central Africa, while classical histoplasmosis is more common in Southern and Northern Africa. Although both classical and African histoplasmosis are common in Africa, the latter is more restricted to Africa, and cases outside the continent usually have a travel history to the continent. Despite the clinical and laboratory difference between African histoplasmosis and classical histoplasmosis, it is not straightforward to distinguish them. The typical manifestation of African histoplasmosis is the appearance of lesions affecting the skin, bones, and lymph nodes and unusually linked to human immunodeficiency virus (HIV)/AIDS. By contrast, classical histoplasmosis mostly affects the lungs and is often associated with immunosuppression, mainly HIV/AIDS. The present perspectives of histoplasmosis in Africa highlight unclear details on the true burden, strain diversity, infection route and genetic basis of African histoplasmosis, availability of specie-specific diagnostic tools, and compliance with recommended antifungal therapy. These knowledge gaps represent research questions that require scientific exploration. Conclusions Despite a subtle increase in identifying histoplasmosis cases in Africa, it remains underdiagnosed and neglected in some parts of the continent. Increasing awareness and training among healthcare workers, bridging diagnostic and therapeutic gaps, and encouraging more research in Africa are crucial to improve the current perspectives of histoplasmosis in Africa.
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Affiliation(s)
- Bright K. Ocansey
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- * E-mail: ,
| | - Chris Kosmidis
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- National Aspergillosis Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Martin Agyei
- Department of Internal Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Améyo M. Dorkenoo
- Department of Biology and Basic Sciences, Faculty of Health Sciences, University of Lomé, Lomé, Togo
- Division of Laboratories, Ministry of Health and Public Hygiene, Lomé, Togo
| | - Olusola O. Ayanlowo
- Department of Medicine, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Rita O. Oladele
- Department of Medical Microbiology & Parasitology, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Tchin Darre
- Department of Pathology, University Teaching Hospital of Lomé, Lomé, Togo
| | - David W. Denning
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
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Chromosome-Level Genome Assembly of a Human Fungal Pathogen Reveals Synteny among Geographically Distinct Species. mBio 2022; 13:e0257421. [PMID: 35089059 PMCID: PMC8725592 DOI: 10.1128/mbio.02574-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Histoplasma capsulatum, a dimorphic fungal pathogen, is the most common cause of fungal respiratory infections in immunocompetent hosts. Histoplasma is endemic in the Ohio and Mississippi River Valleys in the United States and is also distributed worldwide. Previous studies have revealed at least eight clades, each specific to a geographic location: North American classes 1 and 2 (NAm 1 and NAm 2), Latin American groups A and B (LAm A and LAm B), Eurasian, Netherlands, Australian and African, and an additional distinct lineage (H81) comprised of Panamanian isolates. Previously assembled Histoplasma genomes are highly fragmented, with the highly repetitive G217B (NAm 2) strain, which has been used for most whole-genome-scale transcriptome studies, assembled into over 250 contigs. In this study, we set out to fully assemble the repeat regions and characterize the large-scale genome architecture of Histoplasma species. We resequenced five Histoplasma strains (WU24 [NAm 1], G217B [NAm 2], H88 [African], G186AR [Panama], and G184AR [Panama]) using Oxford Nanopore Technologies long-read sequencing technology. Here, we report chromosomal-level assemblies for all five strains, which exhibit extensive synteny among the geographically distant Histoplasma isolates. The new assemblies revealed that RYP2, a major regulator of morphology and virulence, is duplicated in G186AR. In addition, we mapped previously generated transcriptome data sets onto the newly assembled chromosomes. Our analyses revealed that the expression of transposons and transposon-embedded genes are upregulated in yeast phase compared to mycelial phase in the G217B and H88 strains. This study provides an important resource for fungal researchers and further highlights the importance of chromosomal-level assemblies in analyzing high-throughput data sets. IMPORTANCE Histoplasma species are dimorphic fungi causing significant morbidity and mortality worldwide. These fungi grow as mold in the soil and as budding yeast within the human host. Histoplasma can be isolated from soil in diverse regions, including North America, South America, Africa, and Europe. Phylogenetically distinct species of Histoplasma have been isolated and sequenced. However, for the commonly used strains, genome assemblies have been fragmented, leading to underutilization of genome-scale data. This study provides chromosome-level assemblies of the commonly used Histoplasma strains using long-read sequencing technology. Comparative analysis of these genomes shows largely conserved gene order within the chromosomes. Mapping existing transcriptome data on these new assemblies reveals clustering of transcriptionally coregulated genes. The results of this study highlight the importance of obtaining chromosome-level assemblies in understanding the biology of human fungal pathogens.
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Jofre GI, Singh A, Mavengere H, Sundar G, D'Agostino E, Chowdhary A, Matute DR. An Indian lineage of Histoplasma with strong signatures of differentiation and selection. Fungal Genet Biol 2022; 158:103654. [PMID: 34942368 DOI: 10.1016/j.fgb.2021.103654] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 01/04/2023]
Abstract
Histoplasma, a genus of dimorphic fungi, is the etiological agent of histoplasmosis, a pulmonary disease widespread across the globe. Whole genome sequencing has revealed that the genus harbors a previously unrecognized diversity of cryptic species. To date, studies have focused on Histoplasma isolates collected in the Americas with little knowledge of the genomic variation from other localities. In this report, we report the existence of a well-differentiated lineage of Histoplasma occurring in the Indian subcontinent. The group is differentiated enough to satisfy the requirements of a phylogenetic species, as it shows extensive genetic differentiation along the whole genome and has little evidence of gene exchange with other Histoplasma species. Next, we leverage this genetic differentiation to identify genetic changes that are unique to this group and that have putatively evolved through rapid positive selection. We found that none of the previously known virulence factors have evolved rapidly in the Indian lineage but find evidence of strong signatures of selection on other alleles potentially involved in clinically-important phenotypes. Our work serves as an example of the importance of correctly identifying species boundaries to understand the extent of selection in the evolution of pathogenic lineages. IMPORTANCE: Whole genome sequencing has revolutionized our understanding of microbial diversity, including human pathogens. In the case of fungal pathogens, a limiting factor in understanding the extent of their genetic diversity has been the lack of systematic sampling. In this piece, we show the results of a collection in the Indian subcontinent of the pathogenic fungus Histoplasma, the causal agent of a systemic mycosis. We find that Indian samples of Histoplasma form a distinct clade which is highly differentiated from other Histoplasma species. We also show that the genome of this lineage shows unique signals of natural selection. This work exemplifies how the combination of a robust sampling along with population genetics, and phylogenetics can reveal the precise genetic changes that differentiate lineages of fungal pathogens.
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Affiliation(s)
- Gaston I Jofre
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
| | - Ashutosh Singh
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Heidi Mavengere
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
| | - Gandhi Sundar
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Emmanuel D'Agostino
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
| | - Anuradha Chowdhary
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States.
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18
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Li M, Hieno A, Motohashi K, Suga H, Kageyama K. Pythium intermedium, a species complex consisting of three phylogenetic species found in cool-temperate forest ecosystems. Fungal Biol 2021; 125:1017-1025. [PMID: 34776229 DOI: 10.1016/j.funbio.2021.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Pythium intermedium plays a vital role in the carbon cycle of cool-temperate forests and is widely distributed in Japan's forest soils. In this study, we performed a phylogenetic analysis of the P. intermedium species complex using DNA sequences from multiple loci. The study included 35 isolates from cool-temperate forest soils, seven known P. intermedium isolates, and six known Pythium attrantheridium isolates. We also performed morphological observations and mating tests. Our results showed that all the isolates formed one large clade but were divided into three subclades. Furthermore, we observed many mating reactions between isolates from different subclades, including between P. attrantheridium and P. intermedium. Therefore, we suggest that P. intermedium, P. attrantheridium, and another phylogenetic species belong to one species complex. This is the first report of a species complex within P. intermedium and will be helpful in understanding the evolution of Pythium species in natural ecosystems.
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Affiliation(s)
- Mingzhu Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China; River Basin Research Center, Gifu University, Gifu, 501-1193, Japan.
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Keiichi Motohashi
- Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
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19
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Almeida-Silva F, de Melo Teixeira M, Matute DR, de Faria Ferreira M, Barker BM, Almeida-Paes R, Guimarães AJ, Zancopé-Oliveira RM. Genomic Diversity Analysis Reveals a Strong Population Structure in Histoplasma capsulatum LAmA ( Histoplasma suramericanum). J Fungi (Basel) 2021; 7:jof7100865. [PMID: 34682286 PMCID: PMC8540737 DOI: 10.3390/jof7100865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 01/05/2023] Open
Abstract
Histoplasmosis is a severe mycotic disease affecting thousands of immunocompetent and immunocompromised individuals with high incidence in Latin America, where the disease agents are Histoplasma capsulatum and Histoplasma suramericanum. In this work, we used whole-genome sequencing to infer the species diversity and the population structure of H. suramericanum in South America. We find evidence for strong population structure and little admixture within the species. Genome-level phylogenetic trees indicate the existence of at least three different discrete populations. We recovered the existence of a previously identified population, LAmB, and confirm that it is highly differentiated along the whole genome. We also find that H. suramericanum is composed of two populations, one in Northern South America, and another in the southern portion of the continent. Moreover, one of the lineages from the southern population is endemic to Rio de Janeiro and there was no association with clinical data and species isolated from patients with histoplasmosis. Our results point out the need to characterize the symptomatology of histoplasmosis caused by different species and lineages of Histoplasma spp.
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Affiliation(s)
- Fernando Almeida-Silva
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz-INI/Fiocruz, Rio de Janeiro 21040-360, Brazil; (M.d.F.F.); (R.A.-P.)
- Correspondence: (F.A.-S.); (R.M.Z.-O.)
| | - Marcus de Melo Teixeira
- Faculdade de Medicina, Universidadede Brasília, Brasília 70910-900, Brazil;
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA;
| | - Daniel R. Matute
- Biology Department, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Marcela de Faria Ferreira
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz-INI/Fiocruz, Rio de Janeiro 21040-360, Brazil; (M.d.F.F.); (R.A.-P.)
- Serviço Ambulatorial do Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz-INI/Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA;
| | - Rodrigo Almeida-Paes
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz-INI/Fiocruz, Rio de Janeiro 21040-360, Brazil; (M.d.F.F.); (R.A.-P.)
| | - Allan J. Guimarães
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro 24210-130, Brazil;
| | - Rosely M. Zancopé-Oliveira
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz-INI/Fiocruz, Rio de Janeiro 21040-360, Brazil; (M.d.F.F.); (R.A.-P.)
- Correspondence: (F.A.-S.); (R.M.Z.-O.)
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20
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Vite-Garín T, Estrada-Bárcenas DA, Gernandt DS, Reyes-Montes MDR, Sahaza JH, Canteros CE, Ramírez JA, Rodríguez-Arellanes G, Serra-Damasceno L, Zancopé-Oliveira RM, Taylor JW, Taylor ML. Histoplasma capsulatum Isolated from Tadarida brasiliensis Bats Captured in Mexico Form a Sister Group to North American Class 2 Clade. J Fungi (Basel) 2021; 7:529. [PMID: 34209122 PMCID: PMC8305335 DOI: 10.3390/jof7070529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/03/2021] [Accepted: 06/11/2021] [Indexed: 01/11/2023] Open
Abstract
Histoplasma capsulatum is a dimorphic fungus associated with respiratory and systemic infections in mammalian hosts that have inhaled infective mycelial propagules. A phylogenetic reconstruction of this pathogen, using partial sequences of arf, H-anti, ole1, and tub1 protein-coding genes, proposed that H. capsulatum has at least 11 phylogenetic species, highlighting a clade (BAC1) comprising three H. capsulatum isolates from infected bats captured in Mexico. Here, relationships for each individual locus and the concatenated coding regions of these genes were inferred using parsimony, maximum likelihood, and Bayesian inference methods. Coalescent-based analyses, a concatenated sequence-types (CSTs) network, and nucleotide diversities were also evaluated. The results suggest that six H. capsulatum isolates from the migratory bat Tadarida brasiliensis together with one isolate from a Mormoops megalophylla bat support a NAm 3 clade, replacing the formerly reported BAC1 clade. In addition, three H. capsulatum isolates from T. brasiliensis were classified as lineages. The concatenated sequence analyses and the CSTs network validate these findings, suggesting that NAm 3 is related to the North American class 2 clade and that both clades could share a recent common ancestor. Our results provide original information on the geographic distribution, genetic diversity, and host specificity of H. capsulatum.
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Affiliation(s)
- Tania Vite-Garín
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Daniel A. Estrada-Bárcenas
- Colección Nacional de Cepas Microbianas y Cultivos Celulares, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV, IPN), Ciudad de México 07360, Mexico;
| | - David S. Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico;
| | - María del Rocío Reyes-Montes
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Jorge H. Sahaza
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Cristina E. Canteros
- Departamento de Micología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires 1281, Argentina;
| | - José A. Ramírez
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Gabriela Rodríguez-Arellanes
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Lisandra Serra-Damasceno
- Centro de Ciências da Saúde, Departamento de Saúde Comunitária, Universidade Federal do Ceará, Fortaleza 60455-610, Brazil;
| | - Rosely M. Zancopé-Oliveira
- Laboratório de Micologia, Setor Imunodiagnóstico, Instituto Nacional de Infectología Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, Brazil;
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA;
| | - Maria Lucia Taylor
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
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Analyses of the genetic diversity and population structures of Histoplasma capsulatum clinical isolates from Mexico, Guatemala, Colombia and Argentina, using a randomly amplified polymorphic DNA-PCR assay. Epidemiol Infect 2020; 147:e204. [PMID: 31364543 PMCID: PMC6624862 DOI: 10.1017/s0950268819000931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We studied the genetic diversity and the population structure of human isolates of Histoplasma capsulatum, the causative agent of histoplasmosis, using a randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) assay to identify associations with the geographic distribution of isolates from Mexico, Guatemala, Colombia and Argentina. The RAPD-PCR pattern analyses revealed the genetic diversity by estimating the percentage of polymorphic loci, effective number of alleles, Shannon's index and heterozygosity. Population structure was identified by the index of association (IA) test. Thirty-seven isolates were studied and clustered into three groups by the unweighted pair-group method with arithmetic mean (UPGMA). Group I contained five subgroups based on geographic origin. The consistency of the UPGMA dendrogram was estimated by the cophenetic correlation coefficient (CCCr = 0.94, P = 0.001). Isolates from Mexico and Colombia presented higher genetic diversity than isolates from Argentina. Isolates from Guatemala grouped together with the reference strains from the United States of America and Panama. The IA values suggest the presence of a clonal population structure in the Argentinian H. capsulatum isolates and also validate the presence of recombining populations in the Colombian and Mexican isolates. These data contribute to the knowledge on the molecular epidemiology of histoplasmosis in Latin America.
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Rodrigues A, Beale M, Hagen F, Fisher M, Terra P, de Hoog S, Brilhante R, de Aguiar Cordeiro R, de Souza Collares Maia Castelo-Branco D, Rocha M, Sidrim J, de Camargo Z. The global epidemiology of emerging Histoplasma species in recent years. Stud Mycol 2020; 97:100095. [PMID: 33335607 PMCID: PMC7714791 DOI: 10.1016/j.simyco.2020.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Histoplasmosis is a serious infectious disease in humans caused by Histoplasma spp. (Onygenales), whose natural reservoirs are thought to be soil enriched with bird and bat guano. The true global burden of histoplasmosis is underestimated and frequently the pulmonary manifestations are misdiagnosed as tuberculosis. Molecular data on epidemiology of Histoplasma are still scarce, even though there is increasing recognition of histoplasmosis in recent years in areas distant from the traditional endemic regions in the Americas. We used multi-locus sequence data from protein coding loci (ADP-ribosylation factor, H antigen precursor, and delta-9 fatty acid desaturase), DNA barcoding (ITS1/2+5.8s), AFLP markers and mating type analysis to determine the genetic diversity, population structure and recognise the existence of different phylogenetic species among 436 isolates of Histoplasma obtained globally. Our study describes new phylogenetic species and the molecular characteristics of Histoplasma lineages causing outbreaks with a high number of severe outcomes in Northeast Brazil between 2011 and 2015. Genetic diversity levels provide evidence for recombination, common ancestry and clustering of Brazilian isolates at different geographic scales with the emergence of LAm C, a new genotype assigned to a separate population cluster in Northeast Brazil that exhibited low diversity indicative of isolation. The global survey revealed that the high genetic variability among Brazilian isolates along with the presence of divergent cryptic species and/or genotypes may support the hypothesis of Brazil being the center of dispersion of Histoplasma in South America, possibly with the contribution of migratory hosts such as birds and bats. Outside Brazil, the predominant species depends on the region. We confirm that histoplasmosis has significantly broadened its area of occurrence, an important feature of emerging pathogens. From a practical point of view, our data point to the emergence of histoplasmosis caused by a plethora of genotypes, and will enable epidemiological analysis focused on understanding the processes that lead to histoplasmosis. Further, the description of this diversity opens avenues for comparative genomic studies, which will allow progress toward a consensus taxonomy, improve understanding of the presence of hybrids in natural populations of medically relevant fungi, test reproductive barriers and to explore the significance of this variation.
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Affiliation(s)
- A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, 04023-062, Brazil
- Correspondence: A.M. Rodrigues; Z.P. de Camargo
| | - M.A. Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - M.C. Fisher
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - P.P.D. Terra
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, 04023-062, Brazil
| | - S. de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - R.S.N. Brilhante
- Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - R. de Aguiar Cordeiro
- Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - M.F.G. Rocha
- Postgraduate Program in Veterinary Science, State University of Ceará, Fortaleza, Ceará, Brazil
| | - J.J.C. Sidrim
- Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Z.P. de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, 04023-062, Brazil
- Correspondence: A.M. Rodrigues; Z.P. de Camargo
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Pineda J, Merino-Alado R, Mata-Essayag S, Landaeta ME, Garrido L, Rosas MDM. Nasal Septum Perforation Associated to Histoplasmosis: A Retrospective Study. PESQUISA BRASILEIRA EM ODONTOPEDIATRIA E CLÍNICA INTEGRADA 2020. [DOI: 10.1590/pboci.2020.090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Frequency of the Mating-Type (MAT1) in Histoplasma capsulatum Isolates from Buenos Aires, Argentina. Mycopathologia 2019; 185:169-174. [PMID: 31667672 DOI: 10.1007/s11046-019-00402-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
Abstract
Sex is genetically determined in Histoplasma capsulatum, governed by a sex-specific region in the genome called the mating-type locus (MAT1). We investigate the distribution of isolates of two H. capsulatum mating types in the clades circulating in Buenos Aires, Argentina. Forty-nine H. capsulatum isolates were obtained from the culture collection of the Mycology Center. The MAT1 locus was identified by PCR from the yeast suspension. The analysis of forty-eight isolates from clinical samples exhibited a ratio of 1.7 (MAT1-1:MAT1-2) and the only isolate from soil was MAT1-1. Forty-five H. capsulatum isolates belonged to the LAm B clade (H. capsulatum from Latin American group B clade) and showed a ratio of 1.8 (MAT1-1:MAT1-2). These results suggest an association between the mating types in isolates belonging to the LAm B clade. It remains to be defined whether a greater virulence should be attributed to the differences between the strains of the opposite mating type of the LAm B clade.
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25
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Novel clinical and dual infection by Histoplasma capsulatum genotypes in HIV patients from Northeastern, Brazil. Sci Rep 2019; 9:11789. [PMID: 31409874 PMCID: PMC6692370 DOI: 10.1038/s41598-019-48111-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
Histoplasmosis is a worldwide-distributed deep mycosis that affects healthy and immunocompromised hosts. Severe and disseminated disease is especially common in HIV-infected patients. At least 11 phylogenetic species are recognized and the majority of diversity is found in Latin America. The northeastern region of Brazil has one of the highest HIV/AIDS prevalence in Latin America and Ceará State has one of the highest death rates due to histoplasmosis in the world, where the mortality rate varies between 33-42%. The phylogenetic distribution and population genetic structure of 51 clinical isolates from Northeast Brazil was studied. For that morphological characteristics, exoantigens profile, and fungal mating types were evaluated. The genotypes were deduced by a MSLT in order to define local population structure of this fungal pathogen. In addition, the relationships of H. capsulatum genotypes with clinically relevant phenotypes and clinical aspects were investigated. The results suggest two cryptic species, herein named population Northeast BR1 and population Northeast BR2. These populations are recombining, exhibit a high level of haplotype diversity, and contain different ratios of mating types MAT1-1 and MAT1-2. However, differences in phenotypes or clinical aspects were not observed within these new cryptic species. A HIV patient can be co-infected by two or more genotypes from Northeast BR1 and/or Northeast BR2, which may have significant impact on disease progression due to the impaired immune response. We hypothesize that co-infections could be the result of multiple exposure events and may indicate higher risk of disseminated histoplasmosis, especially in HIV infected patients.
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26
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Gómez LF, Arango M, McEwen JG, Gómez OM, Zuluaga A, Peláez CA, Acevedo JM, Taylor ML, Jiménez MDP. Molecular epidemiology of Colombian Histoplasma capsulatum isolates obtained from human and chicken manure samples. Heliyon 2019; 5:e02084. [PMID: 31372546 PMCID: PMC6660563 DOI: 10.1016/j.heliyon.2019.e02084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/11/2019] [Accepted: 07/09/2019] [Indexed: 12/12/2022] Open
Abstract
The thermally dimorphic fungus Histoplasma capsulatum is the causative agent of histoplasmosis, one of the most prevalent endemic mycosis in the Americas. In tropical regions, agro-ecosystems require organic matter replacement, therefore, the use of organic fertilizers has increased disregarding the fact that certain number of such fertilizers might be contaminated with the fungus, and with their handling resulting in human cases and even outbreaks of histoplasmosis. Additionally, in Colombia, chicken manure is the most common raw material used in the production of organic fertilizers. In this work, we reported the isolation of this fungus from chicken manure, and genetically compared with 42 clinical isolates. The genetically compared environmental isolates grouped together with the clinical ones. Our result suggests that chicken manure may be one of H. capsulatum infection sources. Also, the phylogenetic analyses done with other H. capsulatum isolates indicate that the Colombian isolates are widely distributed in the relational tree thus reveling towards the great genetic diversity among the H. capsulatum Colombian isolates.
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Affiliation(s)
- Luisa F Gómez
- Grupo de Micología Médica, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia.,Posgrado de Biología, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Myrtha Arango
- Grupo de Micología Médica, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Juan G McEwen
- Grupo de Micología Médica, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia.,Grupo de Biología Celular y Molecular, Corporación para Investigaciones Biológicas (CIB), Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Oscar M Gómez
- Posgrado de Biología, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Antioquia, Colombia.,Grupo de Biología Celular y Molecular, Corporación para Investigaciones Biológicas (CIB), Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Alejandra Zuluaga
- Grupo de Micología Médica y Experimental, Corporación para Investigaciones Biológicas (CIB). Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Carlos A Peláez
- Grupo Interdisciplinario de Estudios Moleculares, (GIEM), Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Jose M Acevedo
- Grupo Interdisciplinario de Estudios Moleculares, (GIEM), Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - María L Taylor
- Laboratorio de Inmunología de Hongos, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - María Del P Jiménez
- Grupo de Micología Médica, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
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27
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Kroken S, Taylor JW. A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungusLetharia. Mycologia 2019. [DOI: 10.1080/00275514.2001.12061278] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Scott Kroken
- Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, California, USA 94720-3102
| | - John W. Taylor
- Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, California, USA 94720-3102
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28
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Katchy AU, Eyesan SU, Awotunde TO, Adesina SA, Ayandele BO, Sabageh D. Histoplasma duboisii of the femoral bone. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2019; 24:19. [PMID: 31007689 PMCID: PMC6450135 DOI: 10.4103/jrms.jrms_97_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 10/10/2018] [Accepted: 01/21/2019] [Indexed: 11/27/2022]
Abstract
Histoplasmosis due to Histoplasma duboisii is an emerging AIDS-defining opportunistic infection in HIV positive seen predominantly on the African continent between the Tropics of Cancer and Capricorn. Histoplasma duboisii is an invasive fungal organism with tropism for lymph nodes, skin and bones. The infection occurs more in patients with a CD4 count <50/mm3 and is usually dissemnnated Histoplasmosis due to Histoplasma duboisii is an emerging AIDS-defining opportunistic infection in HIV positive seen predominantly on the African continent between the Tropics of Cancer and Capricorn. Histoplasma duboisii is an invasive fungal organism with tropism for lymph nodes, skin and bones. The infection occurs more in patients with a CD4 count <50/mm3 and is usually disseminated. Literature reports of its occurrence in HIV negative patients are scanty. We report a case of histoplasma dubiosii infection of the left femur in a 9 year old HIV negative Nigerian with swelling in the left thigh of 5 months duration. Oral antibiotics and analgesics were prescribed for the patient with satisfactory clinical outcome. To our knowledge, this is the first reported case in an immunocompetent child in Nigeria. Literature reports of its occurrence in HIV negative patients are scanty. We report a case of histoplasma dubiosii infection of the left femur in a 9 year old HIV negative Nigerian with swelling in the left thigh of 5 months duration. Oral antibiotics and analgesics were prescribed for the patient with satisfactory clinical outcome. To our knowledge, this is the first reported case in an immunocompetent child in Nigeria.
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Affiliation(s)
- Amechi Uchenna Katchy
- Department of Orthopaedic Surgery, University of Nigeria Teaching Hospital, Nsukka, Nigeria
| | - Samuel Uwale Eyesan
- Department of Orthopaedic Surgery, Bowen University Teaching Hospital, Ogbomosho, Nigeria
| | | | | | | | - Donatus Sabageh
- Department of Pathology, Lautech Teaching Hospital, Ogbomosho, Nigeria
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29
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Hensel M, Hoffmann AR, Gonzales M, Owston MA, Dick EJ. Phylogenetic analysis of Histoplasma capsulatum var duboisii in baboons from archived formalin-fixed, paraffin embedded tissues. Med Mycol 2019; 57:256-259. [PMID: 29471422 DOI: 10.1093/mmy/myy003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/05/2018] [Indexed: 01/25/2023] Open
Abstract
Histoplasma capsulatum var. duboisii (Hcd) infections have been well documented to cause chronic granulomatous disease, mainly involving the skin of baboons and humans in African countries primarily. This retrospective study classified the subspecies of Histoplasma and developed a phylogenetic tree utilizing DNA sequences extracted from formalin-fixed, paraffin embedded (FFPE) tissues from 9 baboons from a research colony in Texas histologically diagnosed with Hcd. Based on sequence analysis of ITS-2, Tub-1, and ARF, Hcd isolated from the archived samples closely aligns with the African clade and has 88% sequence homology with a sample isolated from an individual in Senegal.
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Affiliation(s)
- M Hensel
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - A Rodrigues Hoffmann
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - M Gonzales
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - M A Owston
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - E J Dick
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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30
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Almeida-Silva F, Barbedo LS, Taylor ML, Muniz MDM, Guimarães AJ, Zancopé-Oliveira RM. Multiplex polymerase chain reaction as an improved method for screening Histoplasma capsulatum mating types. Mem Inst Oswaldo Cruz 2018; 113:e180340. [PMID: 30231112 PMCID: PMC6140378 DOI: 10.1590/0074-02760180340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/17/2018] [Indexed: 12/04/2022] Open
Abstract
Histoplasmosis is a systemic mycosis infection caused by Histoplasma capsulatum, a heterothallic ascomycete. The sexual reproduction of this fungus is regulated by the mating type (MAT1) locus that contains MAT1-1 and MAT1-2 idiomorphs, which were identified by uniplex polymerase chain reaction (PCR). This study aimed to optimise single-step multiplex PCR for the accurate detection of the distinct mating types of H. capsulatum. Among the 26 isolates tested, 20 had MAT1-1 genotype, while six showed MAT1-2 genotype, in agreement with the uniplex PCR results. These results suggest that multiplex PCR is a fast and specific tool for screening H. capsulatum mating types.
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Affiliation(s)
- Fernando Almeida-Silva
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Setor de Imunodiagnóstico, Rio de Janeiro, RJ, Brasil
| | - Leonardo Silva Barbedo
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Setor de Imunodiagnóstico, Rio de Janeiro, RJ, Brasil.,Universidade Federal do Amazonas, Instituto de Saúde e Biotecnologia, Coari, AM, Brasil
| | - Maria Lucia Taylor
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Microbiología-Parasitología, DF, México
| | - Mauro de Medeiros Muniz
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Setor de Imunodiagnóstico, Rio de Janeiro, RJ, Brasil
| | - Allan Jefferson Guimarães
- Universidade Federal Fluminense, Instituto Biomédico, Departamento de Microbiologia e Parasitologia, Niterói, RJ, Brasil
| | - Rosely Maria Zancopé-Oliveira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Setor de Imunodiagnóstico, Rio de Janeiro, RJ, Brasil
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31
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Valero C, Gago S, Monteiro MC, Alastruey-Izquierdo A, Buitrago MJ. African histoplasmosis: new clinical and microbiological insights. Med Mycol 2018; 56:51-59. [PMID: 28431110 DOI: 10.1093/mmy/myx020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
African histoplasmosis is defined as the fungal infection caused by Histoplasma capsulatum var. duboisii (Hcd). Studies focused on distinguishing Hcd and H. capsulatum var. capsulatum (Hcc), which coexist in Africa, are scarce or outdated, and African strains are continuously underrepresented. In this work, 13 cases of African patients with histoplasmosis diagnosed in the Spanish Mycology Reference Laboratory have been reviewed showing that 77% had disseminated disease and AIDS as underlying disease although Hcd infection has been classically considered a rare presentation in AIDS patients. Strains isolated from these patients and other clinical and reference strains were studied by assessing classical identification methods and performing a three-loci multi-locus sequence analysis (MLSA). Classical identification methods based on biochemical tests and measurement of yeast size proved to be useless in distinguishing both varieties. The MLSA defined an African cluster, with a strong statistical support, that included all strains with African origin. Finally, mating type was also determined by using molecular methods revealing an unequal mating type distribution in African strains. In conclusion, historical statements and classical identification methods were useless to distinguish between varieties, whereas molecular analyses revealed that all strains with African origin grouped together suggesting that traditional classification should be revised. Further investigation is required in order to unravel traditional concepts about Hcd infection and support results obtained in this work.
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Affiliation(s)
- C Valero
- Servicio de Micología. Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km 2. 28220 Majadahonda (Madrid), Spain
| | - S Gago
- Servicio de Micología. Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km 2. 28220 Majadahonda (Madrid), Spain
| | - M C Monteiro
- Servicio de Micología. Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km 2. 28220 Majadahonda (Madrid), Spain
| | - A Alastruey-Izquierdo
- Servicio de Micología. Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km 2. 28220 Majadahonda (Madrid), Spain
| | - M J Buitrago
- Servicio de Micología. Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km 2. 28220 Majadahonda (Madrid), Spain
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32
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Maxwell CS, Sepulveda VE, Turissini DA, Goldman WE, Matute DR. Recent admixture between species of the fungal pathogen Histoplasma. Evol Lett 2018; 2:210-220. [PMID: 30283677 PMCID: PMC6121842 DOI: 10.1002/evl3.59] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/03/2018] [Accepted: 05/08/2018] [Indexed: 12/30/2022] Open
Abstract
Hybridization between species of pathogens has the potential to speed evolution of virulence by providing the raw material for adaptation through introgression or by assembling new combinations of virulence traits. Fungal diseases are a source high morbidity, and remain difficult to treat. Yet the frequency of hybridization between fungal species has rarely been explored, and the functional role of introgressed alleles remains largely unknown. Histoplasma mississippiense and H. ohiense are sympatric throughout their range in North America and have distinct virulence strategies, making them an ideal system to examine the role introgression may play in fungal pathogens. We identified introgressed tracts in the genomes of a sample of H. mississippiense and H. ohiense isolates. We found strong evidence in each species for recent admixture, but introgressed alleles were present at low frequencies, suggesting that they were deleterious. Consistent with this, coding and regulatory sequences were strongly depleted within introgressed regions, whereas intergenic regions were enriched, indicating that functional introgressed alleles were frequently deleterious in their new genomic context. Surprisingly, we found only two isolates with substantial admixture: the H. mississippiense and H. ohiense genomic reference strains, WU24 and G217B, respectively. Our results show that recent admixture has occurred, that it is frequently deleterious and that conclusions based on studies of the H. mississippiense and H. ohiense type strains should be revisited with more representative samples from the genus.
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Affiliation(s)
- Colin S Maxwell
- Biology Department University of North Carolina Chapel Hill North Carolina 27599
| | - Victoria E Sepulveda
- Department of Microbiology and Immunology, School of Medicine University of North Carolina Chapel Hill North Carolina 27599
| | - David A Turissini
- Biology Department University of North Carolina Chapel Hill North Carolina 27599
| | - William E Goldman
- Department of Microbiology and Immunology, School of Medicine University of North Carolina Chapel Hill North Carolina 27599
| | - Daniel R Matute
- Biology Department University of North Carolina Chapel Hill North Carolina 27599
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Abstract
Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus.IMPORTANCE The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.
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Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How? Clin Microbiol Rev 2017; 30:671-707. [PMID: 28490578 DOI: 10.1128/cmr.00043-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for Candida spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Cryptococcus neoformans, Pneumocystis jirovecii, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.
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Fisher MC, Koenig GL, White TJ, Taylor JW. Molecular and phenotypic description ofCoccidioides posadasiisp. nov., previously recognized as the non-California population ofCoccidioides immitis. Mycologia 2017. [DOI: 10.1080/15572536.2003.11833250] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- M. C. Fisher
- The Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | | | - T. J. White
- Roche Molecular Systems, 1145 Atlantic Avenue, Alameda, California 94501, USA
| | - J. W. Taylor
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720-3102, USA
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Affiliation(s)
| | | | | | | | - John W. Taylor
- Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, California, USA 94720-3102
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37
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Species in the Cryptococcus gattii Complex Differ in Capsule and Cell Size following Growth under Capsule-Inducing Conditions. mSphere 2016; 1:mSphere00350-16. [PMID: 28066814 PMCID: PMC5196034 DOI: 10.1128/msphere.00350-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/20/2023] Open
Abstract
Infections with the fungal pathogen Cryptococcus gattii have been increasing in recent years. Recently, four different species have been described within C. gattii, which correspond to four previously known molecular genotypes (VGI to VGIV). Examining traits related to infection and disease is important for determining whether these different species have clinical relevance. This study examined variation in attributes that are important for infecting and surviving in the host, including tolerance to various stresses, yeast cell size, and the amount of polysaccharide capsule that covers the cell. The cell size and capsule size were significantly different and inversely correlated across the species. Thermotolerance was highest in C. deuterogattii (VGII), the only species known to cause outbreaks, while most strains of the species C. bacillisporus (VGIII) and C. tetragattii (VGIV) grew poorly at 37°C. These findings argue for increased acceptance of the new species and may be useful for informing diagnosis and prognosis in clinical infection. Cryptococcus gattii causes invasive fungal infections that have been increasing in incidence and global distribution in recent years. The major molecular genotypes of C. gattii that were previously classified as VGI to VGIV have recently been described as four new species: C. gattii (VGI), C. deuterogattii (VGII), C. bacillisporus (VGIII), and C. tetragattii (VGIV). The main driver for their classification has been phylogeny, and phenotypic diversity has not yet been extensively characterized. This study examines variation in attributes related to virulence and pathogenicity, including capsule thickness, cell size, tolerance to temperature, oxidative and osmotic stress, and cell wall integrity. A capsule induction agar using diluted Sabouraud medium revealed significant differences in capsule and cell size across the C. gattii species complex and produced irregularly shaped elongated cells in a number of strains. C. gattii/VGI strains possessed the largest capsules of all species but had smaller cells, while C. deuterogattii/VGII strains possessed the largest cells of all species but had smaller capsules. Overall thermotolerance was highest in C. deuterogattii/VGII strains, while a number of C. bacillisporus/VGIII, and C. tetragattii/VGIV strains had substantially reduced growth at 37°C. There was no significant difference among species in their tolerances to oxidative or osmotic stresses, and there was no evidence for defects in cell wall integrity in strains producing irregular cells. These data support the division of the C. gattii species complex into distinctly identified species and suggest underlying reasons for their differences in virulence, epidemiology, and host preference. IMPORTANCE Infections with the fungal pathogen Cryptococcus gattii have been increasing in recent years. Recently, four different species have been described within C. gattii, which correspond to four previously known molecular genotypes (VGI to VGIV). Examining traits related to infection and disease is important for determining whether these different species have clinical relevance. This study examined variation in attributes that are important for infecting and surviving in the host, including tolerance to various stresses, yeast cell size, and the amount of polysaccharide capsule that covers the cell. The cell size and capsule size were significantly different and inversely correlated across the species. Thermotolerance was highest in C. deuterogattii (VGII), the only species known to cause outbreaks, while most strains of the species C. bacillisporus (VGIII) and C. tetragattii (VGIV) grew poorly at 37°C. These findings argue for increased acceptance of the new species and may be useful for informing diagnosis and prognosis in clinical infection.
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Development and Evaluation of a Molecular Diagnostic Method for Rapid Detection of Histoplasma capsulatum var. farciminosum, the Causative Agent of Epizootic Lymphangitis, in Equine Clinical Samples. J Clin Microbiol 2016; 54:2990-2999. [PMID: 27707938 PMCID: PMC5121390 DOI: 10.1128/jcm.00896-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/17/2016] [Indexed: 11/20/2022] Open
Abstract
Histoplasma capsulatum var. farciminosum, the causative agent of epizootic lymphangitis (EZL), is endemic in parts of Africa. Diagnosis based on clinical signs and microscopy lacks specificity and is a barrier to further understanding this neglected disease. Here, a nested PCR method targeting the internal transcribed spacer (ITS) region of the rRNA operon was validated for application to equine clinical samples. Twenty-nine horses with signs of EZL from different climatic regions of Ethiopia were clinically examined. Blood samples and aspirates of pus from cutaneous nodules were taken, along with blood from a further 20 horses with no cutaneous EZL lesions. Among the 29 horses with suspected cases of EZL, H. capsulatum var. farciminosum was confirmed by extraction of DNA from pus and blood samples from 25 and 17 horses, respectively. Positive PCR results were also obtained with heat-inactivated pus (24 horses) and blood (23 horses) spotted onto Whatman FTA cards. Two positive results were obtained among blood samples from 20 horses that did not exhibit clinical signs of EZL. These are the first reports of the direct detection of H. capsulatum var. farciminosum in equine blood and at high frequency among horses exhibiting cutaneous lesions. The nested PCR outperformed conventional microscopic diagnosis, as characteristic yeast cells could be observed only in 14 pus samples. The presence of H. capsulatum var. farciminosum DNA was confirmed by sequencing the cloned PCR products, and while alignment of the ITS amplicons showed very little sequence variation, there was preliminary single nucleotide polymorphism-based evidence for the existence of two subgroups of H. capsulatum var. farciminosum. This molecular diagnostic method now permits investigation of the epidemiology of EZL.
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Sweet MJ, Scriven LA, Singleton I. Microsatellites for microbiologists. ADVANCES IN APPLIED MICROBIOLOGY 2016; 81:169-207. [PMID: 22958530 DOI: 10.1016/b978-0-12-394382-8.00005-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Microsatellites are repeating sequences of 2-6base pairs of DNA. Currently, they are used as molecular markers in many organisms, specifically in genetic studies analyzing kinship and population structure. In addition, they can be used to study gene duplication and/or deletion. Although they are used in studies on microorganisms including fungi, bacteria, protists, and archaea, it appears that these genetic markers are not being utilized to their full microbiological potential. Microsatellites have many advantages over other genetic markers currently in use as they are in general species specific, and therefore, cross-contamination by nontarget organisms is rare. Furthermore, microsatellites are suitable for use with fast and cheap DNA extraction methods, with ancient DNA or DNA from hair and fecal samples used in noninvasive sampling, making them widely available as a genetic marker. Microsatellites have already proven to be a useful tool for evolutionary studies of pathogenic microorganisms such as Candida albicans and Helicobacter pylori, and the onset of new sequencing techniques (such as 454, PACBIO, and mini-ion sequencing) means the ability to detect such markers will become less time consuming and cheaper, thus further expanding their potential to answer important microbial ecology questions.
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Affiliation(s)
- Michael J Sweet
- School of Biology, Institute for Research on Sustainability, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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Damasceno LS, Leitão TMJS, Taylor ML, Muniz MM, Zancopé-Oliveira RM. The use of genetic markers in the molecular epidemiology of histoplasmosis: a systematic review. Eur J Clin Microbiol Infect Dis 2015; 35:19-27. [PMID: 26589702 DOI: 10.1007/s10096-015-2508-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
Histoplasmosis is a systemic mycosis caused by Histoplasma capsulatum, a dimorphic fungal pathogen that can infect both humans and animals. This disease has worldwide distribution and affects mainly immunocompromised individuals. In the environment, H. capsulatum grows as mold but undergoes a morphologic transition to the yeast morphotype under special conditions. Molecular techniques are important tools to conduct epidemiologic investigations for fungal detection, identification of infection sources, and determination of different fungal genotypes associated to a particular disease symptom. In this study, we performed a systematic review in the PubMed database to improve the understanding about the molecular epidemiology of histoplasmosis. This search was restricted to English and Spanish articles. We included a combination of specific keywords: molecular typing [OR] genetic diversity [OR] polymorphism [AND] H. capsulatum; molecular epidemiology [AND] histoplasmosis; and molecular epidemiology [AND] Histoplasma. In addition, we used the specific terms: histoplasmosis [AND] outbreaks. Non-English or non-Spanish articles, dead links, and duplicate results were excluded from the review. The results reached show that the main methods used for molecular typing of H. capsulatum were: restriction fragment length polymorphism, random amplified polymorphic DNA, microsatellites polymorphism, sequencing of internal transcribed spacers region, and multilocus sequence typing. Different genetic profiles were identified among H. capsulatum isolates, which can be grouped according to their source, geographical origin, and clinical manifestations.
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Affiliation(s)
- L S Damasceno
- FIOCRUZ-Fundação Oswaldo Cruz, Laboratório de Micologia, Setor Imunodiagnóstico, INI-Instituto Nacional de Infectologia Evandro Chagas, 21045-900, Rio de Janeiro, RJ, Brazil
| | - T M J S Leitão
- Departamento de Saúde Comunitária, Faculdade de Medicina, UFC-Universidade Federal do Ceará, 60430-140, Fortaleza, CE, Brazil
| | - M L Taylor
- Departamento de Microbiología y Parasitología, Laboratorio de Inmunología de Hongos, Facultad de Medicina, UNAM-Universidad Nacional Autónoma de México, 04510, México, DF, Mexico
| | - M M Muniz
- FIOCRUZ-Fundação Oswaldo Cruz, Laboratório de Micologia, Setor Imunodiagnóstico, INI-Instituto Nacional de Infectologia Evandro Chagas, 21045-900, Rio de Janeiro, RJ, Brazil
| | - R M Zancopé-Oliveira
- FIOCRUZ-Fundação Oswaldo Cruz, Laboratório de Micologia, Setor Imunodiagnóstico, INI-Instituto Nacional de Infectologia Evandro Chagas, 21045-900, Rio de Janeiro, RJ, Brazil.
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Furuie JL, Sun J, do Nascimento MMF, Gomes RR, Waculicz-Andrade CE, Sessegolo GC, Rodrigues AM, Galvão-Dias MA, de Camargo ZP, Queiroz-Telles F, Najafzadeh MJ, de Hoog SG, Vicente VA. Molecular identification of Histoplasma capsulatum using rolling circle amplification. Mycoses 2015; 59:12-9. [PMID: 26578301 DOI: 10.1111/myc.12426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/30/2015] [Accepted: 10/03/2015] [Indexed: 12/01/2022]
Abstract
Histoplasmosis is a systemic fungal disease that occurs worldwide, causing symptomatic infection mostly in immunocompromised hosts. Etiological agent is the dimorphic fungus, Histoplasma capsulatum, which occurs in soil contaminated with bird or bat droppings. Major limitation in recognition of H. capsulatum infections is the low awareness, since other diseases may have similar symptomatology. The molecular methods have gained importance because of unambiguous diagnostic ability and efficiency. The aim of this study was to develop and evaluate a padlock probe in view of rolling circle amplification (RCA) detection method which targets ITS (Internal Transcribed Spacer) rDNA of H. capsulatum enabling rapid and specific detection of the fungus in clinical samples. Two padlock probes were designed and one of these (HcPL2) allowed specific amplification of H. capsulatum DNA while no cross-reactivity was observed with fungi used as negative controls. This method proved to be effective for H. capsulatum specific identification and demonstrated to be faster than the traditional method of microbiological identification.
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Affiliation(s)
- Jason L Furuie
- Bioprocess Engineering and Biotechnology Department, Post-Graduation Program of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Mariana M F do Nascimento
- Basic Pathology Department, Post-Graduation Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Renata R Gomes
- Basic Pathology Department, Post-Graduation Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Caroline E Waculicz-Andrade
- Basic Pathology Department, Post-Graduation Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, Brazil
| | | | - Anderson M Rodrigues
- Cellular Biology Division, Microbiology, Immunology and Parasitology Department, Federal University of São Paulo, São Paulo, Brazil
| | | | - Zoilo P de Camargo
- Cellular Biology Division, Microbiology, Immunology and Parasitology Department, Federal University of São Paulo, São Paulo, Brazil
| | - Flávio Queiroz-Telles
- Basic Pathology Department, Post-Graduation Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, Brazil.,Clinical Hospital of the Federal University of Paraná, Curitiba, Brazil
| | - Mohammad J Najafzadeh
- Parasitology and Mycology Department, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sybren G de Hoog
- Basic Pathology Department, Post-Graduation Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, Brazil.,CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Vania A Vicente
- Bioprocess Engineering and Biotechnology Department, Post-Graduation Program of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil.,Basic Pathology Department, Post-Graduation Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, Brazil
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Gilmore SA, Voorhies M, Gebhart D, Sil A. Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma. PLoS Genet 2015; 11:e1005395. [PMID: 26177267 PMCID: PMC4503680 DOI: 10.1371/journal.pgen.1005395] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/26/2015] [Indexed: 11/28/2022] Open
Abstract
Eukaryotic cells integrate layers of gene regulation to coordinate complex cellular processes; however, mechanisms of post-transcriptional gene regulation remain poorly studied. The human fungal pathogen Histoplasma capsulatum (Hc) responds to environmental or host temperature by initiating unique transcriptional programs to specify multicellular (hyphae) or unicellular (yeast) developmental states that function in infectivity or pathogenesis, respectively. Here we used recent advances in next-generation sequencing to uncover a novel re-programming of transcript length between Hc developmental cell types. We found that ~2% percent of Hc transcripts exhibit 5’ leader sequences that differ markedly in length between morphogenetic states. Ribosome density and mRNA abundance measurements of differential leader transcripts revealed nuanced transcriptional and translational regulation. One such class of regulated longer leader transcripts exhibited tight transcriptional and translational repression. Further examination of these dually repressed genes revealed that some control Hc morphology and that their strict regulation is necessary for the pathogen to make appropriate developmental decisions in response to temperature. Eukaryotic cells alter their developmental programs in response to environmental signals. Histoplasma capsulatum (Hc), a ubiquitous fungal pathogen of humans, establishes unique transcriptional programs to specify growth in either a multicellular hyphal form or unicellular yeast form in response to temperature. Since hyphae and yeast are specialized to function in infectivity or pathogenesis, respectively, Hc provides a clinically relevant system in which to query eukaryotic regulatory processes. Here we used next-generation sequencing approaches to annotate the transcriptomes of four distinct Hc strains in response to temperature. We found that a fraction of Hc transcripts have differential transcript architecture in hyphae and yeast, exhibiting 5’ leader sequences that differ markedly in length between morphogenetic states. To begin to understand the effect of these differential leader sequences on expression, we performed the first ribosome density and mRNA abundance measurements in Hc, thereby uncovering transcriptional and translational control that contribute to cell-type regulation.
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Affiliation(s)
- Sarah A. Gilmore
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Mark Voorhies
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Dana Gebhart
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Anita Sil
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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Ocular histoplasmosis syndrome. Surv Ophthalmol 2015; 60:279-95. [DOI: 10.1016/j.survophthal.2015.02.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 02/21/2015] [Accepted: 02/27/2015] [Indexed: 11/20/2022]
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Bernhardt A, von Bomhard W, Antweiler E, Tintelnot K. Molecular identification of fungal pathogens in nodular skin lesions of cats. Med Mycol 2014; 53:132-44. [DOI: 10.1093/mmy/myu082] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Abstract
Few among the millions of fungal species fulfill four basic conditions necessary to infect humans: high temperature tolerance, ability to invade the human host, lysis and absorption of human tissue, and resistance to the human immune system. In previously healthy individuals, invasive fungal disease is rare because animals' sophisticated immune systems evolved in constant response to fungal challenges. In contrast, fungal diseases occur frequently in immunocompromised patients. Paradoxically, successes of modern medicine have put increasing numbers of patients at risk for invasive fungal infections. Uncontrolled HIV infection additionally makes millions vulnerable to lethal fungal diseases. A concerted scientific and social effort is needed to meet these challenges.
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Affiliation(s)
- Julia R Köhler
- Division of Infectious Diseases, Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Arturo Casadevall
- Departments of Microbiology and Immunology and Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine, New York, New York 10461
| | - John Perfect
- Division of Infectious Diseases, Duke Medical Center, Durham, North Carolina 27710
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Covey PA, Kuwitzky B, Hanson M, Webb KM. Multilocus analysis using putative fungal effectors to describe a population of Fusarium oxysporum from sugar beet. PHYTOPATHOLOGY 2014; 104:886-896. [PMID: 24502207 DOI: 10.1094/phyto-09-13-0248-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Sugar beet (Beta vulgaris) Fusarium yellows is caused by Fusarium oxysporum f. sp. betae and can lead to significant reductions in root yield, sucrose percentage, juice purity, and storability. F. oxysporum f. sp. betae can be highly variable and many F. oxysporum strains isolated from symptomatic sugar beet are nonpathogenic. Identifying pathogenicity factors and their diversity in the F. oxysporum f. sp. betae population could further understanding of how this pathogen causes disease and potentially provide molecular markers to rapidly identify pathogenic isolates. This study used several previously described fungal effector genes (Fmk1, Fow1, Pda1, PelA, PelD, Pep1, Prt1, Rho1, Sge1, Six1, Six6, Snf1, and Ste12) as genetic markers, in a population of 26 pathogenic and nonpathogenic isolates of F. oxysporum originally isolated from symptomatic sugar beet. Of the genes investigated, six were present in all F. oxysporum isolates from sugar beet (Fmk1, Fow1, PelA, Rho1, Snf1, and Ste12), and seven were found to be dispersed within the population (Pda1, PelD, Pep1, Prt1, Sge1, Six1, and Six6). Of these, Fmk1, Fow1, PelA, Rho1, Sge1, Snf1, and Ste12 were significant in relating clade designations and PelD, and Prt1 were significant for correlating with pathogenicity in F. oxysporum f. sp. betae.
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Comparison of phylogenetically distinct Histoplasma strains reveals evolutionarily divergent virulence strategies. mBio 2014; 5:e01376-14. [PMID: 24987093 PMCID: PMC4161242 DOI: 10.1128/mbio.01376-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infection with the dimorphic fungus Histoplasma capsulatum results from the inhalation of contaminated soil. Disease outcome is variable and depends on the immune status of the host, number of organisms inhaled, and the H. capsulatum strain. H. capsulatum is divided into seven distinct clades based on phylogenetic analyses, and strains from two separate clades have been identified in North America (denoted as NAm strains). We characterized an H. capsulatum isolate (WU24) from the NAm 1 lineage in relation to two other well-characterized Histoplasma isolates, the Panamanian strain G186A and the NAm 2 strain G217B. We determined that WU24 is a chemotype II strain and requires cell wall α-(1,3)-glucan for successful in vitro infection of macrophages. In a mouse model of histoplasmosis, WU24 exhibited a disease profile that was very similar to that of strain G186A at a high sublethal dose; however, at this dose G217B had markedly different kinetics. Surprisingly, infection with a lower dose mitigated many of the differences during the course of infection. The observed differences in fungal burden, disease kinetics, symptomology, and cytokine responses all indicate that there is a sophisticated relationship between host and fungus that drives the development and progression of histoplasmosis. Importance: Histoplasmosis has a wide range of clinical manifestations, presenting as mild respiratory distress, acute respiratory infection, or a life-threatening disseminated disease most often seen in immunocompromised patients. Additionally, the outcome appears to be dependent on the amount and strain of fungus inhaled. In this study, we characterized a recent clinical H. capsulatum isolate that was collected from an HIV(+) individual in North America. In contrast to other isolates from the same lineage, this strain, WU24, infected both macrophages and wild-type mice. We determined that in contrast to many other North American strains, WU24 infection of macrophages is dependent on the presence of cell wall α-(1,3)-glucan. Surprisingly, comparison of WU24 with two previously characterized isolates revealed that many conclusions regarding relative strain virulence and certain hallmarks of histoplasmosis are dependent on the inoculum size.
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Urine antigen tests for the diagnosis of respiratory infections: legionellosis, histoplasmosis, pneumococcal pneumonia. Clin Lab Med 2014; 34:219-36. [PMID: 24856525 DOI: 10.1016/j.cll.2014.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Urinary antigen testing has grown in popularity for several significant respiratory infections, particularly Legionella pneumophila, Streptococcus pneumoniae, and Histoplasma capsulatum. By capitalizing on the concentration of shed antigen from a variety of pathogens in the kidneys for excretion in the urine, urinary antigen testing can be used to obtain rapid test results related to respiratory infection, independent of an invasive collection such as a bronchoalveolar lavage. This article describes the 3 aforementioned organisms, their role in respiratory disease, and the current status of urinary antigen testing in their respective diagnosis.
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Wang Y, Pan B, Wu J, Bi X, Liao W, Pan W, Gu J. Detection and phylogenetic characterization of a case of Histoplasma capsulatum infection in mainland China. Am J Trop Med Hyg 2014; 90:1180-3. [PMID: 24686744 DOI: 10.4269/ajtmh.14-0048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Histoplasmosis usually occurs in specific endemic areas. Sporadic cases have also been reported in mainland China. Here, we described an indigenous case of disseminated histoplasmosis. Phylogenetic analysis revealed that the Histoplasma capsulatum isolated in our case belongs to the Australian clade. Combined with previous studies, it revealed high genetic diversity among Chinese H. capsulatum isolates.
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Affiliation(s)
- Ying Wang
- Department of Dermatology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China; Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Bo Pan
- Department of Dermatology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China; Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Jianhua Wu
- Department of Dermatology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China; Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Xinling Bi
- Department of Dermatology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China; Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Wanqing Liao
- Department of Dermatology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China; Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Weihua Pan
- Department of Dermatology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China; Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Jun Gu
- Department of Dermatology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China; Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
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Stewart JE, Timmer LW, Lawrence CB, Pryor BM, Peever TL. Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen. BMC Evol Biol 2014; 14:38. [PMID: 24593138 PMCID: PMC4015827 DOI: 10.1186/1471-2148-14-38] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/21/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Traditional morphological and biological species concepts are difficult to apply to closely related, asexual taxa because of the lack of an active sexual phase and paucity of morphological characters. Phylogenetic species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been extensively used; however, methods that incorporate gene tree uncertainty into species recognition may more accurately and objectively delineate species. Using a worldwide sample of Alternaria alternata sensu lato, causal agent of citrus brown spot, the evolutionary histories of four nuclear loci including an endo-polygalacturonase gene, two anonymous loci, and one microsatellite flanking region were estimated using the coalescent. Species boundaries were estimated using several approaches including those that incorporate uncertainty in gene genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common. RESULTS Coalescent analyses revealed three phylogenetic lineages strongly influenced by incomplete lineage sorting and recombination. Divergence of the citrus 2 lineage from the citrus 1 and citrus 3 lineages was supported at most loci. A consensus of species tree estimation methods supported two species of Alternaria causing citrus brown spot worldwide. Based on substitution rates at the endo-polygalacturonase locus, divergence of the citrus 2 and the 1 and 3 lineages was estimated to have occurred at least 5, 400 years before present, predating the human-mediated movement of citrus and associated pathogens out of SE Asia. CONCLUSIONS The number of Alternaria species identified as causing brown spot of citrus worldwide using morphological criteria has been overestimated. Little support was found for most of these morphospecies using quantitative species recognition approaches. Correct species delimitation of plant-pathogenic fungi is critical for understanding the evolution of pathogenicity, introductions of pathogens to new areas, and for regulating the movement of pathogens to enforce quarantines. This research shows that multilocus phylogenetic methods that allow for recombination and incomplete lineage sorting can be useful for the quantitative delimitation of asexual species that are morphologically indistinguishable. Two phylogenetic species of Alternaria were identified as causing citrus brown spot worldwide. Further research is needed to determine how these species were introduced worldwide, how they differ phenotypically and how these species are maintained.
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Affiliation(s)
- Jane E Stewart
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
- Current address: Department of Plant Pathology, University of Georgia, Athens, Georgia
| | - Lavern W Timmer
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, USA
| | | | - Barry M Pryor
- Division of Plant Pathology and Microbiology, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Tobin L Peever
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
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