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Tenório BG, Kollath DR, Gade L, Litvintseva AP, Chiller T, Jenness JS, Stajich JE, Matute DR, Hanzlicek AS, Barker BM, Teixeira MDM. Tracing histoplasmosis genomic epidemiology and species occurrence across the USA. Emerg Microbes Infect 2024; 13:2315960. [PMID: 38465644 DOI: 10.1080/22221751.2024.2315960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/04/2024] [Indexed: 03/12/2024]
Abstract
ABSTRACTHistoplasmosis is an endemic mycosis in North America frequently reported along the Ohio and Mississippi River Valleys, although autochthonous cases occur in non-endemic areas. In the United States, the disease is provoked by two genetically distinct clades of Histoplasma capsulatum sensu lato, Histoplasma mississippiense (Nam1) and H. ohiense (Nam2). To bridge the molecular epidemiological gap, we genotyped 93 Histoplasma isolates (62 novel genomes) including clinical, environmental, and veterinarian samples from a broader geographical range by whole-genome sequencing, followed by evolutionary and species niche modelling analyses. We show that histoplasmosis is caused by two major lineages, H. ohiense and H. mississippiense; with sporadic cases caused by H. suramericanum in California and Texas. While H. ohiense is prevalent in eastern states, H. mississipiense was found to be prevalent in the central and western portions of the United States, but also geographically overlapping in some areas suggesting that these species might co-occur. Species Niche Modelling revealed that H. ohiense thrives in places with warmer and drier conditions, while H. mississippiense is endemic to areas with cooler temperatures and more precipitation. In addition, we predicted multiple areas of secondary contact zones where the two species co-occur, potentially facilitating gene exchange and hybridization. This study provides the most comprehensive understanding of the genomic epidemiology of histoplasmosis in the USA and lays a blueprint for the study of invasive fungal diseases.
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Affiliation(s)
| | - Daniel R Kollath
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jeff S Jenness
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Andrew S Hanzlicek
- MiraVista Diagnostics, Indianapolis, IN, USA
- Department of Veterinary Clinical Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Marcus de Melo Teixeira
- Faculty of Medicine, University of Brasília, Brasília, Brazil
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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Eulálio KD, Kollath DR, Martins LMS, Filho ADD, Cavalcanti MDAS, Moreira LM, Tenório BG, Alves LGDB, Yamauchi D, Barrozo LV, Thompson Iii GR, Nacher M, Stajich JE, Benard G, Bagagli E, Felipe MSS, Barker BM, Trilles L, Teixeira MDM. Epidemiological, clinical, and genomic landscape of coccidioidomycosis in northeastern Brazil. Nat Commun 2024; 15:3190. [PMID: 38609393 PMCID: PMC11014852 DOI: 10.1038/s41467-024-47388-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Coccidioidomycosis, listed as a priority mycosis by the WHO, is endemic in the United States but often overlooked in Central and South America. Employing a multi-institutional approach, we investigate how disease characteristics, pathogen genetic variation, and environmental factors impact coccidioidomycosis epidemiology and outcomes in South America. We identified 292 cases (1978-2021) and 42 outbreaks in Piauí and Maranhão states, Brazil, the largest series outside the US/Mexico epidemic zone. The male-to-female ratio was 57.4:1 and the most common activity was armadillo hunting (91.1%) 4 to 30 days before symptom onset. Most patients (92.8%) exhibited typical acute pulmonary disease, with cough (93%), fever (90%), and chest pain (77%) as predominant symptoms. The case fatality rate was 8%. Our negative binomial regression model indicates that reduced precipitation levels in the current (p = 0.015) and preceding year (p = 0.001) predict heightened incidence. Unlike other hotspots, acidic soil characterizes this region. Brazilian strains differ genomically from other C. posadasii lineages. Northeastern Brazil presents a distinctive coccidioidomycosis profile, with armadillo hunters facing elevated risks. Low annual rainfall emerges as a key factor in increasing cases. A unique C. posadasii lineage in Brazil suggests potential differences in environmental, virulence, and/or pathogenesis traits compared to other Coccidioides genotypes.
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Affiliation(s)
- Kelsen Dantas Eulálio
- Hospital de Doenças Infecto Contagiosas-HDIC, Federal University of Piauí-UFPI, Teresina, Piauí, Brazil
| | - Daniel R Kollath
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Antonio de Deus Filho
- Hospital de Doenças Infecto Contagiosas-HDIC, Federal University of Piauí-UFPI, Teresina, Piauí, Brazil
| | | | - Lucas Machado Moreira
- Evandro Chagas National Institute of Infectology, Fiocruz - RJ, Rio de Janeiro, Brazil
| | | | | | - Danielle Yamauchi
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista/UNESP, Botucatu, Brazil
| | - Ligia Vizeu Barrozo
- Department of Geography, Faculty of Philosophy, Languages and Literature, and Human Sciences, University of São Paulo, São Paulo, Brazil
| | - George R Thompson Iii
- Department of Internal Medicine, Division of Infectious Diseases and Department of Medical Microbiology and Immunology, UC-Davis, Sacramento, CA, USA
| | - Mathieu Nacher
- Centre d'Investigations Cliniques, INSERM 1424, Centre hospitalier de Cayenne - French Guiana, Cayenne, French Guiana
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology University of California-Riverside, Riverside, CA, USA
| | - Gil Benard
- Laboratório de Micologia Medica, Departamento de Dermatologia, Instituto de Medicina Tropical, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
| | - Eduardo Bagagli
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista/UNESP, Botucatu, Brazil
| | | | - Bridget M Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Luciana Trilles
- Evandro Chagas National Institute of Infectology, Fiocruz - RJ, Rio de Janeiro, Brazil
| | - Marcus de Melo Teixeira
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
- Faculty of Medicine, University of Brasília, Brasília, Federal District, Brazil.
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Herman C, Barker BM, Bartelli TF, Chandra V, Krajmalnik-Brown R, Jewell M, Li L, Liao C, McAllister F, Nirmalkar K, Xavier JB, Gregory Caporaso J. Assessing Engraftment Following Fecal Microbiota Transplant. ArXiv 2024:arXiv:2404.07325v1. [PMID: 38659636 PMCID: PMC11042410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Fecal Microbiota Transplant (FMT) is an FDA approved treatment for recurrent Clostridium difficile infections, and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to priming the microbiome for cancer treatment, and restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in determining if a recipient didn't respond because the engrafted microbiome didn't produce the desired outcomes (a successful FMT, but negative treatment outcome), or the microbiome didn't engraft (an unsuccessful FMT and negative treatment outcome). The lack of a consistent methodology for quantifying FMT engraftment extent hinders the assessment of FMT success and its relation to clinical outcomes, and presents challenges for comparing FMT results and protocols across studies. Here we review 46 studies of FMT in humans and model organisms and group their approaches for assessing the extent to which an FMT engrafts into three criteria: 1) Chimeric Asymmetric Community Coalescence investigates microbiome shifts following FMT engraftment using methods such as alpha diversity comparisons, beta diversity comparisons, and microbiome source tracking. 2) Donated Microbiome Indicator Features tracks donated microbiome features (e.g., amplicon sequence variants or species of interest) as a signal of engraftment with methods such as differential abundance testing based on the current sample collection, or tracking changes in feature abundances that have been previously identified (e.g., from FMT or disease-relevant literature). 3) Temporal Stability examines how resistant post-FMT recipient's microbiomes are to reverting back to their baseline microbiome. Individually, these criteria each highlight a critical aspect of microbiome engraftment; investigated together, however, they provide a clearer assessment of microbiome engraftment. We discuss the pros and cons of each of these criteria, providing illustrative examples of their application. We also introduce key terminology and recommendations on how FMT studies can be analyzed for rigorous engraftment extent assessment.
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Affiliation(s)
- Chloe Herman
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Thais F Bartelli
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vidhi Chandra
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, U.S.A
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, U.S.A
| | | | - Le Li
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Khemlal Nirmalkar
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, U.S.A
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - J Gregory Caporaso
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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Coyne V, Mead HL, Mongini PKA, Barker BM. B Cell Chronic Lymphocytic Leukemia Development in Mice with Chronic Lung Exposure to Coccidioides Fungal Arthroconidia. Immunohorizons 2023; 7:333-352. [PMID: 37195872 PMCID: PMC10579974 DOI: 10.4049/immunohorizons.2300013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Links between repeated microbial infections and B cell chronic lymphocytic leukemia (B-CLL) have been proposed but not tested directly. This study examines how prolonged exposure to a human fungal pathogen impacts B-CLL development in Eµ-hTCL1-transgenic mice. Monthly lung exposure to inactivated Coccidioides arthroconidia, agents of Valley fever, altered leukemia development in a species-specific manner, with Coccidioides posadasii hastening B-CLL diagnosis/progression in a fraction of mice and Coccidioides immitis delaying aggressive B-CLL development, despite fostering more rapid monoclonal B cell lymphocytosis. Overall survival did not differ significantly between control and C. posadasii-treated cohorts but was significantly extended in C. immitis-exposed mice. In vivo doubling time analyses of pooled B-CLL showed no difference in growth rates of early and late leukemias. However, within C. immitis-treated mice, B-CLL manifests longer doubling times, as compared with B-CLL in control or C. posadasii-treated mice, and/or evidence of clonal contraction over time. Through linear regression, positive relationships were noted between circulating levels of CD5+/B220low B cells and hematopoietic cells previously linked to B-CLL growth, albeit in a cohort-specific manner. Neutrophils were positively linked to accelerated growth in mice exposed to either Coccidioides species, but not in control mice. Conversely, only C. posadasii-exposed and control cohorts displayed positive links between CD5+/B220low B cell frequency and abundance of M2 anti-inflammatory monocytes and T cells. The current study provides evidence that chronic lung exposure to fungal arthroconidia affects B-CLL development in a manner dependent on fungal genotype. Correlative studies suggest that fungal species differences in the modulation of nonleukemic hematopoietic cells are involved.
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Affiliation(s)
- Vanessa Coyne
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, AZ
| | - Heather L. Mead
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, AZ
| | | | - Bridget M. Barker
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, AZ
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Kollath DR, Morales MM, Itogawa AN, Mullaney D, Lee NR, Barker BM. Combating the Dust Devil: Utilizing Naturally Occurring Soil Microbes in Arizona to Inhibit the Growth of Coccidioides spp., the Causative Agent of Valley Fever. J Fungi (Basel) 2023; 9:jof9030345. [PMID: 36983513 PMCID: PMC10056400 DOI: 10.3390/jof9030345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
The fungal disease Valley fever causes a significant medical and financial burden for affected people in the endemic region, and this burden is on the rise. Despite the medical importance of this disease, little is known about ecological factors that influence the geographic point sources of high abundance of the pathogens Coccidioides posadasii and C. immitis, such as competition with co-occurring soil microbes. These “hot spots”, for instance, those in southern Arizona, are areas in which humans are at greater risk of being infected with the fungus due to consistent exposure. The aim of this study was to isolate native microbes from soils collected from Tucson, Arizona (endemic area for C. posadasii) and characterize their relationship (antagonistic, synergistic, or neutral) to the fungal pathogen with in vitro challenge assays. Secreted metabolites from the microbes were extracted and described using analytical techniques including high-performance liquid chromatography (HPLC) and mass spectrometry. Bacteria belonging to the genus Bacillus and fungi in the Fennellomyces and Ovatospora genera were shown to significantly decrease the growth of Coccidioides spp. In vitro. In contrast, other bacteria in the Brevibacillus genus, as well as one species of Bacillus bacteria, were shown to promote growth of Coccidioides when directly challenged. The metabolites secreted from the antagonistic bacteria were described using HPLC and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The microbes identified in this study as antagonists to Coccidioides and/or the metabolites they secrete have the potential to be used as natural biocontrol agents to limit the amount of fungal burden at geographic point sources, and therefore limit the potential for human infection.
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Affiliation(s)
- Daniel R. Kollath
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Correspondence: ; Tel.: +1-708-280-5867
| | - Matthew M. Morales
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Ashley N. Itogawa
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Dustin Mullaney
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Naomi R. Lee
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bridget M. Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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Higgins Keppler EA, Van Dyke MCC, Mead HL, Lake DF, Magee DM, Barker BM, Bean HD. Volatile Metabolites in Lavage Fluid Are Correlated with Cytokine Production in a Valley Fever Murine Model. J Fungi (Basel) 2023; 9:jof9010115. [PMID: 36675936 PMCID: PMC9864585 DOI: 10.3390/jof9010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Coccidioides immitis and Coccidioides posadasii are soil-dwelling fungi of arid regions in North and South America that are responsible for Valley fever (coccidioidomycosis). Forty percent of patients with Valley fever exhibit symptoms ranging from mild, self-limiting respiratory infections to severe, life-threatening pneumonia that requires treatment. Misdiagnosis as bacterial pneumonia commonly occurs in symptomatic Valley fever cases, resulting in inappropriate treatment with antibiotics, increased medical costs, and delay in diagnosis. In this proof-of-concept study, we explored the feasibility of developing breath-based diagnostics for Valley fever using a murine lung infection model. To investigate potential volatile biomarkers of Valley fever that arise from host−pathogen interactions, we infected C57BL/6J mice with C. immitis RS (n = 6), C. posadasii Silveira (n = 6), or phosphate-buffered saline (n = 4) via intranasal inoculation. We measured fungal dissemination and collected bronchoalveolar lavage fluid (BALF) for cytokine profiling and for untargeted volatile metabolomics via solid-phase microextraction (SPME) and two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-TOFMS). We identified 36 volatile organic compounds (VOCs) that were significantly correlated (p < 0.05) with cytokine abundance. These 36 VOCs clustered mice by their cytokine production and were also able to separate mice with moderate-to-high cytokine production by infection strain. The data presented here show that Coccidioides and/or the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test that can detect coccidioidal infection and provide clinically relevant information on primary pulmonary disease severity.
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Affiliation(s)
- Emily A. Higgins Keppler
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | | | - Heather L. Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Douglas F. Lake
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - D. Mitchell Magee
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Heather D. Bean
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Correspondence:
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Dubin CA, Voorhies M, Sil A, Teixeira MM, Barker BM, Brem RB. Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii. J Fungi (Basel) 2022; 8:jof8121235. [PMID: 36547568 PMCID: PMC9782707 DOI: 10.3390/jof8121235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
The human fungal pathogen Coccidioides spp. causes valley fever, a treatment-refractory and sometimes deadly disease prevalent in arid regions of the western hemisphere. Fungal virulence in the mammalian host hinges on a switch between growth as hyphae and as large spherules containing infectious spores. How these virulence programs are encoded in the genome remains poorly understood. Drawing on Coccidioides genomic resources, we first discovered a new facet of genome organization in this system: spherule-gene islands, clusters of genes physically linked in the genome that exhibited specific mRNA induction in the spherule phase. Next, we surveyed copy-number variation genome-wide among strains of C. posadasii. Emerging from this catalog were spherule-gene islands with striking presence-absence differentiation between C. posadasii populations, a pattern expected from virulence factors subjected to different selective pressures across habitats. Finally, analyzing single-nucleotide differences across C. posadasii strains, we identified signatures of natural selection in spherule-expressed genes. Together, our data establish spherule-gene islands as candidate determinants of virulence and targets of selection in Coccidioides.
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Affiliation(s)
- Claire A. Dubin
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720-3102, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, UC San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Department of Microbiology and Immunology, UC San Francisco, San Francisco, CA 94143, USA
| | - Marcus M. Teixeira
- The Translational Genomics Research Institute (TGen)-Affiliate of City of Hope, Flagstaff, AZ 85004, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Bridget M. Barker
- The Translational Genomics Research Institute (TGen)-Affiliate of City of Hope, Flagstaff, AZ 85004, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Rachel B. Brem
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720-3102, USA
- Correspondence:
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Teixeira MM, Almeida-Paes R, Bernardes-Engemann AR, Nicola AM, de Macedo PM, Valle ACF, Gutierrez-Galhardo MC, Freitas DFS, Barker BM, Matute DR, Stajich JE, Zancopé-Oliveira RM. Single nucleotide polymorphisms and chromosomal copy number variation may impact the Sporothrix brasiliensis antifungal susceptibility and sporotrichosis clinical outcomes. Fungal Genet Biol 2022; 163:103743. [PMID: 36152775 DOI: 10.1016/j.fgb.2022.103743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 02/05/2023]
Abstract
Feline-transmitted sporotrichosis has garnered attention due to the recent high incidence and the lack of efficient control in the epicenter of the epidemic, Rio de Janeiro, Brazil. Sporothrix brasiliensis is the major pathogen involved in feline-to-human sporotrichosis in Brazil and displays more virulent genotypes than the closely related species S. schenckii. Over the last two decades, several reports of antifungal-resistant strains have emerged. Sequencing and comparison analysis of the outbreak strains allowed us to observe that the azole non-wild-type S. brasiliensis strain CFP 1054 had significant chromosomal variations compared to wild-type strains. One of these variants includes a region of 231 Kb containing 75 duplicated genes, which were overrepresented for lipid and isoprenoid metabolism. We also identified an additional strain (CFP 1055) that was resistant to itraconazole and amphotericin B, which had a single nucleotide polymorphism in the tac1 gene. The patients infected with these two strains showed protracted clinical course and sequelae. Even though our sample size is modest, these results suggest the possibility of identifying specific point mutations and large chromosomal duplications potentially associated with antifungal resistance and clinical outcomes of sporotrichosis.
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Affiliation(s)
- Marcus M Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA; Faculty of Medicine, University of Brasília-DF, Brazil
| | - Rodrigo Almeida-Paes
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Andréa R Bernardes-Engemann
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | | | - Priscila M de Macedo
- Laboratório de Pesquisa Clínica em Dermatologia Infecciosa, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Antonio Carlos F Valle
- Laboratório de Pesquisa Clínica em Dermatologia Infecciosa, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Maria Clara Gutierrez-Galhardo
- Laboratório de Pesquisa Clínica em Dermatologia Infecciosa, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Dayvison F S Freitas
- Laboratório de Pesquisa Clínica em Dermatologia Infecciosa, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Rosely M Zancopé-Oliveira
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
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de Melo Teixeira M, Stajich JE, Sahl JW, Thompson GR, Brem RB, Dubin CA, Blackmon AV, Mead HL, Keim P, Barker BM. A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain "Silveira". G3 (Bethesda) 2022; 12:jkac031. [PMID: 35137016 PMCID: PMC8982387 DOI: 10.1093/g3journal/jkac031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022]
Abstract
Coccidioidomycosis is a common fungal disease that is endemic to arid and semi-arid regions of both American continents. Coccidioides immitis and Coccidioides posadasii are the etiological agents of the disease, also known as Valley Fever. For several decades, the C. posadasii strain Silveira has been used widely in vaccine studies, is the source strain for production of diagnostic antigens, and is a widely used experimental strain for functional studies. In 2009, the genome was sequenced using Sanger sequencing technology, and a draft assembly and annotation were made available. In this study, the genome of the Silveira strain was sequenced using single molecule real-time sequencing PacBio technology, assembled into chromosomal-level contigs, genotyped, and the genome was reannotated using sophisticated and curated in silico tools. This high-quality genome sequencing effort has improved our understanding of chromosomal structure, gene set annotation, and lays the groundwork for identification of structural variants (e.g. transversions, translocations, and copy number variants), assessment of gene gain and loss, and comparison of transposable elements in future phylogenetic and population genomics studies.
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Affiliation(s)
- Marcus de Melo Teixeira
- Faculty of Medicine, University of Brasília, Brasília 70910-900, Brazil
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jason E Stajich
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - George R Thompson
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA 95616, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Claire A Dubin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Austin V Blackmon
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Heather L Mead
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bridget M Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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Parker CW, Teixeira MDM, Singh NK, Raja HA, Cank KB, Spigolon G, Oberlies NH, Barker BM, Stajich JE, Mason CE, Venkateswaran K. Genomic Characterization of Parengyodontium torokii sp. nov., a Biofilm-Forming Fungus Isolated from Mars 2020 Assembly Facility. J Fungi (Basel) 2022; 8:jof8010066. [PMID: 35050006 PMCID: PMC8778116 DOI: 10.3390/jof8010066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
A fungal strain (FJII-L10-SW-P1) was isolated from the Mars 2020 spacecraft assembly facility and exhibited biofilm formation on spacecraft-qualified Teflon surfaces. The reconstruction of a six-loci gene tree (ITS, LSU, SSU, RPB1 and RPB2, and TEF1) using multi-locus sequence typing (MLST) analyses of the strain FJII-L10-SW-P1 supported a close relationship to other known Parengyodontium album subclade 3 isolates while being phylogenetically distinct from subclade 1 strains. The zig-zag rachides morphology of the conidiogenous cells and spindle-shaped conidia were the distinct morphological characteristics of the P. album subclade 3 strains. The MLST data and morphological analysis supported the conclusion that the P. album subclade 3 strains could be classified as a new species of the genus Parengyodontium and placed in the family Cordycipitaceae. The name Parengyodontium torokii sp. nov. is proposed to accommodate the strain, with FJII-L10-SW-P1 as the holotype. The genome of the FJII-L10-SW-P1 strain was sequenced, annotated, and the secondary metabolite clusters were identified. Genes predicted to be responsible for biofilm formation and adhesion to surfaces were identified. Homology-based assignment of gene ontologies to the predicted proteome of P. torokii revealed the presence of gene clusters responsible for synthesizing several metabolic compounds, including a cytochalasin that was also verified using traditional metabolomic analysis.
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Affiliation(s)
- Ceth W. Parker
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.W.P.); (N.K.S.)
| | - Marcus de Melo Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (M.d.M.T.); (B.M.B.)
- School of Medicine, University of Brasilia, Brasilia 70910-900, Brazil
| | - Nitin K. Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.W.P.); (N.K.S.)
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (H.A.R.); (K.B.C.); (N.H.O.)
| | - Kristof B. Cank
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (H.A.R.); (K.B.C.); (N.H.O.)
| | - Giada Spigolon
- Biological Imaging Facility, California Institute of Technology, Pasadena, CA 91125, USA;
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (H.A.R.); (K.B.C.); (N.H.O.)
| | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (M.d.M.T.); (B.M.B.)
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California—Riverside, Riverside, CA 92521, USA;
| | - Christopher E. Mason
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.W.P.); (N.K.S.)
- Correspondence: ; Tel.: +1-(818)-393-1481; Fax: +1-(818)-393-4176
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11
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Thompson GR, Le T, Chindamporn A, Kauffman CA, Alastruey-Izquierdo A, Ampel NM, Andes DR, Armstrong-James D, Ayanlowo O, Baddley JW, Barker BM, Lopes Bezerra L, Buitrago MJ, Chamani-Tabriz L, Chan JFW, Chayakulkeeree M, Cornely OA, Cunwei C, Gangneux JP, Govender NP, Hagen F, Hedayati MT, Hohl TM, Jouvion G, Kenyon C, Kibbler CC, Klimko N, Kong DCM, Krause R, Lee Lee L, Meintjes G, Miceli MH, Rath PM, Spec A, Queiroz-Telles F, Variava E, Verweij PE, Schwartz IS, Pasqualotto AC. Global guideline for the diagnosis and management of the endemic mycoses: an initiative of the European Confederation of Medical Mycology in cooperation with the International Society for Human and Animal Mycology. Lancet Infect Dis 2021; 21:e364-e374. [PMID: 34364529 PMCID: PMC9450022 DOI: 10.1016/s1473-3099(21)00191-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/20/2022]
Abstract
The global burden of the endemic mycoses (blastomycosis, coccidioidomycosis, emergomycosis, histoplasmosis, paracoccidioidomycosis, sporotrichosis, and talaromycosis) continues to rise yearly and these infectious diseases remain a leading cause of patient morbidity and mortality worldwide. Management of the associated pathogens requires a thorough understanding of the epidemiology, risk factors, diagnostic methods and performance characteristics in different patient populations, and treatment options unique to each infection. Guidance on the management of these infections has the potential to improve prognosis. The recommendations outlined in this Review are part of the "One World, One Guideline" initiative of the European Confederation of Medical Mycology. Experts from 23 countries contributed to the development of these guidelines. The aim of this Review is to provide an up-to-date consensus and practical guidance in clinical decision making, by engaging physicians and scientists involved in various aspects of clinical management.
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Affiliation(s)
- George R Thompson
- Department of Internal Medicine, Division of Infectious Disease, UC Davis Medical Center, Sacramento, CA, USA; Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA.
| | - Thuy Le
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC, USA; Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ariya Chindamporn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Carol A Kauffman
- VA Ann Arbor Healthcare System, Ann Arbor, MI, USA; Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Neil M Ampel
- Division of Infectious Diseases, Mayo Clinic, Phoenix, AZ, USA; Department of Internal Medicine, Division of Infectious Diseases, University of Arizona College of Medicine, Tucson, AZ, USA
| | - David R Andes
- Department of Internal Medicine, Division of Infectious Diseases, and Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | | | - Olusola Ayanlowo
- Department of Medicine, Faculty of Clinical Sciences, University of Lagos, Lagos, Nigeria
| | - John W Baddley
- Department of Internal Medicine, Division of Infectious Disease, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Leila Lopes Bezerra
- Cellular Mycology and Proteomics Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Maria J Buitrago
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Leili Chamani-Tabriz
- Infectious Diseases Unit, Department of Internal Medicine, Saudi German Hospital Dubai, Dubai, UAE
| | - Jasper F W Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Methee Chayakulkeeree
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Oliver A Cornely
- Department of Internal Medicine, Excellence Center for Medical Mycology, University Hospital of Cologne, Cologne, Germany; Department of Internal Medicine, Division of Infectious Diseases, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Cao Cunwei
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jean-Pierre Gangneux
- Department of Internal Medicine, Division of Infectious Diseases, Rennes University, CHU Rennes, Inserm, IRSET-UMR_S 1085, Rennes, France
| | - Nelesh P Govender
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa; Department of Internal Medicine, Division of Infectious Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands; Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands; Laboratory of Medical Mycology, Jining No 1 People's Hospital, Jining, China
| | - Mohammad T Hedayati
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine; Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Grégory Jouvion
- Sorbonne Université, INSERM, Pathophysiology of Pediatric Genetic Diseases, Assistance Publique-Hôpitaux de Paris, Hôpital Armand-Trousseau, UF Génétique Moléculaire, Paris, France; Institut Pasteur, Experimental Neuropathology Unit, Paris, France
| | - Chris Kenyon
- Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Nikolai Klimko
- Department of Clinical Mycology, Allergy, and Immunology, I Mechnikov North-Western State Medical University, St Petersburg, Russia
| | - David C M Kong
- Pharmacy Department, Ballarat Health Services, Ballarat, VIC, Australia; National Centre for Antimicrobial Stewardship, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Low Lee Lee
- Department of Internal Medicine, Hospital Sultanah Bayiyah, Alor Setar, Kedah, Malaysia
| | - Graeme Meintjes
- Wellcome Centre for Infectious Diseases Research, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Marisa H Miceli
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, Essen, Germany
| | - Andrej Spec
- Division of Infectious Disease, Washington University School of Medicine, St Louis, MO, USA
| | - Flavio Queiroz-Telles
- Department of Public Health, Hospital de Clínicas, Federal University of Paraná, Curitiba, Brazil
| | - Ebrahim Variava
- Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa
| | - Paul E Verweij
- Department of Medical Microbiology, Excellence Center for Medical Mycology, Radboudumc-CWZ Center of Expertise for Mycology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ilan S Schwartz
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Alessandro C Pasqualotto
- Department of Clinical Medicine, Federal University of Health Sciences of Porto Alegre Porto Alegre, Brazil; Molecular Biology Laboratory, Santa Casa de Misericordia de Porto Alegre, Porto Alegre, Brazil
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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de Melo Teixeira M, Lang BF, Matute DR, Stajich JE, Barker BM. Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii. G3 (Bethesda) 2021; 11:jkab132. [PMID: 33871031 PMCID: PMC8496281 DOI: 10.1093/g3journal/jkab132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/25/2021] [Indexed: 12/25/2022]
Abstract
Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation in nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify 14 mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.
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Affiliation(s)
- Marcus de Melo Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Faculty of Medicine, University of Brasília-DF, Brasília, Federal District 70910-3300, Brazil
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Génomiques, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jason E Stajich
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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14
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Sun Y, Dong W, Tian L, Rao Y, Qin C, Jaramillo SA, Settles EW, Ma S, Zhang J, Yu K, Xu B, Yan J, Ma R, Li Z, Dadwal SS, Barker BM, Keim PS, Feng P, Caligiuri MA, Yu J. Dual roles of a novel oncolytic viral vector-based SARS-CoV-2 vaccine: preventing COVID-19 and treating tumor progression. bioRxiv 2021. [PMID: 34127971 DOI: 10.1101/2021.06.07.447286] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cancer patients are usually immunocompromised and thus are particularly susceptible to SARS-CoV-2 infection resulting in COVID-19. Although many vaccines against COVID-19 are being preclinically or clinically tested or approved, none have yet been specifically developed for cancer patients or reported as having potential dual functions to prevent COVID-19 and treat cancer. Here, we confirmed that COVID-19 patients with cancer have low levels of antibodies against the spike (S) protein, a viral surface protein mediating the entry of SARS-CoV-2 into host cells, compared with COVID-19 patients without cancer. We developed an oncolytic herpes simplex virus-1 vector-based vaccine named oncolytic virus (OV)-spike. OV-spike induced abundant anti-S protein neutralization antibodies in both tumor-free and tumor-bearing mice, which inhibit infection of VSV-SARS-CoV-2 and wild-type (WT) live SARS-CoV-2 as well as the B.1.1.7 variant in vitro. In the tumor-bearing mice, OV-spike also inhibited tumor growth, leading to better survival in multiple preclinical tumor models than the untreated control. Furthermore, OV-spike induced anti-tumor immune response and SARS-CoV-2-specific T cell response without causing serious adverse events. Thus, OV-spike is a promising vaccine candidate for both preventing COVID-19 and enhancing the anti-tumor response. One Sentence Summary A herpes oncolytic viral vector-based vaccine is a promising vaccine with dual roles in preventing COVID-19 and treating tumor progression.
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15
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Barker BM, Cuomo CA, Govender NP. Editorial: Genomic Characterization of Emerging Human Fungal Pathogens. Front Genet 2021; 12:674765. [PMID: 33841515 PMCID: PMC8027301 DOI: 10.3389/fgene.2021.674765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | | | - Nelesh P Govender
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.,Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
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16
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Mead HL, Hamm PS, Shaffer IN, Teixeira MDM, Wendel CS, Wiederhold NP, Thompson GR, Muñiz-Salazar R, Castañón-Olivares LR, Keim P, Plude C, Terriquez J, Galgiani JN, Orbach MJ, Barker BM. Differential Thermotolerance Adaptation between Species of Coccidioides. J Fungi (Basel) 2020; 6:E366. [PMID: 33327629 PMCID: PMC7765126 DOI: 10.3390/jof6040366] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/24/2020] [Accepted: 12/05/2020] [Indexed: 12/18/2022] Open
Abstract
Coccidioidomycosis, or Valley fever, is caused by two species of dimorphic fungi. Based on molecular phylogenetic evidence, the genus Coccidioides contains two reciprocally monophyletic species: C. immitis and C. posadasii. However, phenotypic variation between species has not been deeply investigated. We therefore explored differences in growth rate under various conditions. A collection of 39 C. posadasii and 46 C. immitis isolates, representing the full geographical range of the two species, was screened for mycelial growth rate at 37 °C and 28 °C on solid media. The radial growth rate was measured for 16 days on yeast extract agar. A linear mixed effect model was used to compare the growth rate of C. posadasii and C. immitis at 37 °C and 28 °C, respectively. C. posadasii grew significantly faster at 37 °C, when compared to C. immitis; whereas both species had similar growth rates at 28 °C. These results indicate thermotolerance differs between these two species. As the ecological niche has not been well-described for Coccidioides spp., and disease variability between species has not been shown, the evolutionary pressure underlying the adaptation is unclear. However, this research reveals the first significant phenotypic difference between the two species that directly applies to ecological research.
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Affiliation(s)
- Heather L. Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (H.L.M.); (P.K.)
| | - Paris S. Hamm
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Isaac N. Shaffer
- School of Informatics, Computers, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA;
| | | | | | - Nathan P. Wiederhold
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 77030, USA;
| | - George R. Thompson
- Departments of Internal Medicine Division of Infectious Diseases, and Medical Microbiology and Immunology, University of California-Davis, Sacramento, CA 95616, USA;
| | - Raquel Muñiz-Salazar
- Laboratorio de Epidemiología y Ecología Molecular, Escuela Ciencias de la Salud, Universidad Autónoma de Baja California, Unidad Valle Dorado, Ensenada 22890, Mexico;
| | - Laura Rosio Castañón-Olivares
- Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Mexico, Ciudad de México 04510, Mexico;
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (H.L.M.); (P.K.)
| | - Carmel Plude
- Northern Arizona Healthcare, Flagstaff, AZ 86001, USA; (C.P.); (J.T.)
| | - Joel Terriquez
- Northern Arizona Healthcare, Flagstaff, AZ 86001, USA; (C.P.); (J.T.)
| | - John N. Galgiani
- Valley Fever Center for Excellence, University of Arizona, Tucson, AZ 85721, USA; (J.N.G.); (M.J.O.)
| | - Marc J. Orbach
- Valley Fever Center for Excellence, University of Arizona, Tucson, AZ 85721, USA; (J.N.G.); (M.J.O.)
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (H.L.M.); (P.K.)
- Valley Fever Center for Excellence, University of Arizona, Tucson, AZ 85721, USA; (J.N.G.); (M.J.O.)
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17
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Eudes Filho J, dos Santos IB, Reis CMS, Patané JSL, Paredes V, Bernardes JPRA, Poggiani SDSC, Castro TDCB, Gomez OM, Pereira SA, Schubach EYP, Gomes KP, Mavengere H, Alves LGDB, Lucas J, Paes HC, Albuquerque P, Cruz LM, McEwen JG, Stajich JE, Almeida-Paes R, Zancopé-Oliveira RM, Matute DR, Barker BM, Felipe MSS, Teixeira MDM, Nicola AM. A novel Sporothrix brasiliensis genomic variant in Midwestern Brazil: evidence for an older and wider sporotrichosis epidemic. Emerg Microbes Infect 2020; 9:2515-2525. [PMID: 33155518 PMCID: PMC7717857 DOI: 10.1080/22221751.2020.1847001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/25/2020] [Indexed: 12/30/2022]
Abstract
Sporotrichosis is a subcutaneous infection caused by fungi from the genus Sporothrix. It is transmitted by inoculation of infective particles found in plant-contaminated material or diseased animals, characterizing the classic sapronotic and emerging zoonotic transmission, respectively. Since 1998, southeastern Brazil has experienced a zoonotic sporotrichosis epidemic caused by S. brasiliensis, centred in the state of Rio de Janeiro. Our observation of feline sporotrichosis cases in Brasília (Midwestern Brazil), around 900 km away from Rio de Janeiro, led us to question whether the epidemic caused by S. brasiliensis has spread from the epicentre in Rio de Janeiro, emerged independently in the two locations, or if the disease has been present and unrecognized in Midwestern Brazil. A retrospective analysis of 91 human and 4 animal cases from Brasília, ranging from 1993 to 2018, suggests the occurrence of both sapronotic and zoonotic transmission. Molecular typing of the calmodulin locus identified S. schenckii as the agent in two animals and all seven human patients from which we were able to recover clinical isolates. In two other animals, the disease was caused by S. brasiliensis. Whole-genome sequence typing of seven Sporothrix spp. strains from Brasília and Rio de Janeiro suggests that S. brasiliensis isolates from Brasília are genetically distinct from those obtained at the epicentre of the outbreak in Rio de Janeiro, both in phylogenomic and population genomic analyses. The two S. brasiliensis populations seem to have separated between 2.2 and 3.1 million years ago, indicating independent outbreaks or that the zoonotic S. brasiliensis outbreak might have started earlier and be more widespread in South America than previously recognized.
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Affiliation(s)
- João Eudes Filho
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
| | | | | | | | | | | | | | | | - Oscar Mauricio Gomez
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - Sandro Antonio Pereira
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | | | - Heidi Mavengere
- Department of Biology, University of North Carolina, Chapel Hill, USA
| | | | - Joaquim Lucas
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
| | | | | | - Laurício Monteiro Cruz
- Office of Environmental Surveillance of Zoonoses, Federal District Health Secretariat, Brasília, Brazil
| | - Juan G. McEwen
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - Jason E. Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, USA
| | - Rodrigo Almeida-Paes
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Daniel R. Matute
- Department of Biology, University of North Carolina, Chapel Hill, USA
| | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, USA
| | - Maria Sueli Soares Felipe
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
- Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Marcus de Melo Teixeira
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
- Faculty of Medicine, University of Brasília, Brazil
| | - André Moraes Nicola
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
- Faculty of Medicine, University of Brasília, Brazil
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18
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Barker BM, Rajan S, De Melo Teixeira M, Sewnarine M, Roe C, Engelthaler DM, Galgiani JN. Coccidioidal Meningitis in New York Traced to Texas by Fungal Genomic Analysis. Clin Infect Dis 2020; 69:1060-1062. [PMID: 30715178 DOI: 10.1093/cid/ciz052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/16/2019] [Indexed: 11/15/2022] Open
Abstract
A child developed hydrocephalus. Sixteen months later, it was discovered to be a complication of coccidioidal meningitis. The infection's source was uncertain until genomic analysis of the fungal isolate identified its origin to be a visit to Beeville, Texas. Improved national reporting of cases of coccidioidomycosis might reduce diagnostic delays.
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Affiliation(s)
- Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff
| | | | - Marcus De Melo Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff.,Faculty of Medicine, University of Brasília, Brazil
| | | | - Chandler Roe
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff.,Translational Genomics Research Institute, Flagstaff
| | | | - John N Galgiani
- Valley Fever Center for Excellence and Department of Medicine, University of Arizona College of Medicine, Tucson
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19
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Mead HL, Van Dyke MCC, Barker BM. Proper Care and Feeding of Coccidioides: A Laboratorian's Guide to Cultivating the Dimorphic Stages of C. immitis and C. posadasii. Curr Protoc Microbiol 2020; 58:e113. [PMID: 32894648 PMCID: PMC9976608 DOI: 10.1002/cpmc.113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Coccidioidomycosis ("Valley fever") is caused by Coccidioides immitis and C. posadasii. These fungi are thermally dimorphic, cycling between mycelia and arthroconidia in the environment and converting into spherules and endospores within a host. Coccidioides can cause a broad spectrum of disease that can be difficult to treat. There has been a steady increase in disease, with an estimated 350,000 new infections per year in the United States. With the increase in disease and difficulty in treatment, there is an unmet need to increase research in basic biology and identify new treatments, diagnostics, and vaccine candidates. Here, we describe protocols required in any Coccidioides laboratory, such as growing, harvesting, and storing the different stages of this dimorphic fungal pathogen. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Growth and harvest of liquid mycelia cultures for extractions Alternate Protocol 1: Large-volume growth and harvest of liquid mycelia cultures Basic Protocol 2: Mycelial growth on solid medium Alternate Protocol 2: Maintaining mycelial growth on solid medium Basic Protocol 3: Harvesting and quantification of arthroconidia Alternate Protocol 3: Long-term storage of arthroconidia Basic Protocol 4: Parasitic spherule growth and harvest Alternate Protocol 4: Obtaining endospores from spherules Basic Protocol 5: Intranasal infection of murine models.
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Affiliation(s)
- Heather L. Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | | | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona,Corresponding author:
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20
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Mead HL, Roe CC, Higgins Keppler EA, Van Dyke MCC, Laux KL, Funke AL, Miller KJ, Bean HD, Sahl JW, Barker BM. Defining Critical Genes During Spherule Remodeling and Endospore Development in the Fungal Pathogen, Coccidioides posadasii. Front Genet 2020; 11:483. [PMID: 32499817 PMCID: PMC7243461 DOI: 10.3389/fgene.2020.00483] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Coccidioides immitis and C. posadasii are soil dwelling dimorphic fungi found in North and South America. Inhalation of aerosolized asexual conidia can result in asymptomatic, acute, or chronic respiratory infection. In the United States there are approximately 350,000 new infections per year. The Coccidioides genus is the only known fungal pathogen to make specialized parasitic spherules, which contain endospores that are released into the host upon spherule rupture. The molecular determinants involved in this key step of infection remain largely elusive as 49% of genes are hypothetical with unknown function. An attenuated mutant strain C. posadasii Δcts2/Δard1/Δcts3 in which chitinase genes 2 and 3 were deleted was previously created for vaccine development. This strain does not complete endospore development, which prevents completion of the parasitic lifecycle. We sought to identify pathways active in the wild-type strain during spherule remodeling and endospore formation that have been affected by gene deletion in the mutant. We compared the transcriptome and volatile metabolome of the mutant Δcts2/Δard1/Δcts3 to the wild-type C735. First, the global transcriptome was compared for both isolates using RNA sequencing. The raw reads were aligned to the reference genome using TOPHAT2 and analyzed using the Cufflinks package. Genes of interest were screened in an in vivo model using NanoString technology. Using solid phase microextraction (SPME) and comprehensive two-dimensional gas chromatography - time-of-flight mass spectrometry (GC × GC-TOFMS) volatile organic compounds (VOCs) were collected and analyzed. Our RNA-Seq analyses reveal approximately 280 significantly differentially regulated transcripts that are either absent or show opposite expression patterns in the mutant compared to the parent strain. This suggests that these genes are tied to networks impacted by deletion and may be critical for endospore development and/or spherule rupture in the wild-type strain. Of these genes, 14 were specific to the Coccidioides genus. We also found that the wild-type and mutant strains differed significantly in their production versus consumption of metabolites, with the mutant displaying increased nutrient scavenging. Overall, our results provide the first targeted list of key genes that are active during endospore formation and demonstrate that this approach can define targets for functional assays in future studies.
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Affiliation(s)
- H L Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - C C Roe
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - E A Higgins Keppler
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - M C Caballero Van Dyke
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - K L Laux
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - A L Funke
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States.,Imaging Histology Core Facility, Northern Arizona University, Flagstaff AZ, United States
| | - K J Miller
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - H D Bean
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - J W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - B M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
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21
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Teixeira MDM, Muszewska A, Travis J, Moreno LF, Ahmed S, Roe C, Mead H, Steczkiewicz K, Lemmer D, de Hoog S, Keim P, Wiederhold N, Barker BM. Genomic characterization of Parengyodontium americanum sp. nov. Fungal Genet Biol 2020; 138:103351. [PMID: 32028048 DOI: 10.1016/j.fgb.2020.103351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 11/29/2022]
Abstract
Modern genome analysis and phylogenomic methods have increased the number of fungal species, as well as enhanced appreciation of the degree of diversity within the fungal kingdom. In this context, we describe a new Parengyodontium species, P. americanum, which is phylogenetically related to the opportunistic human fungal pathogen P. album. Five unusual fungal isolates were recovered from five unique and confirmed coccidioidomycosis patients, and these isolates were subsequently submitted to detailed molecular and morphological identification procedures to determine identity. Molecular and morphological diagnostic analyses showed that the isolates belong to the Cordycipitaceae. Subsequently, three representative genomes were sequenced and annotated, and a new species, P. americanum, was identified. Using various genomic analyses, gene family expansions related to novel compounds and potential for ability to grow in diverse habitats are predicted. A general description of the genomic composition of this newly described species and comparison of genome content with Beauveria bassiana, Isaria fumosorosea and Cordyceps militaris shows a shared core genome of 6371 genes, and 148 genes that appear to be specific for P. americanum. This work provides the framework for future investigations of this interesting fungal species.
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Affiliation(s)
- Marcus de M Teixeira
- Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, AZ, USA; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA; Faculty of Medicine, University of Brasília, Brasília-DF, Brazil
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jason Travis
- Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, AZ, USA
| | - Leandro F Moreno
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Sarah Ahmed
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Chandler Roe
- Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, AZ, USA; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Heather Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Centre of New Technologies, University of Warsaw, Warsaw, Poland.
| | - Darrin Lemmer
- Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, AZ, USA
| | - Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Paul Keim
- Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, AZ, USA; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Nathan Wiederhold
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Bridget M Barker
- Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, AZ, USA; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
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22
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Kollath DR, Miller KJ, Barker BM. The mysterious desert dwellers: Coccidioides immitis and Coccidioides posadasii, causative fungal agents of coccidioidomycosis. Virulence 2019; 10:222-233. [PMID: 30898028 PMCID: PMC6527015 DOI: 10.1080/21505594.2019.1589363] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/07/2019] [Accepted: 02/25/2019] [Indexed: 01/31/2023] Open
Abstract
The genus Coccidioides consists of two species: C. immitis and C. posadasii. Prior to 2000, all disease was thought to be caused by a single species, C. immitis. The organism grows in arid to semiarid alkaline soils throughout western North America and into Central and South America. Regions in the United States, with highest prevalence of disease, include California, Arizona, and Texas. The Mexican states of Baja California, Coahuila, Sonora, and Neuvo Leon currently have the highest skin test positive results. Central America contains isolated endemic areas in Guatemala and Honduras. South America has isolated regions of high endemicity including areas of Colombia, Venezuela, Argentina, Paraguay, and Brazil. Although approximately 15,000 cases per year are reported in the United States, actual disease burden is estimated to be in the hundreds of thousands, as only California and Arizona have dedicated public health outreach, and report and track disease reliably. In this review, we survey genomics, epidemiology, ecology, and summarize aspects of disease, diagnosis, prevention, and treatment.
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Affiliation(s)
- Daniel R. Kollath
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Karis J. Miller
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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23
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Kollath DR, Teixeira MM, Funke A, Miller KJ, Barker BM. Investigating the Role of Animal Burrows on the Ecology and Distribution of Coccidioides spp. in Arizona Soils. Mycopathologia 2019; 185:145-159. [PMID: 31586286 DOI: 10.1007/s11046-019-00391-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/23/2019] [Indexed: 01/08/2023]
Abstract
The lack of knowledge regarding the ecology of Coccidioides spp. makes both modeling the potential for disease outbreaks and predicting the distribution of the organism in the environment challenging. No single ecological parameter explains the biogeography of the pathogen. Previous investigations suggest an association with desert mammals, but these results should be confirmed with modern molecular techniques. Therefore, we used molecular tools to analyze soils associated with animal activity (i.e., burrows) to better define the ecology and biogeography of Coccidioides spp. in Arizona. Soils were collected from locations predicted to have favorable habitat outside of the established endemic regions to better understand the ecological niche of the organism in this state. Our central hypothesis is that soils taken from within animal burrows will have a higher abundance of Coccidioides spp. when compared to soils not directly associated with animal burrows. Our results show that there is a positive relationship with Coccidioides spp. and animal burrows. The organism was detected in two locations in northern Arizona at sites not known previously to harbor the fungus. Moreover, this fungus is able to grow on keratinized tissues (i.e., horse hair). These results provide additional evidence that there is a relationship between Coccidioides spp. and desert animals, which sheds new light on Coccidioides' ecological niche. These results also provide evidence that the geographic range of the organism may be larger than previously thought, and the concept of endemicity should be reevaluated for Coccidioides.
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Affiliation(s)
- Daniel R Kollath
- Pathogen and Microbiome Institute, Northern Arizona University, Applied Research and Development Building, 1298 S Knoles Drive, Flagstaff, AZ, 86011-4073, USA
| | - Marcus M Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Applied Research and Development Building, 1298 S Knoles Drive, Flagstaff, AZ, 86011-4073, USA
- School of Medicine, University of Brasília, Brasília, DF, Brazil
| | - Aubrey Funke
- Imaging and Histology Core Facility, Northern Arizona University, Flagstaff, AZ, USA
| | - Karis J Miller
- Pathogen and Microbiome Institute, Northern Arizona University, Applied Research and Development Building, 1298 S Knoles Drive, Flagstaff, AZ, 86011-4073, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Applied Research and Development Building, 1298 S Knoles Drive, Flagstaff, AZ, 86011-4073, USA.
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24
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Van Dyke MCC, Thompson GR, Galgiani JN, Barker BM. The Rise of Coccidioides: Forces Against the Dust Devil Unleashed. Front Immunol 2019; 10:2188. [PMID: 31572393 PMCID: PMC6749157 DOI: 10.3389/fimmu.2019.02188] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Coccidioidomycosis (Valley fever) is a fungal disease caused by the inhalation of Coccidioides posadasii or C. immitis. This neglected disease occurs in the desert areas of the western United States, most notably in California and Arizona, where infections continue to rise. Clinically, coccidioidomycosis ranges from asymptomatic to severe pulmonary disease and can disseminate to the brain, skin, bones, and elsewhere. New estimates suggest as many as 350,000 new cases of coccidioidomycosis occur in the United States each year. Thus, there is an urgent need for the development of a vaccine and new therapeutic drugs against Coccidioides infection. In this review, we discuss the battle against Coccidioides including the development of potential vaccines, the quest for new therapeutic drugs, and our current understanding of the protective host immune response to Coccidioides infection.
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Affiliation(s)
| | - George R Thompson
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA, United States
| | - John N Galgiani
- Valley Fever Center for Excellence, Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, AZ, United States
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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25
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Bowers JR, Parise KL, Kelley EJ, Lemmer D, Schupp JM, Driebe EM, Engelthaler DM, Keim P, Barker BM. Direct detection of Coccidioides from Arizona soils using CocciENV, a highly sensitive and specific real-time PCR assay. Med Mycol 2019. [PMID: 29534236 DOI: 10.1093/mmy/myy007] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coccidioides immitis and Coccidioides posadasii are soil fungi endemic to desert regions of the southwestern United States, and the causative agents of valley fever, or coccidioidomycosis. Studies have shown that the distribution of Coccidioides in soils is sporadic and cannot be explained by soil characteristics alone, suggesting that biotic and other abiotic factors should be examined. However, tools to reliably and robustly screen the large number of soils needed to investigate these potential associations have not been available. Thus, we developed a real-time polymerase chain reaction (PCR) assay for testing environmental samples by modifying CocciDx, an assay validated for testing clinical specimens to facilitate coccidioidomycosis diagnosis. For this study, we collected soil samples from previously established locations of C. posadasii in Arizona and new locations in fall 2013 and spring 2014, and screened the extracted DNA with the new assay known as CocciEnv. To verify the presence of Coccidioides in soil using an alternate method, we employed next generation amplicon sequencing targeting the ITS2 region. Results show our modified assay, CocciEnv, is a rapid and robust method for detecting Coccidioides DNA in complex environmental samples. The ability to test a large number of soils for the presence of Coccidioides is a much-needed tool in the understanding of the ecology of the organism and epidemiology of the disease and will greatly improve our understanding of this human pathogen.
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Affiliation(s)
- J R Bowers
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - K L Parise
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - E J Kelley
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - D Lemmer
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - J M Schupp
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - E M Driebe
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - D M Engelthaler
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - P Keim
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - B M Barker
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
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26
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Mead HL, Blackmon AV, Vogler AJ, Barker BM. Heat Inactivation of Coccidioides posadasii and Coccidioides immitis for Use in Lower Biosafety Containment. Appl Biosaf 2019; 24:123-128. [PMID: 33833621 DOI: 10.1177/1535676019856525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction The difficulty involved in obtaining sufficient intact genomic deoxyribonucleic acid (DNA) from Coccidioides spp for downstream applications using published protocols prompted the exploration of inactivating mycelia and arthroconidia using heat under biosafety level 3 containment. This was followed by optimizing DNA extraction from mycelia using various methods at lower containment. Methods Various exposure times and temperatures were examined to identify an effective heat inactivation procedure for arthroconidia and mycelia from both C immitis and C posadasii. Heat inactivation of mycelia was followed by DNA extraction using 2 commercially available kits, as well as a phenol:chloroform-based extraction procedure to determine DNA integrity and quantity among extraction methods using both live and heat-inactivated mycelia. Results Ten-minute and 30-minute exposure times at 80°C were sufficient to inactivate Coccidioides spp arthroconidia and mycelia, respectively. DNA yield between live versus heat-inactivated mycelia was similar for each extraction procedure. However, DNA obtained using phenol:chloroform was of higher quantity and integrity compared with DNA obtained using the commercially available kits, which was highly fragmented. Conclusion The ability to heat-inactivate Coccidioides cultures for processing at a lower level of containment greatly increased the efficiency of DNA extractions. Therefore, this is an ideal method for obtaining Coccidioides spp DNA and inactivated arthroconidia.
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Affiliation(s)
- Heather L Mead
- Northern Arizona University, Pathogen and Microbiome Institute, Flagstaff, AZ, USA
| | - Austin V Blackmon
- Northern Arizona University, Pathogen and Microbiome Institute, Flagstaff, AZ, USA
| | - Amy J Vogler
- Northern Arizona University, Pathogen and Microbiome Institute, Flagstaff, AZ, USA
| | - Bridget M Barker
- Northern Arizona University, Pathogen and Microbiome Institute, Flagstaff, AZ, USA
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27
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Van Dyke MCC, Teixeira MM, Barker BM. Fantastic yeasts and where to find them: the hidden diversity of dimorphic fungal pathogens. Curr Opin Microbiol 2019; 52:55-63. [PMID: 31181385 DOI: 10.1016/j.mib.2019.05.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 11/29/2022]
Abstract
Dimorphic fungal pathogens are a significant cause of human disease worldwide. Notably, the dimorphic fungal pathogens within the order Onygenales are considered primary pathogens, causing disease in healthy hosts. Current changes in taxonomy are underway due to advances in molecular phylogenetics, population genetics, and new emerging dimorphic fungal pathogens causing human disease. In this review, we highlight evolutionary relationships of dimorphic fungal pathogens that cause human disease within the order Onygenales and provide rationale to support increased investment in studies understanding the evolutionary relationships of these pathogens to improve rapid diagnostics, help identify mechanisms of antifungal resistance, understand adaptation to human host, and factors associated with virulence.
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Affiliation(s)
| | - Marcus M Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States; Faculty of Medicine, University of Brasília, Brasília-DF, Brazil
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States.
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Mead HL, Teixeira MDM, Galgiani JN, Barker BM. Characterizing in vitro spherule morphogenesis of multiple strains of both species of Coccidioides. Med Mycol 2019; 57:478-488. [PMID: 30053114 DOI: 10.1093/mmy/myy049] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/27/2018] [Indexed: 11/12/2022] Open
Abstract
The disease San Joaquin Valley Fever (coccidioidomycosis) is caused by the inhalation of Coccidioides arthroconidia. In vivo, arthroconidia transform into pathogenic structures termed spherules. Exposure to the host milieu triggers spherule development; however, the molecular mechanisms responsible for the morphological shift are not well characterized. This study compared the morphogenesis of five strains of both species of Coccidioides in two media types to improve the in vitro model of dimorphism that can be easily reproduced, and is amenable to tissue culture. We also sought to establish a modern record of the morphological switch among commonly used lab strains through a detailed account of growth under various conditions. Spherules from five strains were grown in standard (Converse) and experimental media (RPMI-sph). Strain behavior was quantified by median spherule size and spherule concentration, beginning 3 days after inoculation and followed for 10 days of growth. There were significant differences observed among Coccidioides immitis and C. posadasii strains, as well as differences between the in vitro systems.
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Affiliation(s)
- Heather L Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona.,Pathogen Genomics Division, Translational Genomics Research Institute-North, Phoenix, Arizona
| | - Marcus de Melo Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona.,Pathogen Genomics Division, Translational Genomics Research Institute-North, Phoenix, Arizona
| | - John N Galgiani
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona.,Pathogen Genomics Division, Translational Genomics Research Institute-North, Phoenix, Arizona.,Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona
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Abstract
Although the natural history and ecology of Coccidioides spp. have been studied for over 100 years, many fundamental questions about this fungus remain unanswered. Two of the most challenging aspects of the study of Coccidioides have been the undefined ecological niche and the outdated geographic distribution maps dating from midcentury. This review details the history of Coccidioides ecological research, and discusses current strategies and advances in understanding Coccidioides genetics and ecology.
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Affiliation(s)
- Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | | | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, Baja California, 22860, Mexico
| | - Lluvia Vargas-Gastélum
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, Baja California, 22860, Mexico
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Taylor JW, Barker BM. The endozoan, small-mammal reservoir hypothesis and the life cycle of Coccidioides species. Med Mycol 2019; 57:S16-S20. [PMID: 30690603 DOI: 10.1093/mmy/myy039] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 12/23/2022] Open
Abstract
The prevailing hypothesis concerning the ecology of Coccidioides immitis and C. posadasii is that these human pathogenic fungi are soil fungi endemic to hot, dry, salty regions of the New World and that humans and the local, small-mammal fauna are only accidental hosts. Here we advance an alternative hypothesis that Coccidioides spp. live in small mammals as endozoans, which are kept inactive but alive in host granulomas and which transform into spore-producing hyphae when the mammal dies. The endozoan hypothesis incorporates results from comparative genomic analyses of Coccidioides spp. and related taxa that have shown a reduction in gene families associated with deconstruction of plant cell walls and an increase in those associated with digestion of animal protein, consistent with an evolutionary shift in substrate from plants to animals. If true, the endozoan hypothesis requires that models of the prevalence of human coccidioidomycosis account not only for direct effects of climate and soil parameters on the growth and reproduction of Coccidioides spp. but also consider indirect effects on these fungi that come from the plants that support the growth and reproduction of the small mammals that, in turn, support these endozoic fungi.
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Affiliation(s)
- John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
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31
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Maxwell CS, Mattox K, Turissini DA, Teixeira MM, Barker BM, Matute DR. Gene exchange between two divergent species of the fungal human pathogen, Coccidioides. Evolution 2018; 73:42-58. [PMID: 30414183 DOI: 10.1111/evo.13643] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022]
Abstract
The fungal genus Coccidioides is composed of two species, Coccidioides immitis and Coccidioides posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what is the expected size of shared haplotypes that might be inherited from the last common ancestor of the two species and find a cutoff to find what haplotypes have conclusively been exchanged between species. Finally, we precisely identified the breakpoints of the haplotypes that have crossed the species boundary and measure the allele frequency of each introgression in this sample. We find that introgressions are not uniformly distributed across the genome. Most, but not all, of the introgressions segregate at low frequency. Our results show that divergent species can share alleles, that species boundaries can be porous, and highlight the need for a systematic exploration of gene exchange in fungal species.
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Affiliation(s)
- Colin S Maxwell
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Kathleen Mattox
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - David A Turissini
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Marcus M Teixeira
- Núcleo de Medicina Tropical, Faculdade de Medicina, University of Brasília, Brasília, Brazil
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
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Abstract
Although Coccidioides genotypes are highly genetically variable,
they cluster into discrete populations, which has implications for human
infections. During the past 20 years, a general picture of the genetic diversity and population
structure of Coccidioides, the causal agent of coccidioidomycosis
(Valley fever), has emerged. The genus consists of 2 genetically diverse species,
C. immitis and C. posadasii, each of which
contains 1 or more distinct populations with limited gene flow. Genotypic data
indicate that C. immitis is divided into 2 subpopulations (central
and southern California populations) and C. posadasii is divided
into 3 subpopulations (Arizona, Mexico, and Texas/South America populations).
However, admixture within and among these populations and the current paucity of
environmental isolates limit our understanding of the population genetics of
Coccidioides. We assessed population structure of
Coccidioides in Arizona by analyzing 495 clinical and
environmental isolates. Our findings confirm the population structure as previously
described and indicate a finer scale population structure in Arizona. Environmental
isolates appear to have higher genetic diversity than isolates from human
patients.
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Zhang I, Pletcher SD, Goldberg AN, Barker BM, Cope EK. Fungal Microbiota in Chronic Airway Inflammatory Disease and Emerging Relationships with the Host Immune Response. Front Microbiol 2017; 8:2477. [PMID: 29312187 PMCID: PMC5733051 DOI: 10.3389/fmicb.2017.02477] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/29/2017] [Indexed: 12/22/2022] Open
Abstract
The respiratory tract is a complex system that is inhabited by niche-specific communities of microbes including bacteria, fungi, and viruses. These complex microbial assemblages are in constant contact with the mucosal immune system and play a critical role in airway health and immune homeostasis. Changes in the composition and diversity of airway microbiota are frequently observed in patients with chronic inflammatory diseases including chronic rhinosinusitis (CRS), cystic fibrosis, allergy, and asthma. While the bacterial microbiome of the upper and lower airways has been the focus of many recent studies, the contribution of fungal microbiota to inflammation is an emerging research interest. Within the context of allergic airway disease, fungal products are important allergens and fungi are potent inducers of inflammation. In addition, murine models have provided experimental evidence that fungal microbiota in peripheral organs, notably the gastrointestinal (GI) tract, influence pulmonary health. In this review, we explore the role of the respiratory and GI microbial communities in chronic airway inflammatory disease development with a specific focus on fungal microbiome interactions with the airway immune system and fungal-bacterial interactions that likely contribute to inflammatory disease. These findings are discussed in the context of clinical and immunological features of fungal-mediated disease in CRS, allergy, and asthmatic patients. While this field is still nascent, emerging evidence suggests that dysbiotic fungal and bacterial microbiota interact to drive or exacerbate chronic airway inflammatory disease.
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Affiliation(s)
- Irene Zhang
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Steven D. Pletcher
- Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Andrew N. Goldberg
- Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Emily K. Cope
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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Teixeira MDM, Patané JSL, Taylor ML, Gómez BL, Theodoro RC, de Hoog S, Engelthaler DM, Zancopé-Oliveira RM, Felipe MSS, Barker BM. Worldwide Phylogenetic Distributions and Population Dynamics of the Genus Histoplasma. PLoS Negl Trop Dis 2016; 10:e0004732. [PMID: 27248851 PMCID: PMC4889077 DOI: 10.1371/journal.pntd.0004732] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/03/2016] [Indexed: 12/11/2022] Open
Abstract
Background Histoplasma capsulatum comprises a worldwide complex of saprobiotic fungi mainly found in nitrogen/phosphate (often bird guano) enriched soils. The microconidia of Histoplasma species may be inhaled by mammalian hosts, and is followed by a rapid conversion to yeast that can persist in host tissues causing histoplasmosis, a deep pulmonary/systemic mycosis. Histoplasma capsulatum sensu lato is a complex of at least eight clades geographically distributed as follows: Australia, Netherlands, Eurasia, North American classes 1 and 2 (NAm 1 and NAm 2), Latin American groups A and B (LAm A and LAm B) and Africa. With the exception of the Eurasian cluster, those clades are considered phylogenetic species. Methodology/Principal Findings Increased Histoplasma sampling (n = 234) resulted in the revision of the phylogenetic distribution and population structure using 1,563 aligned nucleotides from four protein-coding regions. The LAm B clade appears to be divided into at least two highly supported clades, which are geographically restricted to either Colombia/Argentina or Brazil respectively. Moreover, a complex population genetic structure was identified within LAm A clade supporting multiple monophylogenetic species, which could be driven by rapid host or environmental adaptation (~0.5 MYA). We found two divergent clades, which include Latin American isolates (newly named as LAm A1 and LAm A2), harboring a cryptic cluster in association with bats. Conclusions/Significance At least six new phylogenetic species are proposed in the Histoplasma species complex supported by different phylogenetic and population genetics methods, comprising LAm A1, LAm A2, LAm B1, LAm B2, RJ and BAC-1 phylogenetic species. The genetic isolation of Histoplasma could be a result of differential dispersion potential of naturally infected bats and other mammals. In addition, the present study guides isolate selection for future population genomics and genome wide association studies in this important pathogen complex. Histoplasmosis is a potentially severe fungal disease of mammals caused by Histoplasma capsulatum. The highest incidence of the disease is reported on the American continent, and approximately 30% of HIV and histoplasmosis co-infections are fatal. Previous studies have suggested at least 7 phylogenetic species within H. capsulatum, however by increasing taxon sampling and using different phylogenetic and population genetic methods, we detect at least 5 additional phylogenetic species within Latin America (LAm A1, LAm A2, LAm B1, LAm B2, RJ and BAC-1). These phylogenetic species are nested in the former LAm A clade. We found evidence that bats may be a cause of speciation in Histoplasma, as well-supported monophyletic clades were found in association with different species of bats. The radiation of the Latin American H. capsulatum species took a place around 5 million years ago, which is consistent with the radiation and diversification of bat species. Previous phylogenetic distribution of Histoplasma is upheld and strong support is indicated for the species delineation and evolution of this important pathogen.
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Affiliation(s)
- Marcus de M. Teixeira
- Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, Arizona, United States of America
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - José S. L. Patané
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Maria L. Taylor
- Department of Microbiology and Parasitology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Beatriz L. Gómez
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
| | - Raquel C. Theodoro
- Department of Cell Biology and Genetics/ Institute of Tropical Medicine, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands
| | - David M. Engelthaler
- Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, Arizona, United States of America
| | - Rosely M. Zancopé-Oliveira
- Mycology Laboratory, National Institute of Infectology Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Bridget M. Barker
- Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, Arizona, United States of America
- * E-mail:
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35
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Chow NA, Griffin DW, Barker BM, Loparev VN, Litvintseva AP. Molecular detection of airborne Coccidioides in Tucson, Arizona. Med Mycol 2016; 54:584-92. [PMID: 27143633 DOI: 10.1093/mmy/myw022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 02/03/2016] [Indexed: 11/12/2022] Open
Abstract
Environmental surveillance of the soil-dwelling fungus Coccidioides is essential for the prevention of Valley fever, a disease primarily caused by inhalation of the arthroconidia. Methods for collecting and detecting Coccidioides in soil samples are currently in use by several laboratories; however, a method utilizing current air sampling technologies has not been formally demonstrated for the capture of airborne arthroconidia. In this study, we collected air/dust samples at two sites (Site A and Site B) in the endemic region of Tucson, Arizona, and tested a variety of air samplers and membrane matrices. We then employed a single-tube nested qPCR assay for molecular detection. At both sites, numerous soil samples (n = 10 at Site A and n = 24 at Site B) were collected and Coccidioides was detected in two samples (20%) at Site A and in eight samples (33%) at Site B. Of the 25 air/dust samples collected at both sites using five different air sampling methods, we detected Coccidioides in three samples from site B. All three samples were collected using a high-volume sampler with glass-fiber filters. In this report, we describe these methods and propose the use of these air sampling and molecular detection strategies for environmental surveillance of Coccidioides.
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Affiliation(s)
- Nancy A Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Dale W Griffin
- US Geological Survey, Coastal and Marine Science Center, St. Petersburg, Florida
| | - Bridget M Barker
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona
| | - Vladimir N Loparev
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, GA
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Abstract
The lack of published data on effective disinfectants and contact times for use on the fungal pathogens Coccidioides immitis and C. posadasii prompted the authors to investigate the fungicidal activity of three commonly used laboratory disinfectants on arthroconidia harvested from C. immitis strain 2009. They tested the ability of 10% bleach, 70% ethanol, and Vesphene® IIse to inactivate 107 arthroconidia in an aqueous suspension within 1, 2, 5, 10, or 20 minutes of contact time. Both 10% bleach and 70% ethanol provided a 7-log10 reduction in arthroconidia in less than 1 minute, with no growth observed at any of the tested time points. Vesphene® IIse was less effective, providing a 6-log10 reduction in arthroconidia after 5 minutes, but was unable to completely inactivate all of the arthroconidia, even after 20 minutes of contact time.
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Affiliation(s)
| | | | | | - Paul Keim
- Northern Arizona University, Flagstaff, Arizona
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37
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Lee MJ, Liu H, Barker BM, Snarr BD, Gravelat FN, Al Abdallah Q, Gavino C, Baistrocchi SR, Ostapska H, Xiao T, Ralph B, Solis NV, Lehoux M, Baptista SD, Thammahong A, Cerone RP, Kaminskyj SGW, Guiot MC, Latgé JP, Fontaine T, Vinh DC, Filler SG, Sheppard DC. The Fungal Exopolysaccharide Galactosaminogalactan Mediates Virulence by Enhancing Resistance to Neutrophil Extracellular Traps. PLoS Pathog 2015; 11:e1005187. [PMID: 26492565 PMCID: PMC4619649 DOI: 10.1371/journal.ppat.1005187] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 09/03/2015] [Indexed: 11/18/2022] Open
Abstract
Of the over 250 Aspergillus species, Aspergillus fumigatus accounts for up to 80% of invasive human infections. A. fumigatus produces galactosaminogalactan (GAG), an exopolysaccharide composed of galactose and N-acetyl-galactosamine (GalNAc) that mediates adherence and is required for full virulence. Less pathogenic Aspergillus species were found to produce GAG with a lower GalNAc content than A. fumigatus and expressed minimal amounts of cell wall-bound GAG. Increasing the GalNAc content of GAG of the minimally pathogenic A. nidulans, either through overexpression of the A. nidulans epimerase UgeB or by heterologous expression of the A. fumigatus epimerase Uge3 increased the amount of cell wall bound GAG, augmented adherence in vitro and enhanced virulence in corticosteroid-treated mice to levels similar to A. fumigatus. The enhanced virulence of the overexpression strain of A. nidulans was associated with increased resistance to NADPH oxidase-dependent neutrophil extracellular traps (NETs) in vitro, and was not observed in neutropenic mice or mice deficient in NADPH-oxidase that are unable to form NETs. Collectively, these data suggest that cell wall-bound GAG enhances virulence through mediating resistance to NETs. The ubiquitous mold A. fumigatus is isolated in over 80% of all patients with invasive aspergillosis (IA). A. nidulans is a relatively non-pathogenic species that rarely causes IA except in patients with chronic granulomatous disease (CGD), a hereditary disease characterized by impaired neutrophil function due to mutations in the NADPH oxidase complex. Here, we demonstrate that one factor underlying the differences in the intrinsic virulence between A. fumigatus and A. nidulans is the amount of the exopolysaccharide galactosaminogalactan that is associated with the cell wall of these species. A. fumigatus produces higher amounts of cell wall-associated galactosaminogalactan and is more resistant than A. nidulans to neutrophil killing by NADPH-oxidase dependent extracellular traps (NETs). Increasing cell wall-associated galactosaminogalactan in A. nidulans enhanced resistance to NETs and increased the virulence of this species to the same level as A. fumigatus in mice with intact NET formation. Collectively, these data suggest that A. nidulans is more sensitive than A. fumigatus to NADPH-oxidase dependent NETosis due to lower levels of cell wall-associated GAG.
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Affiliation(s)
- Mark J. Lee
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Hong Liu
- Division of Infectious Diseases, LA Biomedical Research Institute at Harbor—UCLA, Torrance, California, United States of America
| | - Bridget M. Barker
- Department of Immunology and Infectious Diseases, Montana State University, Bozeman, Montana, United States of America
| | - Brendan D. Snarr
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Fabrice N. Gravelat
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Qusai Al Abdallah
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Christina Gavino
- Infectious Disease Susceptibility Program, McGill University Health Centre, Montreal, Quebec, Canada
| | - Shane R. Baistrocchi
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Hanna Ostapska
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Tianli Xiao
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Benjamin Ralph
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Norma V. Solis
- Division of Infectious Diseases, LA Biomedical Research Institute at Harbor—UCLA, Torrance, California, United States of America
| | - Mélanie Lehoux
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Stefanie D. Baptista
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Arsa Thammahong
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover
| | - Robert P. Cerone
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | | | | | | | | | - Donald C. Vinh
- Infectious Disease Susceptibility Program, McGill University Health Centre, Montreal, Quebec, Canada
| | - Scott G. Filler
- Division of Infectious Diseases, LA Biomedical Research Institute at Harbor—UCLA, Torrance, California, United States of America
- David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, United States of America
| | - Donald C. Sheppard
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- * E-mail:
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38
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Affiliation(s)
- Eric R. G. Lewis
- Pathogen Genomics Division, Translational Genomics Institute, Flagstaff, Arizona, United States of America
- Northern Arizona Center for Valley Fever Research, Translational Genomics Institute, Flagstaff, Arizona, United States of America
- * E-mail: (ERGL); (JRB); (BMB)
| | - Jolene R. Bowers
- Pathogen Genomics Division, Translational Genomics Institute, Flagstaff, Arizona, United States of America
- * E-mail: (ERGL); (JRB); (BMB)
| | - Bridget M. Barker
- Pathogen Genomics Division, Translational Genomics Institute, Flagstaff, Arizona, United States of America
- Northern Arizona Center for Valley Fever Research, Translational Genomics Institute, Flagstaff, Arizona, United States of America
- Center for Microbial Genetic and Genomics, Department of Biology, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail: (ERGL); (JRB); (BMB)
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39
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Caffrey AK, Lehmann MM, Zickovich JM, Espinosa V, Shepardson KM, Watschke CP, Hilmer KM, Thammahong A, Barker BM, Rivera A, Cramer RA, Obar JJ. IL-1α signaling is critical for leukocyte recruitment after pulmonary Aspergillus fumigatus challenge. PLoS Pathog 2015; 11:e1004625. [PMID: 25629406 PMCID: PMC4309569 DOI: 10.1371/journal.ppat.1004625] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/11/2014] [Indexed: 11/21/2022] Open
Abstract
Aspergillus fumigatus is a mold that causes severe pulmonary infections. Our knowledge of how A. fumigatus growth is controlled in the respiratory tract is developing, but still limited. Alveolar macrophages, lung resident macrophages, and airway epithelial cells constitute the first lines of defense against inhaled A. fumigatus conidia. Subsequently, neutrophils and inflammatory CCR2+ monocytes are recruited to the respiratory tract to prevent fungal growth. However, the mechanism of neutrophil and macrophage recruitment to the respiratory tract after A. fumigatus exposure remains an area of ongoing investigation. Here we show that A. fumigatus pulmonary challenge induces expression of the inflammasome-dependent cytokines IL-1β and IL-18 within the first 12 hours, while IL-1α expression continually increases over at least the first 48 hours. Strikingly, Il1r1-deficient mice are highly susceptible to pulmonary A. fumigatus challenge exemplified by robust fungal proliferation in the lung parenchyma. Enhanced susceptibility of Il1r1-deficient mice correlated with defects in leukocyte recruitment and anti-fungal activity. Importantly, IL-1α rather than IL-1β was crucial for optimal leukocyte recruitment. IL-1α signaling enhanced the production of CXCL1. Moreover, CCR2+ monocytes are required for optimal early IL-1α and CXCL1 expression in the lungs, as selective depletion of these cells resulted in their diminished expression, which in turn regulated the early accumulation of neutrophils in the lung after A. fumigatus challenge. Enhancement of pulmonary neutrophil recruitment and anti-fungal activity by CXCL1 treatment could limit fungal growth in the absence of IL-1α signaling. In contrast to the role of IL-1α in neutrophil recruitment, the inflammasome and IL-1β were only essential for optimal activation of anti-fungal activity of macrophages. As such, Pycard-deficient mice are mildly susceptible to A. fumigatus infection. Taken together, our data reveal central, non-redundant roles for IL-1α and IL-1β in controlling A. fumigatus infection in the murine lung. Aspergillus spp. are ubiquitous in the environment, and even though individuals are regularly exposed to fungal spores clinical invasive disease is a rare manifestation. In contrast, individuals with weakened immune systems develop severe disease, such as invasive pulmonary aspergillosis (IPA). IPA is associated with extremely poor prognoses and unacceptably high mortality rates. Knowledge gained from understanding how immunocompetent mammals control Aspergillus challenge will help develop new immunomodulatory strategies aimed at improving patient outcomes. It is well known that neutrophils and monocytes are crucial immune cells that act to limit fungal growth. Our work demonstrates a central role for the cytokine IL-1α in orchestrating the optimal recruitment of neutrophils and monocytes, whereas IL-1β and the inflammasome are more important in activation of anti-fungal activity of the monocytes. Moreover, our studies indicate that CCR2+ monocytes are required for optimal production of IL-1α in the lungs of A. fumigatus challenged mice. Thus, our data highlight a crucial role of the IL-1 cytokine in mediating anti-fungal immunity which might be harnessed to treat clinical cases of IPA.
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Affiliation(s)
- Alayna K. Caffrey
- Montana State University, Department of Immunology & Infectious Diseases, Bozeman, Montana, United States of America
| | - Margaret M. Lehmann
- Montana State University, Department of Immunology & Infectious Diseases, Bozeman, Montana, United States of America
| | - Julianne M. Zickovich
- Montana State University, Department of Immunology & Infectious Diseases, Bozeman, Montana, United States of America
| | - Vanessa Espinosa
- Rutgers, New Jersey Medical School, Department of Pediatrics, Center for Immunity and Inflammation, Newark, New Jersey, United States of America
| | - Kelly M. Shepardson
- Geisel School of Medicine at Dartmouth, Department of Microbiology & Immunology, Hanover, New Hampshire, United States of America
| | - Christopher P. Watschke
- Montana State University, Department of Immunology & Infectious Diseases, Bozeman, Montana, United States of America
| | - Kimberly M. Hilmer
- Montana State University, Department of Immunology & Infectious Diseases, Bozeman, Montana, United States of America
| | - Arsa Thammahong
- Geisel School of Medicine at Dartmouth, Department of Microbiology & Immunology, Hanover, New Hampshire, United States of America
| | - Bridget M. Barker
- TGen North, Pathogen Genomics Research Division, Flagstaff, Arizona, United States of America
| | - Amariliz Rivera
- Rutgers, New Jersey Medical School, Department of Pediatrics, Center for Immunity and Inflammation, Newark, New Jersey, United States of America
| | - Robert A. Cramer
- Geisel School of Medicine at Dartmouth, Department of Microbiology & Immunology, Hanover, New Hampshire, United States of America
| | - Joshua J. Obar
- Montana State University, Department of Immunology & Infectious Diseases, Bozeman, Montana, United States of America
- * E-mail:
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Litvintseva AP, Marsden-Haug N, Hurst S, Hill H, Gade L, Driebe EM, Ralston C, Roe C, Barker BM, Goldoft M, Keim P, Wohrle R, Thompson GR, Engelthaler DM, Brandt ME, Chiller T. Valley fever: finding new places for an old disease: Coccidioides immitis found in Washington State soil associated with recent human infection. Clin Infect Dis 2014; 60:e1-3. [PMID: 25165087 DOI: 10.1093/cid/ciu681] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We used real-time polymerase chain reaction and culture to demonstrate persistent colonization of soils by Coccidioides immitis, an agent of valley fever, in Washington State linked to recent human infections and located outside the endemic range. Whole-genome sequencing confirmed genetic identity between isolates from soil and one of the case-patients.
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Affiliation(s)
| | | | - Steven Hurst
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Heather Hill
- Benton-Franklin Health District, Kennewick, Washington
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Cindy Ralston
- Benton-Franklin Health District, Kennewick, Washington
| | - Chandler Roe
- Translational Genomics Research Institute, Flagstaff, Arizona
| | | | - Marcia Goldoft
- Washington State Department of Health, Shoreline and Tumwater
| | - Paul Keim
- Translational Genomics Research Institute, Flagstaff, Arizona
| | - Ron Wohrle
- Washington State Department of Health, Shoreline and Tumwater
| | - George R Thompson
- Coccidioidomycosis Serology Laboratory, University of California, Davis
| | | | - Mary E Brandt
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
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Shepardson KM, Ngo LY, Aimanianda V, Latgé JP, Barker BM, Blosser SJ, Iwakura Y, Hohl TM, Cramer RA. Hypoxia enhances innate immune activation to Aspergillus fumigatus through cell wall modulation. Microbes Infect 2012; 15:259-69. [PMID: 23220005 DOI: 10.1016/j.micinf.2012.11.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/24/2012] [Accepted: 11/23/2012] [Indexed: 12/31/2022]
Abstract
Infection by the human fungal pathogen Aspergillus fumigatus induces hypoxic microenvironments within the lung that can alter the course of fungal pathogenesis. How hypoxic microenvironments shape the composition and immune activating potential of the fungal cell wall remains undefined. Herein we demonstrate that hypoxic conditions increase the hyphal cell wall thickness and alter its composition particularly by augmenting total and surface-exposed β-glucan content. In addition, hypoxia-induced cell wall alterations increase macrophage and neutrophil responsiveness and antifungal activity as judged by inflammatory cytokine production and ability to induce hyphal damage. We observe that these effects are largely dependent on the mammalian β-glucan receptor dectin-1. In a corticosteroid model of invasive pulmonary aspergillosis, A. fumigatus β-glucan exposure correlates with the presence of hypoxia in situ. Our data suggest that hypoxia-induced fungal cell wall changes influence the activation of innate effector cells at sites of hyphal tissue invasion, which has potential implications for therapeutic outcomes of invasive pulmonary aspergillosis.
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Affiliation(s)
- Kelly M Shepardson
- Department of Immunology and Infectious Diseases, Montana State University, Bozeman, MT 59717, USA
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Barker BM, Tabor JA, Shubitz LF, Perrill R, Orbach MJ. Detection and phylogenetic analysis of Coccidioides posadasii in Arizona soil samples. FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2011.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Barker BM, Kroll K, Vödisch M, Mazurie A, Kniemeyer O, Cramer RA. Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter. BMC Genomics 2012; 13:62. [PMID: 22309491 PMCID: PMC3293747 DOI: 10.1186/1471-2164-13-62] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 02/06/2012] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Aspergillus fumigatus is a mold responsible for the majority of cases of aspergillosis in humans. To survive in the human body, A. fumigatus must adapt to microenvironments that are often characterized by low nutrient and oxygen availability. Recent research suggests that the ability of A. fumigatus and other pathogenic fungi to adapt to hypoxia contributes to their virulence. However, molecular mechanisms of A. fumigatus hypoxia adaptation are poorly understood. Thus, to better understand how A. fumigatus adapts to hypoxic microenvironments found in vivo during human fungal pathogenesis, the dynamic changes of the fungal transcriptome and proteome in hypoxia were investigated over a period of 24 hours utilizing an oxygen-controlled fermenter system. RESULTS Significant increases in transcripts associated with iron and sterol metabolism, the cell wall, the GABA shunt, and transcriptional regulators were observed in response to hypoxia. A concomitant reduction in transcripts was observed with ribosome and terpenoid backbone biosynthesis, TCA cycle, amino acid metabolism and RNA degradation. Analysis of changes in transcription factor mRNA abundance shows that hypoxia induces significant positive and negative changes that may be important for regulating the hypoxia response in this pathogenic mold. Growth in hypoxia resulted in changes in the protein levels of several glycolytic enzymes, but these changes were not always reflected by the corresponding transcriptional profiling data. However, a good correlation overall (R(2) = 0.2, p < 0.05) existed between the transcriptomic and proteomics datasets for all time points. The lack of correlation between some transcript levels and their subsequent protein levels suggests another regulatory layer of the hypoxia response in A. fumigatus. CONCLUSIONS Taken together, our data suggest a robust cellular response that is likely regulated both at the transcriptional and post-transcriptional level in response to hypoxia by the human pathogenic mold A. fumigatus. As with other pathogenic fungi, the induction of glycolysis and transcriptional down-regulation of the TCA cycle and oxidative phosphorylation appear to major components of the hypoxia response in this pathogenic mold. In addition, a significant induction of the transcripts involved in ergosterol biosynthesis is consistent with previous observations in the pathogenic yeasts Candida albicans and Cryptococcus neoformans indicating conservation of this response to hypoxia in pathogenic fungi. Because ergosterol biosynthesis enzymes also require iron as a co-factor, the increase in iron uptake transcripts is consistent with an increased need for iron under hypoxia. However, unlike C. albicans and C. neoformans, the GABA shunt appears to play an important role in reducing NADH levels in response to hypoxia in A. fumigatus and it will be intriguing to determine whether this is critical for fungal virulence. Overall, regulatory mechanisms of the A. fumigatus hypoxia response appear to involve both transcriptional and post-transcriptional control of transcript and protein levels and thus provide candidate genes for future analysis of their role in hypoxia adaptation and fungal virulence.
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Affiliation(s)
- Bridget M Barker
- Department of Immunology and Infectious Disease, Montana State University, Bozeman, MT, USA
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Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, Hung CY, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, Bessette D, Brown A, FitzGerald M, Lui A, Macdonald JP, Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, Henn MR, Taylor JW, Rounsley SD. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Res 2010; 20:938-46. [PMID: 20516208 PMCID: PMC2892095 DOI: 10.1101/gr.103911.109] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 04/28/2010] [Indexed: 11/24/2022]
Abstract
We have sequenced the genomes of 18 isolates of the closely related human pathogenic fungi Coccidioides immitis and Coccidioides posadasii to more clearly elucidate population genomic structure, bringing the total number of sequenced genomes for each species to 10. Our data confirm earlier microsatellite-based findings that these species are genetically differentiated, but our population genomics approach reveals that hybridization and genetic introgression have recently occurred between the two species. The directionality of introgression is primarily from C. posadasii to C. immitis, and we find more than 800 genes exhibiting strong evidence of introgression in one or more sequenced isolates. We performed PCR-based sequencing of one region exhibiting introgression in 40 C. immitis isolates to confirm and better define the extent of gene flow between the species. We find more coding sequence than expected by chance in the introgressed regions, suggesting that natural selection may play a role in the observed genetic exchange. We find notable heterogeneity in repetitive sequence composition among the sequenced genomes and present the first detailed genome-wide profile of a repeat-induced point mutation (RIP) process distinctly different from what has been observed in Neurospora. We identify promiscuous HLA-I and HLA-II epitopes in both proteomes and discuss the possible implications of introgression and population genomic data for public health and vaccine candidate prioritization. This study highlights the importance of population genomic data for detecting subtle but potentially important phenomena such as introgression.
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Sheff KW, York ER, Driebe EM, Barker BM, Rounsley SD, Waddell VG, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS, Keim PS, Engelthaler DM. Development of a rapid, cost-effective TaqMan Real-Time PCR Assay for identification and differentiation of Coccidioides immitis and Coccidioides posadasii. Med Mycol 2010; 48:466-9. [PMID: 20370360 DOI: 10.3109/13693780903218990] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Coccidioidomycosis is an infection caused by Coccidioides immitis or C. posadasii. We developed a TaqMan real-time PCR assay that rapidly and accurately differentiates the species. This assay can be used as a tool to improve disease surveillance, increase understanding of the natural history of the infection, and assist in clinical differentiation studies.
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Affiliation(s)
- Kelly W Sheff
- Translational Genomics Research Institute, Pathogen Genomics Division (TGen North), 3051 West Shamrell Boulevard, Flagstaff, Arizona, USA
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Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung CY, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res 2009; 19:1722-31. [PMID: 19717792 DOI: 10.1101/gr.087551.108] [Citation(s) in RCA: 214] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
While most Ascomycetes tend to associate principally with plants, the dimorphic fungi Coccidioides immitis and Coccidioides posadasii are primary pathogens of immunocompetent mammals, including humans. Infection results from environmental exposure to Coccidiodies, which is believed to grow as a soil saprophyte in arid deserts. To investigate hypotheses about the life history and evolution of Coccidioides, the genomes of several Onygenales, including C. immitis and C. posadasii; a close, nonpathogenic relative, Uncinocarpus reesii; and a more diverged pathogenic fungus, Histoplasma capsulatum, were sequenced and compared with those of 13 more distantly related Ascomycetes. This analysis identified increases and decreases in gene family size associated with a host/substrate shift from plants to animals in the Onygenales. In addition, comparison among Onygenales genomes revealed evolutionary changes in Coccidioides that may underlie its infectious phenotype, the identification of which may facilitate improved treatment and prevention of coccidioidomycosis. Overall, the results suggest that Coccidioides species are not soil saprophytes, but that they have evolved to remain associated with their dead animal hosts in soil, and that Coccidioides metabolism genes, membrane-related proteins, and putatively antigenic compounds have evolved in response to interaction with an animal host.
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Affiliation(s)
- Thomas J Sharpton
- Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA.
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Mandel MA, Barker BM, Kroken S, Rounsley SD, Orbach MJ. Genomic and population analyses of the mating type loci in Coccidioides species reveal evidence for sexual reproduction and gene acquisition. Eukaryot Cell 2007; 6:1189-99. [PMID: 17513566 PMCID: PMC1951113 DOI: 10.1128/ec.00117-07] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Coccidioides species, the fungi responsible for the valley fever disease, are known to reproduce asexually through the production of arthroconidia that are the infectious propagules. The possible role of sexual reproduction in the survival and dispersal of these pathogens is unexplored. To determine the potential for mating of Coccidioides, we analyzed genome sequences and identified mating type loci characteristic of heterothallic ascomycetes. Coccidioides strains contain either a MAT1-1 or a MAT1-2 idiomorph, which is 8.1 or 9 kb in length, respectively, the longest reported for any ascomycete species. These idiomorphs contain four or five genes, respectively, more than are present in the MAT loci of most ascomycetes. Along with their cDNA structures, we determined that all genes in the MAT loci are transcribed. Two genes frequently found in common sequences flanking MAT idiomorphs, APN2 and COX13, are within the MAT loci in Coccidioides, but the MAT1-1 and MAT1-2 copies have diverged dramatically from each other. Data indicate that the acquisition of these genes in the MAT loci occurred prior to the separation of Coccidioides from Uncinocarpus reesii. An analysis of 436 Coccidioides isolates from patients and the environment indicates that in both Coccidioides immitis and C. posadasii, there is a 1:1 distribution of MAT loci, as would be expected for sexually reproducing species. In addition, an analysis of isolates obtained from 11 soil samples demonstrated that at three sampling sites, strains of both mating types were present, indicating that compatible strains were in close proximity in the environment.
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Affiliation(s)
- M Alejandra Mandel
- Division of Plant Pathology and Microbiology, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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Abstract
Studies of field- and patient-derived isolates conducted over the past 75 years have provided a general picture of the population structure of Coccidioides, the cause of coccidioidomycosis. Premolecular studies provided a general outline of the geographical range, epidemiology and distribution of the fungus. Recent studies based on molecular markers have demonstrated that the genus is comprised of two genetically diverse, and genetically isolated, species: Coccidioides immitis and C. posadasii. Both species are composed of biogeographically distinct populations. Structure for two of these populations (C. immitis from central California, and C. posadasii from southern Arizona) indicates that frequent genetic recombination occurs within the entire geographic range of each population, even though sex has never been observed in the genus. Outbreaks of coccidioidomycosis are not the result of the spread of a single clonal isolate, but are caused by a diversity of genotypes. Although it is now possible to match patient isolates to populations, the lack of apparent structure within each population and the current paucity of environmental isolates limit map-based epidemiological approaches to understanding outbreaks. Therefore, a comprehensive database comprised of soil-derived isolates from across the biogeographic range of Coccidioides will improve the utility of this approach. Appropriate collection of environmental isolates will assist the investigation of remaining questions regarding the population biology of Coccidioides. The comparative genomics of representative genotypes from both species and all populations of Coccidioides will provide a thorough set of genetic markers in order to resolve the population genetics of this pathogenic fungus.
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Affiliation(s)
- B M Barker
- Department of Plant Sciences, Division of Plant Pathology and Microbiology, University of Arizona, Tucson, AZ 85721, USA.
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Vandemark GJ, Barker BM, Gritsenko MA. Quantifying Aphanomyces euteiches in Alfalfa with a Fluorescent Polymerase Chain Reaction Assay. Phytopathology 2002; 92:265-72. [PMID: 18943997 DOI: 10.1094/phyto.2002.92.3.265] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
ABSTRACT A polymerase chain reaction (PCR) assay using a set of specific primers and a dual-labeled probe (TaqMan) was developed to quantify the amount of Aphanomyces euteiches DNA in alfalfa plants exhibiting varying levels of disease severity. The study included isolates of race 1 and race 2 of A. euteiches. The assay also discriminated between alfalfa populations for resistance based on analysis of DNA extracted from bulked plant samples. Analysis of individual plants and bulked plant samples of standard check populations with both pathogen isolates resulted in Spearman rank correlations between pathogen DNA content and disease severity index ratings that were greater than 0.75 and highly significant (P < 0.0005). In experiments with a race 1 isolate, the amount of pathogen DNA present in the resistant check WAPH-1 was significantly less than in the susceptible check Saranac. In experiments with a race 2 isolate, the amount of pathogen DNA in the resistant check WAPH-5 was significantly less than in either of the susceptible checks, Saranac and WAPH-1. Discrimination between commercial cultivars based on quantitative PCR analysis of bulked plant samples was similar to classification based on visual assessment of disease severity.
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Abstract
The present investigation was designed to determine by factor analysis the nature of the items that comprise the A-State and A-Trait scales of the State-Trait Anxiety Inventory. Three factors were identified. Factor I was defined exclusively by items from the A-State scale. The underlying dimension tapped by the scale was interpreted as state anxiety (how one feels at a particular moment in time); support thus was provided for Spielberger's A-State concept. Items from the A-Trait scale, however, identified two separate factors, neither of which was clearly consonant with Spielberger's concept of A-Trait. Factor II appeared to tap state anxiety according to how the individual generally feels or a typical level of state anxiety as remembered over an indefinite period of time. Factor III was interpreted as a measure of neuroticism.
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