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Voorhies M, Joehnk B, Uehling J, Walcott K, Dubin C, Mead HL, Homer CM, Galgiani JN, Barker BM, Brem RB, Sil A. Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606565. [PMID: 39149389 PMCID: PMC11326141 DOI: 10.1101/2024.08.05.606565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Next generation sequencing has unlocked a wealth of genotype information for microbial populations, but phenotyping remains a bottleneck for exploiting this information, particularly for pathogens that are difficult to manipulate. Here, we establish a method for high-throughput phenotyping of mixed cultures, in which the pattern of naturally occurring single-nucleotide polymorphisms in each isolate is used as intrinsic barcodes which can be read out by sequencing. We demonstrate that our method can correctly deconvolute strain proportions in simulated mixed-strain pools. As an experimental test of our method, we perform whole genome sequencing of 66 natural isolates of the thermally dimorphic pathogenic fungus Coccidioides posadasii and infer the strain compositions for large mixed pools of these strains after competition at 37°C and room temperature. We validate the results of these selection experiments by recapitulating the temperature-specific enrichment results in smaller pools. Additionally, we demonstrate that strain fitness estimated by our method can be used as a quantitative trait for genome-wide association studies. We anticipate that our method will be broadly applicable to natural populations of microbes and allow high-throughput phenotyping to match the rate of genomic data acquisition.
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Affiliation(s)
- Mark Voorhies
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Bastian Joehnk
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Jessie Uehling
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Claire Dubin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Heather L. Mead
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Christina M. Homer
- Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - John N. Galgiani
- Valley Fever Center for Excellence, Department of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Bridget M. Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Rachel B. Brem
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Anita Sil
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Biohub – San Francisco, San Francisco, California, United States of America
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2
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Tejeda-Garibay S, Zhao L, Hum NR, Pimentel M, Diep AL, Amiri B, Sindi SS, Weilhammer DR, Loots GG, Hoyer KK. Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro. Microbiol Spectr 2024; 12:e0297823. [PMID: 38832766 PMCID: PMC11218535 DOI: 10.1128/spectrum.02978-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/19/2024] [Indexed: 06/05/2024] Open
Abstract
Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia, leading to inappropriate antibiotic treatment. The soil Bacillus subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides, while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2×GYE (GYE) and Columbia colistin and nalidixic acid with 5% sheep's blood agar inhibited the growth of Coccidioides, but microbiota grown on chocolate agar did not. Partial depletion of the microbiota through antibiotic disk diffusion revealed diminished inhibition and comparable growth of Coccidioides to controls. To characterize the bacteria grown and identify potential candidates contributing to the inhibition of Coccidioides, 16S rRNA sequencing was performed on tracheal and intestinal agar cultures and murine lung extracts. We found that the host bacteria likely responsible for this inhibition primarily included Lactobacillus and Staphylococcus. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo. IMPORTANCE Coccidioidomycosis is caused by a fungal pathogen that invades the host lungs, causing respiratory distress. In 2019, 20,003 cases of Valley fever were reported to the CDC. However, this number likely vastly underrepresents the true number of Valley fever cases, as many go undetected due to poor testing strategies and a lack of diagnostic models. Valley fever is also often misdiagnosed as bacterial pneumonia, resulting in 60%-80% of patients being treated with antibiotics prior to an accurate diagnosis. Misdiagnosis contributes to a growing problem of antibiotic resistance and antibiotic-induced microbiome dysbiosis; the implications for disease outcomes are currently unknown. About 5%-10% of symptomatic Valley fever patients develop chronic pulmonary disease. Valley fever causes a significant financial burden and a reduced quality of life. Little is known regarding what factors contribute to the development of chronic infections and treatments for the disease are limited.
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Affiliation(s)
- Susana Tejeda-Garibay
- Quantitative and Systems Biology, Graduate Program, University of California, Merced, Merced, California, USA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Lihong Zhao
- Department of Applied Mathematics, University of California, Merced, Merced, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
| | - Nicholas R. Hum
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Maria Pimentel
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, Merced, California, USA
| | - Anh L. Diep
- Quantitative and Systems Biology, Graduate Program, University of California, Merced, Merced, California, USA
| | - Beheshta Amiri
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Suzanne S. Sindi
- Department of Applied Mathematics, University of California, Merced, Merced, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
| | - Dina R. Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Gabriela G. Loots
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
- />Department of Orthopaedic Surgery, Lawrence J. Ellison Musculoskeletal Research Center, University of California Davis Health, Sacramento, California, USA
| | - Katrina K. Hoyer
- Quantitative and Systems Biology, Graduate Program, University of California, Merced, Merced, California, USA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, Merced, California, USA
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3
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Saucier CJ, Ma Z, Montoya JA, Plant A, Suresh S, Robbins CL, Fraser R. Overcoming Health Information Inequities: Valley fever Information Repertoires Among Vulnerable Communities in California. HEALTH COMMUNICATION 2024:1-18. [PMID: 38177098 DOI: 10.1080/10410236.2023.2288380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Although Valley fever represents a growing public health challenge for Central and Southern Californian residents, awareness remains severely limited. The California Department of Public Health (CDPH) ran a cross-platform campaign to mitigate this awareness gap and impact prevention behavior. This study evaluates exposure to the CDPH campaign, followed by an examination of the information consumption patterns associated with key health outcomes. Results suggest that the CDPH campaign successfully improved knowledge accuracy, reduced misperceptions, and increased the likelihood of prevention behavior. Using an information repertoire lens revealed a more nuanced account. Most information repertoires positively influenced accurate knowledge retention and prevention behavior compared to those who were not exposed. The most diverse information repertoire, including interpersonal and media channels, was associated with increased knowledge accuracy, affective risk concerns, personal susceptibility, and prevention behavior. However, exposure to this repertoire was also associated with greater misperceptions. In addition, medical professional and radio-based repertoires positively influenced personal susceptibility perceptions. Overall, this research illustrates the importance of examining not only the general outcomes of health campaigns but also the patterns of information acquisition - particularly when working with underserved communities whose health information consumption preferences may not be comprehensively reflected in the literature.
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Affiliation(s)
| | - Zexin Ma
- Department of Communication, University of Connecticut
| | | | | | - Sapna Suresh
- Department of Medical Social Sciences, Northwestern University
| | - Chris L Robbins
- Department of Medical Social Sciences, Northwestern University
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4
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Cai J, Sin D, Tomassetti S. Unexpected coccidioidomycosis presenting as lung nodules with presumptive diagnosis of malignancy. Clin Case Rep 2023; 11:e8316. [PMID: 38084359 PMCID: PMC10710529 DOI: 10.1002/ccr3.8316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 10/16/2024] Open
Abstract
Coccidioidomycosis can present as fluorodeoxyglucose (FDG) avid lung nodules which may be mistaken as relapse in patients with a history of malignancy. Detailed clinical history, relevant laboratory testing, and/or tissue biopsy with histologic evaluation are necessary for correct diagnosis.
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Affiliation(s)
- Jennifer Cai
- Department of PathologyHarbor‐UCLA Medical CenterTorranceCaliforniaUSA
- University of California at IrvineIrvineCaliforniaUSA
| | - David Sin
- Department of RadiologyHarbor‐UCLA Medical CenterTorranceCaliforniaUSA
| | - Sarah Tomassetti
- Division of Hematology and OncologyHarbor‐UCLA Medical CenterTorranceCaliforniaUSA
- David Geffen School of Medicine at UCLALos AngelesCaliforniaUSA
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5
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Tejeda-Garibay S, Zhao L, Hum NR, Pimentel M, Diep AL, Amiri B, Sindi SS, Weilhammer DR, Loots GG, Hoyer KK. Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563655. [PMID: 37961490 PMCID: PMC10634762 DOI: 10.1101/2023.10.23.563655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia leading to inappropriate antibiotic treatment. Soil bacteria B. subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2xGYE (GYE) and CNA w/ 5% sheep's blood agar (5%SB-CNA) inhibited the growth of Coccidioides, but that grown on chocolate agar does not. Partial depletion of the microbiota through antibiotic disk diffusion revealed that microbiota depletion leads to diminished inhibition and comparable growth of Coccidioides growth to controls. To characterize the bacteria grown and narrow down potential candidates contributing to the inhibition of Coccidioides, 16s rRNA sequencing of tracheal and intestinal agar cultures and murine lung extracts was performed. The identity of host bacteria that may be responsible for this inhibition was revealed. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo.
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Affiliation(s)
- Susana Tejeda-Garibay
- Quantitative and Systems Biology, Graduate Program, University of California Merced, CA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Lihong Zhao
- Department of Applied Mathematics, University of California, Merced, CA
- Health Sciences Research Institute, University of California Merced, Merced, CA
| | - Nicholas R Hum
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Maria Pimentel
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, CA
| | - Anh L Diep
- Quantitative and Systems Biology, Graduate Program, University of California Merced, CA
| | - Beheshta Amiri
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Suzanne S Sindi
- Department of Applied Mathematics, University of California, Merced, CA
- Health Sciences Research Institute, University of California Merced, Merced, CA
| | - Dina R Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Gabriela G Loots
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
- University of California Davis Health, Department of Orthopaedic Surgery, Lawrence J. Ellison Musculo-skeletal Research Center, 2700 Stockton Blvd, Sacramento, CA 95817, CA
| | - Katrina K Hoyer
- Quantitative and Systems Biology, Graduate Program, University of California Merced, CA
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, CA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
- Health Sciences Research Institute, University of California Merced, Merced, CA
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6
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Miranda N, Hoyer KK. Coccidioidomycosis Granulomas Informed by Other Diseases: Advancements, Gaps, and Challenges. J Fungi (Basel) 2023; 9:650. [PMID: 37367586 DOI: 10.3390/jof9060650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
Valley fever is a respiratory disease caused by a soil fungus, Coccidioides, that is inhaled upon soil disruption. One mechanism by which the host immune system attempts to control and eliminate Coccidioides is through granuloma formation. However, very little is known about granulomas during Coccidioides infection. Granulomas were first identified in tuberculosis (TB) lungs as early as 1679, and yet many gaps in our understanding of granuloma formation, maintenance, and regulation remain. Granulomas are best defined in TB, providing clues that may be leveraged to understand Coccidioides infections. Granulomas also form during several other infectious and spontaneous diseases including sarcoidosis, chronic granulomatous disease (CGD), and others. This review explores our current understanding of granulomas, as well as potential mechanisms, and applies this knowledge to unraveling coccidioidomycosis granulomas.
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Affiliation(s)
- Nadia Miranda
- Quantitative Systems Biology Graduate Program, University of California Merced, Merced, CA 95343, USA
| | - Katrina K Hoyer
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA 95343, USA
- Health Sciences Research Institute, University of California Merced, Merced, CA 95343, USA
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7
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Peterson MW, Jain R, Hildebrandt K, Carson WK, Fayed MA. Differentiating Lung Nodules Due to Coccidioides from Those Due to Lung Cancer Based on Radiographic Appearance. J Fungi (Basel) 2023; 9:641. [PMID: 37367577 DOI: 10.3390/jof9060641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Coccidioidomycosis (cocci) is an endemic fungal disease that can cause asymptomatic or post-symptomatic lung nodules which are visible on chest CT scanning. Lung nodules are common and can represent early lung cancer. Differentiating lung nodules due to cocci from those due to lung cancer can be difficult and lead to invasive and expensive evaluations. MATERIALS AND METHODS We identified 302 patients with biopsy-proven cocci or bronchogenic carcinoma seen in our multidisciplinary nodule clinic. Two experienced radiologists who were blinded to the diagnosis read the chest CT scans and identified radiographic characteristics to determine their utility in differentiating lung cancer nodules from those due to cocci. RESULTS Using univariate analysis, we identified several radiographic findings that differed between lung cancer and cocci infection. We then entered these variables along with age and gender into a multivariate model and found that age, nodule diameter, nodule cavitation, presence of satellite nodules and radiographic presence of chronic lung disease differed significantly between the two diagnoses. Three findings, cavitary nodules, satellite nodules and chronic lung disease, have sufficient discrimination to potentially be useful in clinical decision-making. CONCLUSIONS Careful evaluation of the three obtained radiographic findings can significantly improve our ability to differentiate benign coccidioidomycosis infection from lung cancer in an endemic region for the fungal disease. Using these data may significantly reduce the cost and risk associated with distinguishing the cause of lung nodules in these patients by preventing unnecessary invasive studies.
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Affiliation(s)
- Michael W Peterson
- Fresno Department of Medicine, University of California (San Francisco), San Francisco, CA 93701, USA
- UCSF Fresno/Community Medical Centers' Multidisciplinary Lung Nodule Clinic, Fresno, CA 93701, USA
| | - Ratnali Jain
- Fresno Department of Medicine, University of California (San Francisco), San Francisco, CA 93701, USA
| | - Kurt Hildebrandt
- Community Medical Imaging Radiology Group, Fresno, CA 93721, USA
| | | | - Mohamed A Fayed
- Fresno Department of Medicine, University of California (San Francisco), San Francisco, CA 93701, USA
- UCSF Fresno/Community Medical Centers' Multidisciplinary Lung Nodule Clinic, Fresno, CA 93701, USA
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8
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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] [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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9
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Mandel MA, Beyhan S, Voorhies M, Shubitz LF, Galgiani JN, Orbach MJ, Sil A. The WOPR family protein Ryp1 is a key regulator of gene expression, development, and virulence in the thermally dimorphic fungal pathogen Coccidioides posadasii. PLoS Pathog 2022; 18:e1009832. [PMID: 35385558 PMCID: PMC9015156 DOI: 10.1371/journal.ppat.1009832] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 04/18/2022] [Accepted: 03/01/2022] [Indexed: 12/03/2022] Open
Abstract
Coccidioides spp. are mammalian fungal pathogens endemic to the Southwestern US and other desert regions of Mexico, Central and South America, with the bulk of US infections occurring in California and Arizona. In the soil, Coccidioides grows in a hyphal form that differentiates into 3-5 micron asexual spores (arthroconidia). When arthroconidia are inhaled by mammals they undergo a unique developmental transition from polar hyphal growth to isotropic expansion with multiple rounds of nuclear division, prior to segmentation, forming large spherules filled with endospores. Very little is understood about the molecular basis of spherule formation. Here we characterize the role of the conserved transcription factor Ryp1 in Coccidioides development. We show that Coccidioides Δryp1 mutants have altered colony morphology under hypha-promoting conditions and are unable to form mature spherules under spherule-promoting conditions. We analyze the transcriptional profile of wild-type and Δryp1 mutant cells under hypha- and spherule-promoting conditions, thereby defining a set of hypha- or spherule-enriched transcripts ("morphology-regulated" genes) that are dependent on Ryp1 for their expression. Forty percent of morphology-regulated expression is Ryp1-dependent, indicating that Ryp1 plays a dual role in both hyphal and spherule development. Ryp1-dependent transcripts include key virulence factors such as SOWgp, which encodes the spherule outer wall glycoprotein. Concordant with its role in spherule development, we find that the Δryp1 mutant is completely avirulent in the mouse model of coccidioidomycosis, indicating that Ryp1-dependent pathways are essential for the ability of Coccidioides to cause disease. Vaccination of C57BL/6 mice with live Δryp1 spores does not provide any protection from lethal C. posadasii intranasal infection, consistent with our findings that the Δryp1 mutant fails to make mature spherules and likely does not express key antigens required for effective vaccination. Taken together, this work identifies the first transcription factor that drives mature spherulation and virulence in Coccidioides.
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Affiliation(s)
- M. Alejandra Mandel
- School of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, United States of America
| | - Sinem Beyhan
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Mark Voorhies
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Lisa F. Shubitz
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, United States of America
| | - John N. Galgiani
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, United States of America
| | - Marc J. Orbach
- School of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (MJO); (AS)
| | - Anita Sil
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (MJO); (AS)
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10
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Diep AL, Hoyer KK. Host Response to Coccidioides Infection: Fungal Immunity. Front Cell Infect Microbiol 2020; 10:581101. [PMID: 33262956 PMCID: PMC7686801 DOI: 10.3389/fcimb.2020.581101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/15/2020] [Indexed: 12/22/2022] Open
Abstract
Coccidioidomycosis is a fungal, respiratory disease caused by Coccidioides immitis and Coccidioides posadasii. This emerging infectious disease ranges from asymptomatic to pulmonary disease and disseminated infection. Most infections are cleared with little to no medical intervention whereas chronic disease often requires life-long medication with severe impairment in quality of life. It is unclear what differentiates hosts immunity resulting in disease resolution versus chronic infection. Current understanding in mycology-immunology suggests that chronic infection could be due to maladaptive immune responses. Immunosuppressed patients develop more severe disease and mouse studies show adaptive Th1 and Th17 responses are required for clearance. This is supported by heightened immunosuppressive regulatory responses and lowered anti-fungal T helper responses in chronic Coccidioides patients. Diagnosis and prognosis is difficult as symptoms are broad and overlapping with community acquired pneumonia, often resulting in misdiagnosis and delayed treatment. Furthermore, we lack clear biomarkers of disease severity which could aid prognosis for more effective healthcare. As the endemic region grows and population increases in endemic areas, the need to understand Coccidioides infection is becoming urgent. There is a growing effort to identify fungal virulence factors and host immune components that influence fungal immunity and relate these to patient disease outcome and treatment. This review compiles the known immune responses to Coccidioides spp. infection and various related fungal pathogens to provide speculation on Coccidioides immunity.
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Affiliation(s)
- Anh L. Diep
- Quantitative and Systems Biology, Graduate Program, University of California Merced, Merced, CA, United States
| | - Katrina K. Hoyer
- Quantitative and Systems Biology, Graduate Program, University of California Merced, Merced, CA, United States
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, United States
- Health Sciences Research Institute, University of California Merced, Merced, CA, United States
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11
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Pearson D, Ebisu K, Wu X, Basu R. A Review of Coccidioidomycosis in California: Exploring the Intersection of Land Use, Population Movement, and Climate Change. Epidemiol Rev 2020; 41:145-157. [PMID: 31497853 DOI: 10.1093/epirev/mxz004] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 01/12/2023] Open
Abstract
California has seen a surge in coccidioidomycosis (valley fever), a disease spread by the Coccidioides immitis fungus found in soil throughout the state, particularly in the San Joaquin Valley. We reviewed epidemiologic studies in which outbreak and sporadic cases of coccidioidomycosis were examined, and we considered the possible relationship of these cases to environmental conditions, particularly the state's increasing aridity, drought, and wildfire conditions. Most of the studies we reviewed pertained to cases occupationally acquired in construction, military, archeological, and correctional institutional settings where workers were exposed to dust in C. immitis-endemic areas. A few reviewed outbreaks in the general population related to dust exposure from natural disasters, including an earthquake-associated landslide and a dust storm that carried particles long distances from endemic areas. Although many of California's coccidioidomycosis outbreaks have been occupationally related, changing demographics and new, immunologically naïve populations in dry, endemic areas could expose the general population to C. immitis spores. Given the high rate of infection among workers who, for the most part, are healthy, the general population, including some elderly and immunocompromised individuals, could face additional risk. With climate-related events like drought and wildfires also increasing in endemic areas, research is needed to address the possible associations between these phenomena and coccidioidomycosis outbreaks.
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Affiliation(s)
- Dharshani Pearson
- Air and Climate Epidemiology Section, Office of Environmental Health Hazard Assessment, California Environmental Protection Agency, Oakland, California
| | - Keita Ebisu
- Air and Climate Epidemiology Section, Office of Environmental Health Hazard Assessment, California Environmental Protection Agency, Oakland, California
| | - Xiangmei Wu
- Air and Climate Epidemiology Section, Office of Environmental Health Hazard Assessment, California Environmental Protection Agency, Oakland, California
| | - Rupa Basu
- Air and Climate Epidemiology Section, Office of Environmental Health Hazard Assessment, California Environmental Protection Agency, Oakland, California
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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: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [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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Reyes-Montes MDR, Frías-De-León MG, Victoriano-Pastelín I, Acosta-Altamirano G, Duarte-Escalante E. Design and evaluation of an AFLP molecular marker for the detection of Coccidioides spp. in biological samples. Braz J Infect Dis 2019; 23:322-330. [PMID: 31539511 PMCID: PMC9428003 DOI: 10.1016/j.bjid.2019.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 12/01/2022] Open
Abstract
At present, there is no standardized marker that is routinely used in clinical laboratories to diagnose coccidioidomycosis. Thus, the goals of this study were to obtain a sequence characterized amplified region (SCAR) marker for the identification of Coccidioides spp., evaluate its specificity and sensitivity in fungal DNA-spiked blood and sputum samples, and compare it with previously described molecular markers. Specific amplified fragment length polymorphism (AFLP) amplicons for Coccidioides immitis and Coccidioides posadasii were cloned into the vector pGEM® -T Easy vector and sequenced to develop a SCAR marker. Oligonucleotides were designed to identify Coccidioides spp. by polymerase chain reaction (PCR), and the specificity and sensitivity of these oligonucleotides were tested with the DNA from related pathogens. The specificity and sensitivity of the SCAR marker was evaluated with blood and sputum samples spiked with Coccidioides DNA and compared with other previously described markers (621, GAC2, and Ag2/PRA). In addition, the conditions for its use were established using biological samples. A specific marker named SCAR300 was obtained to identify Coccidioides spp. that exhibited good sensitivity and specificity. The results showed that all of the markers tested in this study can identify Coccidioides spp. However, the SCAR300 and 621 markers were the most sensitive, whereas the SCAR300 marker was the most specific. Thus, the SCAR300 marker is a useful tool to identify Coccidioides spp.
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Affiliation(s)
- María Del Rocío Reyes-Montes
- Facultad de Medicina (UNAM), Departamento de Microbiología y Parasitología, Laboratorio de Micología Molecular, Ciudad de México, Mexico
| | | | - Isai Victoriano-Pastelín
- Facultad de Medicina (UNAM), Departamento de Microbiología y Parasitología, Laboratorio de Micología Molecular, Ciudad de México, Mexico
| | - Gustavo Acosta-Altamirano
- Hospital Regional de Alta Especialidad de Ixtapaluca, Dirección de Investigación, Ixtapaluca, Mexico
| | - Esperanza Duarte-Escalante
- Facultad de Medicina (UNAM), Departamento de Microbiología y Parasitología, Laboratorio de Micología Molecular, Ciudad de México, Mexico.
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Lang R, Stokes W, Lemaire J, Johnson A, Conly J. A case report of Coccidioides posadasii meningoencephalitis in an immunocompetent host. BMC Infect Dis 2019; 19:722. [PMID: 31420023 PMCID: PMC6697908 DOI: 10.1186/s12879-019-4329-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/29/2019] [Indexed: 11/26/2022] Open
Abstract
Background Coccidioides spp. are dimorphic fungi endemic to Central America, regions of South America and southwestern USA. Two species cause most human disease: Coccidioides immitis (primarily California isolates) and Coccidioides posadasii. Coccidioidomycosis is typically acquired through inhalation of soil or dust containing spores. Coccidioidal meningitis (CM), most common in the immunocompromised host, can also affect immunocompetent hosts. Case presentation We report a case of C. posadasii meningoencephalitis in a previously healthy 42-year-old Caucasian male who returned to Canada after spending time working in New Mexico. He presented with a 3-week history of headache, malaise and low-grade fevers. He developed progressive confusion and decreasing level of consciousness following hospitalization. Evidence of hydrocephalus and leptomeningeal enhancement was demonstrated on magnetic resonance imaging (MRI) of his brain. Serologic and PCR testing of the patient's CSF confirmed Coccidioides posadasii. Despite appropriate antifungal therapy he continues to have significant short-term memory deficits and has not returned to his full baseline functional status. Conclusions Travel to endemic regions can result in disease secondary to Coccidioides spp. and requires physicians in non-endemic areas to have a high index of suspicion. Effective therapeutic options have reduced the mortality rate of CM, however, it is still associated with significant morbidity and requires life-long therapy.
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Affiliation(s)
- Raynell Lang
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada.
| | - William Stokes
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
| | - Jane Lemaire
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
| | - Andrew Johnson
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
| | - John Conly
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada.,Departments of Medicine, Microbiology, immunology & Infectious Diseases, Pathology & Laboratory Medicine. Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
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15
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Watson IT, Murzaku E. Cutaneous coccidiomycosis presenting with a facial plaque. Proc AMIA Symp 2019; 32:88-89. [PMID: 30956593 DOI: 10.1080/08998280.2018.1523643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/08/2018] [Accepted: 09/11/2018] [Indexed: 10/27/2022] Open
Abstract
We present the case of a 55-year-old black man with coccidiomycosis presenting as a cutaneous plaque on the upper lip. Coccidiomycosis, or "valley fever," is caused by the virulent, dimorphic, soil-dwelling fungus Coccidiodes immitis. Seen in up to 50% of symptomatic patients, skin involvement by coccidiomycosis can present as papules, pustules, plaques, nodules, abscesses, or ulcerations. Diagnosis of coccidiomycosis relies on serology and identification in clinical specimens, and first-line treatment includes fluconazole, ketoconazole, or itraconazole. Recognizing the cutaneous manifestations of this mycotic infection is essential for diagnosis in otherwise asymptomatic patients.
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Affiliation(s)
| | - Era Murzaku
- Department of Dermatology, University of Texas Southwestern Medical CenterDallasTexas
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16
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Davini D, Naeem F, Phong A, Al-Kuhlani M, Valentine KM, McCarty J, Ojcius DM, Gravano DM, Hoyer KK. Elevated regulatory T cells at diagnosis of Coccidioides infection associates with chronicity in pediatric patients. J Allergy Clin Immunol 2018; 142:1971-1974.e7. [PMID: 30539725 DOI: 10.1016/j.jaci.2018.10.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Dan Davini
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, Calif
| | | | - Aron Phong
- Stem Cell Instrumentation Foundry, University of California Merced, Merced, Calif
| | - Mufadhal Al-Kuhlani
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, Calif
| | - Kristen M Valentine
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, Calif; Health Sciences Research Institute, University of California Merced, Merced, Calif
| | - James McCarty
- Stanford University School of Medicine, Stanford, Calif
| | - David M Ojcius
- Health Sciences Research Institute, University of California Merced, Merced, Calif; Arthur Dugoni Dental School, University of the Pacific, San Francisco, Calif
| | - David M Gravano
- Stem Cell Instrumentation Foundry, University of California Merced, Merced, Calif; Health Sciences Research Institute, University of California Merced, Merced, Calif
| | - Katrina K Hoyer
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, Calif; Health Sciences Research Institute, University of California Merced, Merced, Calif.
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Alvarado P, Teixeira MDM, Andrews L, Fernandez A, Santander G, Doyle A, Perez M, Yegres F, Barker BM. Detection of Coccidioides posadasii from xerophytic environments in Venezuela reveals risk of naturally acquired coccidioidomycosis infections. Emerg Microbes Infect 2018; 7:46. [PMID: 29593263 PMCID: PMC5874253 DOI: 10.1038/s41426-018-0049-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/10/2018] [Accepted: 01/29/2018] [Indexed: 01/09/2023]
Abstract
A wide range of mammals are susceptible to infection by the fungal species Coccidioides immitis and C. posadasii. In humans, 60% of infections are asymptomatic; however, certain patients may develop a severe and deep systemic mycosis called coccidioidomycosis. Genetic analysis suggests that the majority of clinical isolates recovered from South America are C. posadasii; however, little is known about the prevalence, species distribution, and ecological factors that favor the occurrence of this pathogen in those areas. By using a combined quantitative polymerase chain reaction (qPCR)-based approach and mycobiome amplicon sequencing, we provide evidence that at least two genotypes of C. posadasii are found in the xerophytic environment in Venezuela. We detected a 3806-fold range in the amount of Coccidioides DNA when comparing among the sampled locations, which indicates that human exposure risk is variable, and is one critical factor for disease manifestation. We identified fungal communities that are correlated with a higher prevalence of C. posadasii, suggesting that a combination of specific microbes and a xeric microenvironment may favor the growth of Coccidioides in certain locations. Moreover, we discuss the use of a combinatorial approach, using both qPCR and deep-sequencing methods to assess and monitor fungal pathogen burden at outbreak sources.
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Affiliation(s)
- Primavera Alvarado
- Laboratorio de Micología, Servicio Autonomo Instituto de Biomedicina Dr. Jacinto Convit, Caracas, 4043, Venezuela
| | | | - Lela Andrews
- Environmental Genetics and Genomics Laboratory, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Alexis Fernandez
- Laboratorio de Inmunología II, Servicio Autónomo Instituto de Biomedicina Dr. Jacinto Convit, Caracas, 4043, Venezuela
| | - Gerardo Santander
- Laboratory Geomatics, Universidad Bolivariana de Venezuela, Caracas, 1040, Venezuela
| | - Adina Doyle
- Division of Pathogen Genomics, Translational Genomics Research Institute-North, Flagstaff, AZ, 86005, USA
| | - Magaly Perez
- Laboratory Geomatics, Universidad Bolivariana de Venezuela, Caracas, 1040, Venezuela
| | - Francisco Yegres
- Laboratorio de Investigación y Apoyo Docente del Santa Ana (LIADSA), Universidad Nacional Experimental Francisco de Miranda (UNEFM), Coro, 4101, Venezuela
| | - Bridget Marie Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
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Abstract
Fungi must meet four criteria to infect humans: growth at human body temperatures, circumvention or penetration of surface barriers, lysis and absorption of tissue, and resistance to immune defenses, including elevated body temperatures. Morphogenesis between small round, detachable cells and long, connected cells is the mechanism by which fungi solve problems of locomotion around or through host barriers. Secretion of lytic enzymes, and uptake systems for the released nutrients, are necessary if a fungus is to nutritionally utilize human tissue. Last, the potent human immune system evolved in the interaction with potential fungal pathogens, so few fungi meet all four conditions for a healthy human host. Paradoxically, the advances of modern medicine have made millions of people newly susceptible to fungal infections by disrupting immune defenses. This article explores how different members of four fungal phyla use different strategies to fulfill the four criteria to infect humans: the Entomophthorales, the Mucorales, the Ascomycota, and the Basidiomycota. Unique traits confer human pathogenic potential on various important members of these phyla: pathogenic Onygenales comprising thermal dimorphs such as Histoplasma and Coccidioides; the Cryptococcus spp. that infect immunocompromised as well as healthy humans; and important pathogens of immunocompromised patients-Candida, Pneumocystis, and Aspergillus spp. Also discussed are agents of neglected tropical diseases important in global health such as mycetoma and paracoccidiomycosis and common pathogens rarely implicated in serious illness such as dermatophytes. Commensalism is considered, as well as parasitism, in shaping genomes and physiological systems of hosts and fungi during evolution.
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Shriber J, Conlon KC, Benedict K, McCotter OZ, Bell JE. Assessment of Vulnerability to Coccidioidomycosis in Arizona and California. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:E680. [PMID: 28644403 PMCID: PMC5551118 DOI: 10.3390/ijerph14070680] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 11/17/2022]
Abstract
Coccidioidomycosis is a fungal infection endemic to the southwestern United States, particularly Arizona and California. Its incidence has increased, potentially due in part to the effects of changing climatic variables on fungal growth and spore dissemination. This study aims to quantify the county-level vulnerability to coccidioidomycosis in Arizona and California and to assess the relationships between population vulnerability and climate variability. The variables representing exposure, sensitivity, and adaptive capacity were combined to calculate county level vulnerability indices. Three methods were used: (1) principal components analysis; (2) quartile weighting; and (3) percentile weighting. Two sets of indices, "unsupervised" and "supervised", were created. Each index was correlated with coccidioidomycosis incidence data from 2000-2014. The supervised percentile index had the highest correlation; it was then correlated with variability measures for temperature, precipitation, and drought. The supervised percentile index was significantly correlated (p < 0.05) with coccidioidomycosis incidence in both states. Moderate, positive significant associations (p < 0.05) were found between index scores and climate variability when both states were concurrently analyzed and when California was analyzed separately. This research adds to the body of knowledge that could be used to target interventions to vulnerable counties and provides support for the hypothesis that population vulnerability to coccidioidomycosis is associated with climate variability.
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Affiliation(s)
- Jennifer Shriber
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
| | - Kathryn C Conlon
- Climate and Health Program, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA.
| | - Kaitlin Benedict
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, GA 30333, USA.
| | - Orion Z McCotter
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, GA 30333, USA.
| | - Jesse E Bell
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
- Climate and Health Program, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA.
- North Carolina Institute for Climate Studies, North Carolina State University, Asheville, NC 28801, USA.
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20
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Colson AJ, Vredenburgh L, Guevara RE, Rangel NP, Kloock CT, Lauer A. Large-Scale Land Development, Fugitive Dust, and Increased Coccidioidomycosis Incidence in the Antelope Valley of California, 1999-2014. Mycopathologia 2017; 182:439-458. [PMID: 28084574 DOI: 10.1007/s11046-016-0105-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 12/16/2016] [Indexed: 11/26/2022]
Abstract
Ongoing large-scale land development for renewable energy projects in the Antelope Valley, located in the Western Mojave Desert, has been blamed for increased fugitive dust emissions and coccidioidomycosis incidence among the general public in recent years. Soil samples were collected at six sites that were destined for solar farm construction and were analyzed for the presence of the soil-borne fungal pathogen Coccidioides immitis which is endemic to many areas of central and southern California. We used a modified culture-independent nested PCR approach to identify the pathogen in all soil samples and also compared the sampling sites in regard to soil physical and chemical parameters, degree of disturbance, and vegetation. Our results indicated the presence of C. immitis at four of the six sites, predominantly in non-disturbed soils of the Pond-Oban complex, which are characterized by an elevated pH and salt bush communities, but also in grassland characterized by different soil parameters and covered with native and non-native annuals. Overall, we were able to detect the pathogen in 40% of the soil samples (n = 42). Incidence of coccidioidomycosis in the Antelope Valley was positively correlated with land use and particulate matter in the air (PM10) (Pearson correlation coefficient >0.5). With the predicted population growth and ongoing large-scale disturbance of soil in the Antelope Valley in coming years, incidence of coccidioidomycosis will likely further increase if policy makers and land developers continue to ignore the risk of grading land without implementing long-term dust mitigation plans in Environmental Impact Reports.
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Affiliation(s)
- Aaron J Colson
- Department of Biology, California State University Bakersfield (CSUB), 9001 Stockdale Highway, Bakersfield, CA, 93311-1022, USA
| | - Larry Vredenburgh
- Bureau of Land Management, Bakersfield Field Office, 3801 Pegasus Drive, Bakersfield, CA, 93308, USA
| | - Ramon E Guevara
- County of Los Angeles Department of Public Health, 600 S. Commonwealth Ave, Suite 700, Los Angeles, CA, 90005, USA
| | - Natalia P Rangel
- Department of Biology, California State University Bakersfield (CSUB), 9001 Stockdale Highway, Bakersfield, CA, 93311-1022, USA
| | - Carl T Kloock
- Department of Biology, California State University Bakersfield (CSUB), 9001 Stockdale Highway, Bakersfield, CA, 93311-1022, USA
| | - Antje Lauer
- Department of Biology, California State University Bakersfield (CSUB), 9001 Stockdale Highway, Bakersfield, CA, 93311-1022, USA.
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21
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Wheeler ML, Limon JJ, Underhill DM. Immunity to Commensal Fungi: Detente and Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 12:359-385. [PMID: 28068483 DOI: 10.1146/annurev-pathol-052016-100342] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fungi are ubiquitous in our environment, and a healthy immune system is essential to maintain adequate protection from fungal infections. When this protection breaks down, superficial and invasive fungal infections cause diseases that range from irritating to life-threatening. Millions of people worldwide develop invasive infections during their lives, and mortality for these infections often exceeds 50%. Nevertheless, we are normally colonized with many of the same disease-causing fungi (e.g., on the skin or in the gut). Recent research is dramatically expanding our understanding of the mechanisms by which our immune systems interact with these organisms in health and disease. In this review, we discuss what is currently known about where and how the immune system interacts with common fungi.
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Affiliation(s)
- Matthew L Wheeler
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048; , ,
| | - Jose J Limon
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048; , ,
| | - David M Underhill
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048; , , .,Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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Abstract
Dimorphic fungi cause several endemic mycoses which range from subclinical respiratory infections to life-threatening systemic disease. Pathogenic-phase cells of Histoplasma, Blastomyces, Paracoccidioides and Coccidioides escape elimination by the innate immune response with control ultimately requiring activation of cell-mediated immunity. Clinical management of disease relies primarily on antifungal compounds; however, dimorphic fungal pathogens create a number of challenges for antifungal drug therapy. In addition to the drug toxicity issues known for current antifungals, barriers to efficient drug treatment of dimorphic fungal infections include natural resistance to the echinocandins, residence of fungal cells within immune cells, the requirement for systemic delivery of drugs, prolonged treatment times, potential for latent infections, and lack of optimized standardized methodology for in vitro testing of drug susceptibilities. This review will highlight recent advances, current therapeutic options, and new compounds on the horizon for treating infections by dimorphic fungal pathogens.
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Affiliation(s)
| | - Chad A Rappleye
- a Department of Microbiology , Ohio State University , Columbus , OH , USA
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Primary and Disseminated Cutaneous Coccidioidomycosis: Clinical Aspects and Diagnosis. CURRENT FUNGAL INFECTION REPORTS 2016. [DOI: 10.1007/s12281-016-0263-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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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] [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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Chan O, Low SW, Urcis R, Mahmoud N, Yumul IKT, Po JLZ, Zangeneh TT. Coccidioidomycosis with Pericardial Involvement: Case Report and Literature Review. Am J Med 2016; 129:e21-5. [PMID: 26642905 DOI: 10.1016/j.amjmed.2015.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 11/17/2022]
Affiliation(s)
- Onyee Chan
- Department of Medicine, University of Arizona, Banner University Medical Center - Tucson, Tucson
| | - See Wei Low
- Department of Medicine, University of Arizona, Banner University Medical Center - Tucson, Tucson
| | - Rafael Urcis
- Department of Medicine, University of Arizona, Banner University Medical Center - Tucson, Tucson; Division of Infectious Diseases, University of Arizona, Banner University Medical Center - Tucson, Tucson
| | - Naser Mahmoud
- Department of Medicine, University of Arizona, Banner University Medical Center - Tucson, Tucson; Division of Pulmonary and Critical Care, University of Arizona, Banner University Medical Center - Tucson, Tucson
| | - Ily Kristine T Yumul
- Department of Medicine, University of Arizona, Banner University Medical Center - Tucson, Tucson; Department of Cardiology, University of Arizona, Banner University Medical Center - Tucson, Tucson
| | - John Leander Z Po
- Department of Medicine, University of Arizona, Banner University Medical Center - Tucson, Tucson; Division of Infectious Diseases, University of Arizona, Banner University Medical Center - Tucson, Tucson
| | - Tirdad T Zangeneh
- Department of Medicine, University of Arizona, Banner University Medical Center - Tucson, Tucson; Division of Infectious Diseases, University of Arizona, Banner University Medical Center - Tucson, Tucson.
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26
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Gaab EM, Naeem F. Pediatric Coccidioidomycosis Patients: Perceptions, Quality of Life and Psychosocial Factors. Healthcare (Basel) 2015; 3:775-95. [PMID: 27417796 PMCID: PMC4939562 DOI: 10.3390/healthcare3030775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/06/2015] [Accepted: 08/13/2015] [Indexed: 11/17/2022] Open
Abstract
Research investigating the effects of coccidioidomycosis (valley fever) on children and the psychosocial implications of this disease in general is lacking. This study reviews what is known about pediatric coccidioidomycosis patients. It documents the psychological functioning, quality of life, and illness perceptions of a sample of coccidioidomycosis patient families. Primary caregivers of pediatric patients and patients from a major hospital in the San Joaquin Valley of California were interviewed regarding their perceptions of disease detection, access to care and the patient/family experience.
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Affiliation(s)
- Erin Mary Gaab
- Health Sciences Research Institute, University of California, Merced, CA 95343, USA.
| | - Fouzia Naeem
- Valley Children's Hospital, 9300 Valley Children's Pl, Madera, CA 93636, USA.
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Nenoff P, Reinel D, Krüger C, Grob H, Mugisha P, Süß A, Mayser P. Tropen- und Reise-assoziierte Dermatomykosen. Hautarzt 2015; 66:522-32. [DOI: 10.1007/s00105-015-3635-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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