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Kahn D, Chen W, Linden Y, Corbeil KA, Lowry S, Higham CA, Mendez KS, Burch P, DiFondi T, Verhougstraete M, De Roos AJ, Haas CN, Gerba C, Hamilton KA. A microbial risk assessor's guide to Valley Fever (Coccidioides spp.): Case study and review of risk factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170141. [PMID: 38242485 PMCID: PMC10923130 DOI: 10.1016/j.scitotenv.2024.170141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/07/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Valley Fever is a respiratory disease caused by inhalation of arthroconidia, a type of spore produced by fungi within the genus Coccidioides spp. which are found in dry, hot ecosystems of the Western Hemisphere. A quantitative microbial risk assessment (QMRA) for the disease has not yet been performed due to a lack of dose-response models and a scarcity of quantitative occurrence data from environmental samples. A literature review was performed to gather data on experimental animal dosing studies, environmental occurrence, human disease outbreaks, and meteorological associations. As a result, a risk framework is presented with information for parameterizing QMRA models for Coccidioides spp., with eight new dose-response models proposed. A probabilistic QMRA was conducted for a Southwestern US agricultural case study, evaluating eight scenarios related to farming occupational exposures. Median daily workday risks for developing severe Valley Fever ranged from 2.53 × 10-7 (planting by hand while wearing an N95 facemask) to 1.33 × 10-3 (machine harvesting while not wearing a facemask). The literature review and QMRA synthesis confirmed that exposure to aerosolized arthroconidia has the potential to result in high attack rates but highlighted that the mechanistic relationships between environmental conditions and disease remain poorly understood. Recommendations for Valley Fever risk assessment research needs in order to reduce disease risks are discussed, including interventions for farmers.
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Affiliation(s)
- David Kahn
- Department of Civil Architectural and Environmental Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - William Chen
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Yarrow Linden
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karalee A Corbeil
- Department of Water Management and Hydrological Science, Texas A&M University, College Station, TX 79016, USA
| | - Sarah Lowry
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
| | - Ciara A Higham
- Leeds Institute for Fluid Dynamics, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Karla S Mendez
- The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX 77030, USA
| | - Paige Burch
- Seaford High School, 1575 Seamans Neck Rd, Seaford, NY 11783, USA
| | - Taylor DiFondi
- Seaford High School, 1575 Seamans Neck Rd, Seaford, NY 11783, USA
| | - Marc Verhougstraete
- University of Arizona, Mel and Enid Zuckerman College of Public Health, 1295 N. Marton Ave., Tucson, AZ 85724, USA
| | - Anneclaire J De Roos
- Department of Environmental and Occupational Health, Dornsife School of Public Health, Drexel University, Philadelphia, PA 19104, USA
| | - Charles N Haas
- Department of Civil Architectural and Environmental Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Charles Gerba
- University of Arizona, Mel and Enid Zuckerman College of Public Health, 1295 N. Marton Ave., Tucson, AZ 85724, USA
| | - Kerry A Hamilton
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85281, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85281, USA.
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Wilmes D, Hagen F, Verissimo C, Alanio A, Rickerts V, Buitrago MJ. A multicentre external quality assessment: A first step to standardise PCR protocols for the diagnosis of histoplasmosis and coccidioidomycosis. Mycoses 2023. [PMID: 37169736 DOI: 10.1111/myc.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND In-house real-time PCR (qPCR) is increasingly used to diagnose the so-called endemic mycoses as commercial assays are not widely available. OBJECTIVES To compare the performance of different molecular diagnostic assays for detecting Histoplasma capsulatum and Coccidioides spp. in five European reference laboratories. METHODS Two blinded external quality assessment (EQA) panels were sent to each laboratory that performed the analysis with their in-house assays. Both panels included a range of concentrations of H. capsulatum (n = 7) and Coccidioides spp. (n = 6), negative control and DNA from other fungi. Four laboratories used specific qPCRs, and one laboratory a broad-range fungal conventional PCR (cPCR) and a specific cPCR for H. capsulatum with subsequent sequencing. RESULTS qPCR assays were the most sensitive for the detection of H. capsulatum DNA. The lowest amount of H. capsulatum DNA detected was 1-4 fg, 0.1 pg and 10 pg for qPCRs, specific cPCR and broad-range cPCR, respectively. False positive results occurred with high concentrations of Blastomyces dermatitidis DNA in two laboratories and with Emergomyces spp. in one laboratory. For the Coccidioides panel, the lowest amount of DNA detected was 1-16 fg by qPCRs and 10 pg with the broad-range cPCR. One laboratory reported a false positive result by qPCR with high load of Uncinocarpus DNA. CONCLUSION All five laboratories were able to correctly detect H. capsulatum and Coccidioides spp. DNA and qPCRs had a better performance than specific cPCR and broad-range cPCR. EQAs may help standardise in-house molecular tests for the so-called endemic mycoses improving patient management.
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Affiliation(s)
- Dunja Wilmes
- FG16, Unit for Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute (WI-KNAW), Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cristina Verissimo
- Department of Infectious Diseases, Reference Laboratory for Parasites and Fungal infections, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Alexandre Alanio
- Mycology Department, Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Institut Pasteur, Université Paris Cité, Paris, France
- Laboratoire de Parasitologie-Mycologie, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Volker Rickerts
- FG16, Unit for Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
- Konsiliarlabor für Kryptokokkose und Seltene Systemmykosen, Robert Koch Institute, Berlin, Germany
| | - Maria José Buitrago
- Reference Mycology Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBERINFEC, ISCIII-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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Wagner R, Montoya L, Head JR, Campo S, Remais J, Taylor JW. Coccidioides undetected in soils from agricultural land and uncorrelated with time or the greater soil fungal community on undeveloped land. PLoS Pathog 2023; 19:e1011391. [PMID: 37228157 PMCID: PMC10246812 DOI: 10.1371/journal.ppat.1011391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 06/07/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Coccidioidomycosis is a typically respiratory fungal disease that, in the United States, occurs primarily in Arizona and California. In California, most coccidioidomycosis cases occur in the San Joaquin Valley, a primarily agricultural region where the disease poses a risk for outdoor workers. We collected 710 soil samples and 265 settled dust samples from nine sites in the San Joaquin Valley and examined how Coccidioides detection varied by month, site, and the presence and abundance of other fungal species. We detected Coccidioides in 89 of 238 (37.4%) rodent burrow soil samples at five undeveloped sites and were unable to detect Coccidioides in any of 472 surface and subsurface soil samples at four agricultural sites. In what is the largest sampling effort undertaken on agricultural land, our results provide no evidence that agricultural soils in the San Joaquin Valley harbor Coccidioides. We found no clear association between Coccidioides and the greater soil fungal community, but we identified 19 fungal indicator species that were significantly associated with Coccidioides detection in burrows. We also did not find a seasonal pattern in Coccidioides detection in the rodent burrow soils we sampled. These findings suggest both the presence of a spore bank and that coccidioidomycosis incidence may be more strongly associated with Coccidioides dispersal than Coccidioides growth. Finally, we were able to detect Coccidioides in only five of our 265 near-surface settled dust samples, one from agricultural land, where Coccidioides was undetected in soils, and four from undeveloped land, where Coccidioides was common in the rodent burrow soils we sampled. Our ability to detect Coccidioides in few settled dust samples indicates that improved methods are likely needed moving forward, though raises questions regarding aerial dispersal in Coccidioides, whose key transmission event likely occurs over short distances in rodent burrows from soil to naïve rodent lungs.
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Affiliation(s)
- Robert Wagner
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Liliam Montoya
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Jennifer R. Head
- Division of Epidemiology, University of California Berkeley, Berkeley, California, United States of America
| | - Simon Campo
- Division of Environmental Health Sciences, University of California Berkeley, Berkeley, California, United States of America
| | - Justin Remais
- Division of Environmental Health Sciences, University of California Berkeley, Berkeley, California, United States of America
| | - John W. Taylor
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
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Kaur J, Harder CB, Sharma J. Congeneric temperate orchids recruit similar-yet differentially abundant-endophytic bacterial communities that are uncoupled from soil, but linked to host phenology and population size. AMERICAN JOURNAL OF BOTANY 2023; 110:e16168. [PMID: 37052191 DOI: 10.1002/ajb2.16168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 05/16/2023]
Abstract
PREMISE Besides the beneficial plant-fungus symbiosis in mycorrhizal plants, bacteria also enhance plant fitness via tripartite interactions. While bacterial associations are presumably just as important for the obligate mycorrhizal family Orchidaceae, little is known about orchid associating bacteria (OAB). METHODS We examined the OAB communities of two, congeneric, terrestrial orchids, Platanthera cooperi and Platanthera praeclara, which represent widely disparate North American ecosystems. We tested whether they recruit distinct OAB communities, and whether variability in OAB communities can be linked to phenology, population size, or habitat soil. Genomic DNAs from roots of seedling, vegetative, and reproductive plants and from soil were subjected to Illumina sequencing of V4 and V5 regions of the 16S rRNA gene. RESULTS We obtained 809 OAB Zero-radius Operational Taxonomic Units (ZOTUs). Despite an overlap of 209 ZOTUs that accounted for >75% relative abundances of their respective OAB communities, the overall community structures of the two orchids were distinct. Within each orchid, distinctions were detected in the OAB communities of large and small populations and the three phenological stages. The OAB ZOTUs were either absent or present with low abundances in soil associated with both orchids. CONCLUSIONS The two orchids exhibited preferential recruitment of known growth-promoting OAB communities from soil. Their OAB communities also showed considerable overlap despite the large environmental and geographical separation of the two host taxa. Our results lend further support to the emerging evidence that not only the fungi, but root-associated bacteria also have functional importance for orchid ecology.
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Affiliation(s)
- Jaspreet Kaur
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA
- Department of Biology, University of Wisconsin-La Crosse, La Crosse, Wisconsin, USA
| | - Christoffer B Harder
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA
- Department of Biology, MEMEG, Lund University, Ekologihuset, Sölvegatan, Sweden
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, Denmark
| | - Jyotsna Sharma
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA
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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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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Coccidioidomycosis in Northern Arizona: an Investigation of the Host, Pathogen, and Environment Using a Disease Triangle Approach. mSphere 2022; 7:e0035222. [PMID: 35972134 PMCID: PMC9599602 DOI: 10.1128/msphere.00352-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coccidioides immitis and Coccidioides posadasii are the etiological agents of coccidioidomycosis (Valley fever [VF]). Disease manifestation ranges from mild pneumonia to chronic or extrapulmonary infection. If diagnosis is delayed, the risk of severe disease increases. In this report, we investigated the intersection of pathogen, host, and environment for VF cases in Northern Arizona (NAZ), where the risk of acquiring the disease is much lower than in Southern Arizona. We investigated reported cases and assessed pathogen origin by comparing genomes of NAZ clinical isolates to isolates from other regions. Lastly, we surveyed regional soils for presence of Coccidioides. We found that cases of VF increased in NAZ in 2019, and Coccidioides NAZ isolates are assigned to Arizona populations using phylogenetic inference. Importantly, we detected Coccidioides DNA in NAZ soil. Given recent climate modeling of the disease that predicts that cases will continue to increase throughout the region, and the evidence presented in this report, we propose that disease awareness outreach to clinicians throughout the western United States is crucial for improving patient outcomes, and further environmental sampling across the western U.S. is warranted. IMPORTANCE Our work is the first description of the Valley fever disease triangle in Northern Arizona, which addresses the host, the pathogen, and the environmental source in the region. Our data suggest that the prevalence of diagnosed cases rose in 2019 in this region, and some severe cases necessitate hospitalization. We present the first evidence of Coccidioides spp. in Northern Arizona soils, suggesting that the pathogen is maintained in the local environment. Until disease prevention is an achievable option via vaccination, we predict that incidence of Valley fever will rise in the area. Therefore, enhanced awareness of and surveillance for coccidioidomycosis is vital to community health in Northern Arizona.
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Revillini D, David AS, Menges ES, Main KN, Afkhami ME, Searcy CA. Microbiome-mediated response to pulse fire disturbance outweighs the effects of fire legacy on plant performance. THE NEW PHYTOLOGIST 2022; 233:2071-2082. [PMID: 34432894 DOI: 10.1111/nph.17689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/31/2021] [Indexed: 06/13/2023]
Abstract
Fire plays a major role in structuring plant communities across the globe. Interactions with soil microbes impact plant fitness, scaling up to influence plant populations and distributions. Here we present the first factorial manipulation of both fire and soil microbiome presence to investigate their interactive effects on plant performance across a suite of plant species with varying life history traits. We conducted fully factorial experiments on 11 species from the Florida scrub ecosystem to test plant performance responses to soils with varying fire histories (36 soil sources), the presence/absence of a microbiome, and exposure to an experimental burn. Results revealed interactive 'pulse' effects between fire and the soil microbiome on plant performance. On average, post-fire soil microbiomes strongly reduced plant productivity compared to unburned or sterilized soils. Interestingly, longer-term fire 'legacy' effects had minor impacts on plant performance and were unrelated to soil microbiomes. While pulse fire effects on plant-microbiome interactions are short-term, they could have long-term consequences for plant communities by establishing differential microbiome-mediated priority effects during post-disturbance succession. The prominence of pulse fire effects on plant-microbe interactions has even greater import due to expected increases in fire disturbances resulting from anthropogenic climate change.
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Affiliation(s)
- Daniel Revillini
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33146, USA
| | - Aaron S David
- Archbold Biological Station, 123 Main Drive, Venus, FL, 33960, USA
| | - Eric S Menges
- Archbold Biological Station, 123 Main Drive, Venus, FL, 33960, USA
| | - Kevin N Main
- Archbold Biological Station, 123 Main Drive, Venus, FL, 33960, USA
| | - Michelle E Afkhami
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33146, USA
| | - Christopher A Searcy
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33146, USA
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Effect of Climate Change on the Incidence and Geographical Distribution of Coccidioidomycosis. Fungal Biol 2022. [DOI: 10.1007/978-3-030-89664-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Yamauchi DH, Garcia Garces H, Teixeira MDM, Rodrigues GFB, Ullmann LS, Garcia Garces A, Hebeler-Barbosa F, Bagagli E. Soil Mycobiome Is Shaped by Vegetation and Microhabitats: A Regional-Scale Study in Southeastern Brazil. J Fungi (Basel) 2021; 7:587. [PMID: 34436126 PMCID: PMC8396882 DOI: 10.3390/jof7080587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 11/20/2022] Open
Abstract
Soil is the principal habitat and reservoir of fungi that act on ecological processes vital for life on Earth. Understanding soil fungal community structures and the patterns of species distribution is crucial, considering climatic change and the increasing anthropic impacts affecting nature. We evaluated the soil fungal diversity in southeastern Brazil, in a transitional region that harbors patches of distinct biomes and ecoregions. The samples originated from eight habitats, namely: semi-deciduous forest, Brazilian savanna, pasture, coffee and sugarcane plantation, abandoned buildings, owls' and armadillos' burrows. Forty-four soil samples collected in two periods were evaluated by metagenomic approaches, focusing on the high-throughput DNA sequencing of the ITS2 rDNA region in the Illumina platform. Normalized difference vegetation index (NDVI) was used for vegetation cover analysis. NDVI values showed a linear relationship with both diversity and richness, reinforcing the importance of a healthy vegetation for the establishment of a diverse and complex fungal community. The owls' burrows presented a peculiar fungal composition, including high rates of Onygenales, commonly associated with keratinous animal wastes, and Trichosporonales, a group of basidiomycetous yeasts. Levels of organic matter and copper influenced all guild communities analyzed, supporting them as important drivers in shaping the fungal communities' structures.
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Affiliation(s)
- Danielle Hamae Yamauchi
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-689, SP, Brazil; (H.G.G.); (A.G.G.)
| | - Hans Garcia Garces
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-689, SP, Brazil; (H.G.G.); (A.G.G.)
| | - Marcus de Melo Teixeira
- Center for Tropical Medicine, Faculty of Medicine, University of Brasília (UnB), Brasília 70910-900, DF, Brazil;
| | - Gabriel Fellipe Barros Rodrigues
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Biosciences, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-689, SP, Brazil;
| | - Leila Sabrina Ullmann
- Institute for Biotechnology, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18607-440, SP, Brazil;
| | - Adalberto Garcia Garces
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-689, SP, Brazil; (H.G.G.); (A.G.G.)
| | - Flavia Hebeler-Barbosa
- Laboratory of Molecular Biology, Medical School, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-687, SP, Brazil;
| | - Eduardo Bagagli
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-689, SP, Brazil; (H.G.G.); (A.G.G.)
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Cordeiro R, Moura S, Castelo-Branco D, Rocha MF, Lima-Neto R, Sidrim JJ. Coccidioidomycosis in Brazil: Historical Challenges of a Neglected Disease. J Fungi (Basel) 2021; 7:85. [PMID: 33513773 PMCID: PMC7911456 DOI: 10.3390/jof7020085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/11/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
Coccidioidomycosis is a deep-seated fungal infection that occurs exclusively in semiarid areas in the Americas. In Brazil, coccidioidomycosis occurs exclusively in rural areas in the northeast region and affects counties that are hit by recurrent droughts, poverty and economic stagnation. Since 1978, approximately 136 cases of the disease have been reported in Brazil, according to scientific publications. However, a lack of governmental epidemiological data as well as a similarity to tuberculosis have led scientists and experts to assume that a greater number of cases occur in the country, which are not diagnosed and/or reported. In this review, general characteristics of coccidioidomycosis are presented, followed by a description of the main clinical and epidemiological data of cases in Brazil. The purpose of this article is to discuss the inclusion of coccidioidomycosis in the list of neglected tropical diseases. We believe that the adoption of coccidioidomycosis as a neglected tropical disease will enable the creation of an effective epidemiological surveillance system and the development of feasible public health solutions for its control in vulnerable populations.
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Affiliation(s)
- Rossana Cordeiro
- Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza 60430-270, Brazil
| | - Santiago Moura
- Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza 60430-270, Brazil
| | - Débora Castelo-Branco
- Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza 60430-270, Brazil
| | - Marcos Fábio Rocha
- Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza 60430-270, Brazil
- Postgraduate Program in Veterinary Sciences, School of Veterinary Medicine, Ceará State University, Fortaleza 60740-000, Brazil
| | - Reginaldo Lima-Neto
- Center of Medical Sciences, Department of Tropical Medicine, Federal University of Pernambuco (UFPE), Recife-PE 50740-600, Brazil
| | - José Júlio Sidrim
- Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza 60430-270, Brazil
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Kaur J, Phillips C, Sharma J. Host population size is linked to orchid mycorrhizal fungal communities in roots and soil, which are shaped by microenvironment. MYCORRHIZA 2021; 31:17-30. [PMID: 33113039 DOI: 10.1007/s00572-020-00993-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 10/12/2020] [Indexed: 05/04/2023]
Abstract
Interaction with orchid mycorrhizal fungi (OMF) is essential to all members of the Orchidaceae, yet we know little about whether or how OMF abundances in substrates shape orchid populations. While root-associated OMF diversity is catalogued frequently, technological constraints have impeded the assessments of OMF communities in substrates until recently, thereby limiting the ability to link OMF communities in a habitat to population responses. Furthermore, there is some evidence that edaphic and microclimatic conditions impact OMF in soil, yet we lack an understanding of the coupled influences of abiotic environment and OMF structure on orchid population dynamics. To discover the linkages between abiotic environment, OMF community structure, and population size, we characterized the microclimatic conditions, soil physicochemistry, and OMF communities hosted by roots and soil across large and small populations of a terrestrial orchid endemic to California Floristic Province in North America. By using high-throughput sequencing of the ITS2 region of nrDNA amplified from root and soil DNAs, we determined that both roots and soil of larger populations, which were high in phosphorus but low in zinc, organic matter, and silt, were dominated by Tulasnellaceae OTUs. In comparison, roots and soil from smaller populations of the orchid hosted higher relative abundances of the Ceratobasidiaceae. In this multiyear, range-wide study that simultaneously measured habitat environmental conditions, and soil and root OMF communities, our results suggest that soil chemistry is clearly linked to soil and root OMF communities, which then likely alter and shape orchid populations.
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Affiliation(s)
- Jaspreet Kaur
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA.
| | - Caleb Phillips
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Jyotsna Sharma
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
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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] [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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Identifying Mechanisms for Successful Ecological Restoration with Salvaged Topsoil in Coastal Sage Scrub Communities. DIVERSITY 2020. [DOI: 10.3390/d12040150] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although aboveground metrics remain the standard, restoring functional ecosystems should promote both aboveground and belowground biotic communities. Restoration using salvaged soil—removal and translocation of topsoil from areas planned for development, with subsequent deposition at degraded sites—is an alternative to traditional methods. Salvaged soil contains both seed and spore banks, which may holistically augment restoration. Salvaged soil methods may reduce non-native germination by burying non-native seeds, increase native diversity by adding native seeds, or transfer soil microbiomes, including arbuscular mycorrhizal fungi (AMF), to recipient sites. We transferred soil to three degraded recipient sites and monitored soil microbes, using flow cytometry and molecular analyses, and characterized the plant community composition. Our findings suggest that salvaged soil at depths ≥5 cm reduced non-native grass cover and increased native plant density and species richness. Bacterial abundance at recipient sites were statistically equivalent to donor sites in abundance. Overall, topsoil additions affected AMF alpha diversity and community composition and increased rhizophilic AMF richness. Because salvaged soil restoration combines multiple soil components, including native plant and microbial propagules, it may promote both aboveground and belowground qualities of the donor site, when applying this method for restoring invaded and degraded ecosystems.
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Ashraf N, Kubat RC, Poplin V, Adenis AA, Denning DW, Wright L, McCotter O, Schwartz IS, Jackson BR, Chiller T, Bahr NC. Re-drawing the Maps for Endemic Mycoses. Mycopathologia 2020; 185:843-865. [PMID: 32040709 PMCID: PMC7416457 DOI: 10.1007/s11046-020-00431-2] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/24/2020] [Indexed: 01/19/2023]
Abstract
Endemic mycoses such as histoplasmosis, coccidioidomycosis, blastomycosis, paracoccidioidomycosis, and talaromycosis are well-known causes of focal and systemic disease within specific geographic areas of known endemicity. However, over the past few decades, there have been increasingly frequent reports of infections due to endemic fungi in areas previously thought to be “non-endemic.” There are numerous potential reasons for this shift such as increased use of immune suppressive medications, improved diagnostic tests, increased disease recognition, and global factors such as migration, increased travel, and climate change. Regardless of the causes, it has become evident that our previous understanding of endemic regions for these fungal diseases needs to evolve. The epidemiology of the newly described Emergomyces is incomplete; our understanding of it continues to evolve. This review will focus on the evidence underlying the established areas of endemicity for these mycoses as well as new data and reports from medical literature that support the re-thinking these geographic boundaries. Updating the endemic fungi maps would inform clinical practice and global surveillance of these diseases.
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Affiliation(s)
- Nida Ashraf
- Division of Infectious Diseases, Department of Internal Medicine, University of Kansas, Kansas City, KS, USA
| | - Ryan C Kubat
- Division of Infectious Diseases, Department of Internal Medicine, University of Kansas, Kansas City, KS, USA
| | - Victoria Poplin
- Department of Internal Medicine, University of Kansas, Kansas City, KS, USA
| | - Antoine A Adenis
- Centre d'Investigation Clinique Antilles-Guyane, Inserm 1424, Centre Hospitalier de Cayenne, Cayenne, French Guiana
| | - David W Denning
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Laura Wright
- Geographic Research Analysis and Services Program, Division of Toxicology and Human Health Services, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Orion McCotter
- Mycotic Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ilan S Schwartz
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Brendan R Jackson
- Mycotic Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tom Chiller
- Mycotic Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nathan C Bahr
- Division of Infectious Diseases, Department of Internal Medicine, University of Kansas, Kansas City, KS, USA.
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Population Structure and Genetic Diversity among Isolates of Coccidioides posadasii in Venezuela and Surrounding Regions. mBio 2019; 10:mBio.01976-19. [PMID: 31772050 PMCID: PMC6879716 DOI: 10.1128/mbio.01976-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coccidioides posadasii is a pathogenic fungus that causes coccidioidomycosis in many arid regions of the Americas. One of these regions is bordered by the Caribbean Sea, and the surrounding landscape may play an important role in the dispersion of C. posadasii across South America through southeastern Mexico, Honduras, Guatemala, and Venezuela. Comparative phylogenomic analyses of C. posadasii reveal that clinical strains from Venezuela are genetically distinct from the North American populations found in (i) Arizona and (ii) Texas, Mexico, and the rest of South America (TX/MX/SA). We find evidence for admixture between the Venezuela and the North American populations of C. posadasii in Central America. Additionally, the proportion of Venezuelan alleles in the admixed population decreases as latitude (and distance from Venezuela) increases. Our results indicate that the population in Venezuela may have been subjected to a recent bottleneck and shows a strong population structure. This analysis provides insight into potential for Coccidioides spp. to invade new regions.IMPORTANCE Valley Fever is a fungal disease caused by two species of fungi: Coccidioides immitis and C. posadasii These fungi are found throughout the arid regions of North and South America; however, our understanding of genetic diversity and disease in South America is limited. In this report, we analyze 10 new genomes of Coccidioides posadasii from regions bordering the Caribbean Sea. We show that these populations are distinct and that isolates from Venezuela are likely a result of a recent bottleneck. These data point to patterns that might be observed when investigating recently established populations.
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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] [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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Weber SE, Diez JM, Andrews LV, Goulden ML, Aronson EL, Allen MF. Responses of arbuscular mycorrhizal fungi to multiple coinciding global change drivers. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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