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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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2
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Carlin AF, Beyhan S, Peña JF, Stajich JE, Viriyakosol S, Fierer J, Kirkland TN. Transcriptional Analysis of Coccidioides immitis Mycelia and Spherules by RNA Sequencing. J Fungi (Basel) 2021; 7:jof7050366. [PMID: 34067070 PMCID: PMC8150946 DOI: 10.3390/jof7050366] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/13/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
Coccidioides immitis and C. posadasii are dimorphic fungi that transform from mycelia with internal arthroconidia in the soil to a tissue form known as a spherule in mammals. This process can be recapitulated in vitro by increasing the temperature, CO2 and changing other culture conditions. In this study, we have analyzed changes in gene expression in mycelia and young and mature spherules. Genes that were highly upregulated in young spherules include a spherule surface protein and iron and copper membrane transporters. Genes that are unique to Coccidioides spp. are also overrepresented in this group, suggesting that they may be important for spherule differentiation. Enriched GO terms in young spherule upregulated genes include oxidation-reduction, response to stress and membrane proteins. Downregulated genes are enriched for transcription factors, especially helix–loop–helix and C2H2 type zinc finger domain-containing proteins, which is consistent with the dramatic change in transcriptional profile. Almost all genes that are upregulated in young spherules remain upregulated in mature spherules, but a small number of genes are differentially expressed in those two stages of spherule development. Mature spherules express more Hsp31 and amylase and less tyrosinase than young spherules. Some expression of transposons was detected and most of the differentially expressed transposons were upregulated in spherules.
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Affiliation(s)
- Aaron F. Carlin
- Department of Medicine, Division of Infectious Disease, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA; (A.F.C.); (S.V.); (J.F.)
| | - Sinem Beyhan
- J. Craig Venter Institute, La Jolla, CA 92037, USA;
| | - Jesús F. Peña
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA; (J.F.P.); (J.E.S.)
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA; (J.F.P.); (J.E.S.)
| | - Suganya Viriyakosol
- Department of Medicine, Division of Infectious Disease, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA; (A.F.C.); (S.V.); (J.F.)
| | - Joshua Fierer
- Department of Medicine, Division of Infectious Disease, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA; (A.F.C.); (S.V.); (J.F.)
- Infectious Diseases Section, VA Healthcare San Diego, San Diego, CA 92161, USA
- Department of Pathology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Theo N. Kirkland
- Department of Medicine, Division of Infectious Disease, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA; (A.F.C.); (S.V.); (J.F.)
- Department of Pathology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
- Correspondence:
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Boniche C, Rossi SA, Kischkel B, Vieira Barbalho F, Nogueira D’Aurea Moura Á, Nosanchuk JD, Travassos LR, Pelleschi Taborda C. Immunotherapy against Systemic Fungal Infections Based on Monoclonal Antibodies. J Fungi (Basel) 2020; 6:jof6010031. [PMID: 32121415 PMCID: PMC7151209 DOI: 10.3390/jof6010031] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 12/17/2022] Open
Abstract
The increasing incidence in systemic fungal infections in humans has increased focus for the development of fungal vaccines and use of monoclonal antibodies. Invasive mycoses are generally difficult to treat, as most occur in vulnerable individuals, with compromised innate and adaptive immune responses. Mortality rates in the setting of our current antifungal drugs remain excessively high. Moreover, systemic mycoses require prolonged durations of antifungal treatment and side effects frequently occur, particularly drug-induced liver and/or kidney injury. The use of monoclonal antibodies with or without concomitant administration of antifungal drugs emerges as a potentially efficient treatment modality to improve outcomes and reduce chemotherapy toxicities. In this review, we focus on the use of monoclonal antibodies with experimental evidence on the reduction of fungal burden and prolongation of survival in in vivo disease models. Presently, there are no licensed monoclonal antibodies for use in the treatment of systemic mycoses, although the potential of such a vaccine is very high as indicated by the substantial promising results from several experimental models.
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Affiliation(s)
- Camila Boniche
- Biomedical Sciences Institute, Department of Microbiology, University of São Paulo, Sao Paulo 05508-000, Brazil; (C.B.); (S.A.R.); (B.K.); (F.V.B.)
| | - Suélen Andreia Rossi
- Biomedical Sciences Institute, Department of Microbiology, University of São Paulo, Sao Paulo 05508-000, Brazil; (C.B.); (S.A.R.); (B.K.); (F.V.B.)
| | - Brenda Kischkel
- Biomedical Sciences Institute, Department of Microbiology, University of São Paulo, Sao Paulo 05508-000, Brazil; (C.B.); (S.A.R.); (B.K.); (F.V.B.)
| | - Filipe Vieira Barbalho
- Biomedical Sciences Institute, Department of Microbiology, University of São Paulo, Sao Paulo 05508-000, Brazil; (C.B.); (S.A.R.); (B.K.); (F.V.B.)
| | - Ágata Nogueira D’Aurea Moura
- Tropical Medicine Institute, Department of Dermatology, Faculty of Medicine, University of Sao Paulo, Sao Paulo 05403-000, Brazil;
| | - Joshua D. Nosanchuk
- Departments of Medicine (Division of Infectious Diseases) and Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10461, USA;
| | - Luiz R. Travassos
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, Sao Paulo 04021-001, Brazil;
| | - Carlos Pelleschi Taborda
- Biomedical Sciences Institute, Department of Microbiology, University of São Paulo, Sao Paulo 05508-000, Brazil; (C.B.); (S.A.R.); (B.K.); (F.V.B.)
- Tropical Medicine Institute, Department of Dermatology, Faculty of Medicine, University of Sao Paulo, Sao Paulo 05403-000, Brazil;
- Correspondence:
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4
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Mead HL, Blackmon AV, Vogler AJ, Barker BM. Heat Inactivation of Coccidioides posadasii and Coccidioides immitis for Use in Lower Biosafety Containment. APPLIED BIOSAFETY 2019; 24:123-128. [PMID: 33833621 DOI: 10.1177/1535676019856525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction The difficulty involved in obtaining sufficient intact genomic deoxyribonucleic acid (DNA) from Coccidioides spp for downstream applications using published protocols prompted the exploration of inactivating mycelia and arthroconidia using heat under biosafety level 3 containment. This was followed by optimizing DNA extraction from mycelia using various methods at lower containment. Methods Various exposure times and temperatures were examined to identify an effective heat inactivation procedure for arthroconidia and mycelia from both C immitis and C posadasii. Heat inactivation of mycelia was followed by DNA extraction using 2 commercially available kits, as well as a phenol:chloroform-based extraction procedure to determine DNA integrity and quantity among extraction methods using both live and heat-inactivated mycelia. Results Ten-minute and 30-minute exposure times at 80°C were sufficient to inactivate Coccidioides spp arthroconidia and mycelia, respectively. DNA yield between live versus heat-inactivated mycelia was similar for each extraction procedure. However, DNA obtained using phenol:chloroform was of higher quantity and integrity compared with DNA obtained using the commercially available kits, which was highly fragmented. Conclusion The ability to heat-inactivate Coccidioides cultures for processing at a lower level of containment greatly increased the efficiency of DNA extractions. Therefore, this is an ideal method for obtaining Coccidioides spp DNA and inactivated arthroconidia.
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Affiliation(s)
- Heather L Mead
- Northern Arizona University, Pathogen and Microbiome Institute, Flagstaff, AZ, USA
| | - Austin V Blackmon
- Northern Arizona University, Pathogen and Microbiome Institute, Flagstaff, AZ, USA
| | - Amy J Vogler
- Northern Arizona University, Pathogen and Microbiome Institute, Flagstaff, AZ, USA
| | - Bridget M Barker
- Northern Arizona University, Pathogen and Microbiome Institute, Flagstaff, AZ, USA
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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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6
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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7
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Fernandez JA, Hidalgo MN, Hodzic E, Diab SS, Uzal FA. Pathology of coccidioidomycosis in llamas and alpacas. J Vet Diagn Invest 2018; 30:560-564. [PMID: 29790449 DOI: 10.1177/1040638718777282] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Coccidioidomycosis is a fungal disease caused by either Coccidioides immitis or Coccidioides posadasii. Anecdotal evidence suggests that camelids are particularly susceptible to this disease and that a relatively large percentage of pneumonias in these animals are caused by Coccidioides spp. In a search of 21 y (1992-2013) of records from the California Animal Health and Food Safety Laboratory, we found 79 cases of coccidioidomycosis diagnosed in camelids; 66 (84%) had pneumonia and 13 (16%) had lesions only in organs other than the lungs. The organs most frequently affected were lung (84%) and liver (78%). Coccidioides spp. were the cause of pneumonia in 66 of 362 (18%) camelid cases during the study period. The lesions in affected organs were multifocal-to-coalescing pyogranulomas, which in most cases were visible grossly. Ten of the 12 formalin-fixed, paraffin-embedded lung samples tested by a universal Coccidioides spp. PCR assay were positive (4 C. immitis, 2 C. posadasii); the species could not be determined in 4 of the 10 cases positive by PCR. Coccidioidomycosis is an important cause of pneumonia in camelids in California, and can be caused by either C. immitis or C. posadasii.
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Affiliation(s)
- Julian A Fernandez
- Basic and Agricultural Studies Department, Veterinary School, National University of Rio Cuarto, Rio Cuarto, Argentina (Fernandez).,Pathology Department, Veterinary School, Autonomous University of Barcelona, Barcelona, Spain (Hidalgo).,Real-time PCR Research and Diagnostics Core Facility (Hodzic), School of Veterinary Medicine, University of California, Davis, CA.,California Animal Health and Food Safety Laboratory, Davis (Diab), School of Veterinary Medicine, University of California, Davis, CA.,San Bernardino (Uzal) branches, School of Veterinary Medicine, University of California, Davis, CA
| | - Mireia N Hidalgo
- Basic and Agricultural Studies Department, Veterinary School, National University of Rio Cuarto, Rio Cuarto, Argentina (Fernandez).,Pathology Department, Veterinary School, Autonomous University of Barcelona, Barcelona, Spain (Hidalgo).,Real-time PCR Research and Diagnostics Core Facility (Hodzic), School of Veterinary Medicine, University of California, Davis, CA.,California Animal Health and Food Safety Laboratory, Davis (Diab), School of Veterinary Medicine, University of California, Davis, CA.,San Bernardino (Uzal) branches, School of Veterinary Medicine, University of California, Davis, CA
| | - Emir Hodzic
- Basic and Agricultural Studies Department, Veterinary School, National University of Rio Cuarto, Rio Cuarto, Argentina (Fernandez).,Pathology Department, Veterinary School, Autonomous University of Barcelona, Barcelona, Spain (Hidalgo).,Real-time PCR Research and Diagnostics Core Facility (Hodzic), School of Veterinary Medicine, University of California, Davis, CA.,California Animal Health and Food Safety Laboratory, Davis (Diab), School of Veterinary Medicine, University of California, Davis, CA.,San Bernardino (Uzal) branches, School of Veterinary Medicine, University of California, Davis, CA
| | - Santiago S Diab
- Basic and Agricultural Studies Department, Veterinary School, National University of Rio Cuarto, Rio Cuarto, Argentina (Fernandez).,Pathology Department, Veterinary School, Autonomous University of Barcelona, Barcelona, Spain (Hidalgo).,Real-time PCR Research and Diagnostics Core Facility (Hodzic), School of Veterinary Medicine, University of California, Davis, CA.,California Animal Health and Food Safety Laboratory, Davis (Diab), School of Veterinary Medicine, University of California, Davis, CA.,San Bernardino (Uzal) branches, School of Veterinary Medicine, University of California, Davis, CA
| | - Francisco A Uzal
- Basic and Agricultural Studies Department, Veterinary School, National University of Rio Cuarto, Rio Cuarto, Argentina (Fernandez).,Pathology Department, Veterinary School, Autonomous University of Barcelona, Barcelona, Spain (Hidalgo).,Real-time PCR Research and Diagnostics Core Facility (Hodzic), School of Veterinary Medicine, University of California, Davis, CA.,California Animal Health and Food Safety Laboratory, Davis (Diab), School of Veterinary Medicine, University of California, Davis, CA.,San Bernardino (Uzal) branches, School of Veterinary Medicine, University of California, Davis, CA
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8
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Abstract
The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.
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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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10
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Teixeira MM, Barker BM. Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides. Emerg Infect Dis 2018; 22:1022-30. [PMID: 27191589 PMCID: PMC4880095 DOI: 10.3201/eid2206.151565] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Although Coccidioides genotypes are highly genetically variable,
they cluster into discrete populations, which has implications for human
infections. During the past 20 years, a general picture of the genetic diversity and population
structure of Coccidioides, the causal agent of coccidioidomycosis
(Valley fever), has emerged. The genus consists of 2 genetically diverse species,
C. immitis and C. posadasii, each of which
contains 1 or more distinct populations with limited gene flow. Genotypic data
indicate that C. immitis is divided into 2 subpopulations (central
and southern California populations) and C. posadasii is divided
into 3 subpopulations (Arizona, Mexico, and Texas/South America populations).
However, admixture within and among these populations and the current paucity of
environmental isolates limit our understanding of the population genetics of
Coccidioides. We assessed population structure of
Coccidioides in Arizona by analyzing 495 clinical and
environmental isolates. Our findings confirm the population structure as previously
described and indicate a finer scale population structure in Arizona. Environmental
isolates appear to have higher genetic diversity than isolates from human
patients.
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11
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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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Enoch DA, Yang H, Aliyu SH, Micallef C. The Changing Epidemiology of Invasive Fungal Infections. Methods Mol Biol 2017; 1508:17-65. [PMID: 27837497 DOI: 10.1007/978-1-4939-6515-1_2] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Invasive fungal infections (IFI) are an emerging problem worldwide with invasive candidiasis and candidemia responsible for the majority of cases. This is predominantly driven by the widespread adoption of aggressive immunosuppressive therapy among certain patient populations (e.g., chemotherapy, transplants) and the increasing use of invasive devices such as central venous catheters (CVCs). The use of new immune modifying drugs has also opened up an entirely new spectrum of patients at risk of IFIs. While the epidemiology of candida infections has changed in the last decade, with a gradual shift from C. albicans to non-albicans candida (NAC) strains which may be less susceptible to azoles, these changes vary between hospitals and regions depending on the type of population risk factors and antifungal use. In certain parts of the world, the incidence of IFI is strongly linked to the prevalence of other disease conditions and the ecological niche for the organism; for instance cryptococcal and pneumocystis infections are particularly common in areas with a high prevalence of HIV disease. Poorly controlled diabetes is a major risk factor for invasive mould infections. Environmental factors and trauma also play a unique role in the epidemiology of mould infections, with well-described hospital outbreaks linked to the use of contaminated instruments and devices. Blastomycosis is associated with occupational exposure (e.g., forest rangers) and recreational activities (e.g., camping and fishing).The true burden of IFI is probably an underestimate because of the absence of reliable diagnostics and lack of universal application. For example, the sensitivity of most blood culture systems for detecting candida is typically 50 %. The advent of new technology including molecular techniques such as 18S ribosomal RNA PCR and genome sequencing is leading to an improved understanding of the epidemiology of the less common mould and dimorphic fungal infections. Molecular techniques are also providing a platform for improved diagnosis and management of IFI.Many factors affect mortality in IFI, not least the underlying medical condition, choice of therapy, and the ability to achieve early source control. For instance, mortality due to pneumocystis pneumonia in HIV-seronegative individuals is now higher than in seropositive patients. Of significant concern is the progressive increase in resistance to azoles and echinocandins among candida isolates, which appears to worsen the already significant mortality associated with invasive candidiasis. Mortality with mould infections approaches 50 % in most studies and varies depending on the site, underlying disease and the use of antifungal agents such as echinocandins and voriconazole. Nevertheless, mortality for most IFIs has generally fallen with advances in medical technology, improved care of CVCs, improved diagnostics, and more effective preemptive therapy and prophylaxis.
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Affiliation(s)
- David A Enoch
- National Infection Service, Public Health England, Cambridge Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Box 236, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0QW, UK.
| | - Huina Yang
- National Infection Service, Public Health England, Cambridge Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Box 236, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0QW, UK
| | - Sani H Aliyu
- National Infection Service, Public Health England, Cambridge Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Box 236, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0QW, UK
| | - Christianne Micallef
- National Infection Service, Public Health England, Cambridge Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Box 236, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0QW, UK
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Del Rocío Reyes-Montes M, Pérez-Huitrón MA, Ocaña-Monroy JL, Frías-De-León MG, Martínez-Herrera E, Arenas R, Duarte-Escalante E. The habitat of Coccidioides spp. and the role of animals as reservoirs and disseminators in nature. BMC Infect Dis 2016; 16:550. [PMID: 27724885 PMCID: PMC5057265 DOI: 10.1186/s12879-016-1902-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 10/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coccidioidomycosis, a potentially fatal fungal infection, is considered an emergent mycotic disease because of the increased incidence of fungal infections registered over recent years. Infection occurs through the inhalation of arthroconidia from two main species of Coccidioides: Coccidioides immitis and C. posadasii, which are both endemic to arid and semi-arid regions of North America. Coccidioides species not only infect humans but can also infect other mammals (land, aquatic, wild or domestic), reptiles and birds. OBJECTIVE To obtain information regarding the habitat of Coccidioides spp. and the animals infected by this fungus and to identify the role that infected animals play as reservoirs and disseminators of this fungus in nature. MATERIALS A literature review was conducted to identify the habitat of Coccidioides spp. and the infected non-human animal species targeted by this fungus. RESULTS AND CONCLUSIONS This review allows us to suggest that Coccidioides spp. may be classified as halotolerant organisms; nevertheless, to perpetuate their life cycle, these organisms depend on different animal species (reservoirs) that serve as a link with the environment, by acting as disseminators of the fungi in nature.
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Affiliation(s)
- María Del Rocío Reyes-Montes
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Coyoacán, 04510, México Cd.Mx., Mexico
| | - María Ameyali Pérez-Huitrón
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Coyoacán, 04510, México Cd.Mx., Mexico
| | - Jorge Luis Ocaña-Monroy
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Coyoacán, 04510, México Cd.Mx., Mexico
| | - María Guadalupe Frías-De-León
- División de Investigación, Hospital Juárez de México, Edificio E. Av. Instituto Politécnico Nacional 5160, Col. Magdalena de las Salinas, 07760, México Cd.Mx., Mexico
| | - Erick Martínez-Herrera
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Coyoacán, 04510, México Cd.Mx., Mexico
| | - Roberto Arenas
- Unidad de Micología, Hospital General "Manuel Gea González", Av. Calzada de Tlalpan 4800, Tlalpan, 14080, México, Cd.Mx., Mexico
| | - Esperanza Duarte-Escalante
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Coyoacán, 04510, México Cd.Mx., Mexico.
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Kracher D, Scheiblbrandner S, Felice AKG, Breslmayr E, Preims M, Ludwicka K, Haltrich D, Eijsink VGH, Ludwig R. Extracellular electron transfer systems fuel cellulose oxidative degradation. Science 2016; 352:1098-101. [DOI: 10.1126/science.aaf3165] [Citation(s) in RCA: 257] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/15/2016] [Indexed: 01/19/2023]
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Local Population Structure and Patterns of Western Hemisphere Dispersal for Coccidioides spp., the Fungal Cause of Valley Fever. mBio 2016; 7:e00550-16. [PMID: 27118594 PMCID: PMC4850269 DOI: 10.1128/mbio.00550-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Coccidioidomycosis (or valley fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year. This infection is caused by two sibling species, Coccidioides immitis and C. posadasii, which are endemic to specific arid locales throughout the Western Hemisphere, particularly the desert southwest of the United States. Recent epidemiological and population genetic data suggest that the geographic range of coccidioidomycosis is expanding, as new endemic clusters have been identified in the state of Washington, well outside the established endemic range. The genetic mechanisms and epidemiological consequences of this expansion are unknown and require better understanding of the population structure and evolutionary history of these pathogens. Here we performed multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure in C. posadasii and demonstrate the presence of distinct geographic clades in central and southern Arizona as well as dispersed populations in Texas, Mexico, South America, and Central America. Although a smaller number of C. immitis strains were included in the analyses, some evidence of phylogeographic structure was also detected in this species, which has been historically limited to California and Baja, Mexico. Bayesian analyses indicated that C. posadasii is the more ancient of the two species and that Arizona contains the most diverse subpopulations. We propose a southern Arizona-northern Mexico origin for C. posadasii and describe a pathway for dispersal and distribution out of this region. Coccidioidomycosis, or valley fever, is caused by the pathogenic fungi Coccidioides posadasii and C. immitis. The fungal species and disease are primarily found in the American desert southwest, with spotted distribution throughout the Western Hemisphere. Initial molecular studies suggested a likely anthropogenic movement of C. posadasii from North America to South America. Here we comparatively analyze eighty-six genomes of the two Coccidioides species and establish local and species-wide population structures to not only clarify the earlier dispersal hypothesis but also provide evidence of likely ancestral populations and patterns of dispersal for the known subpopulations of C. posadasii.
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