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Camponuri SK, Heaney AK, Cooksey GS, Vugia DJ, Jain S, Swain DL, Balmes J, Remais JV, Head JR. Recent and forecasted increases in coccidioidomycosis incidence in California linked to hydroclimatic swings. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.30.24312858. [PMID: 39252900 PMCID: PMC11383451 DOI: 10.1101/2024.08.30.24312858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Coccidioidomycosis, or Valley fever, is an infectious disease caused by inhalation of Coccidioides spp., fungi found primarily in soils of the southwestern United States. Prior work showed that coccidioidomycosis cases in California sharply increase by nearly 2-fold following wet winters that occur one- and two-years following drought. Statewide drought between 2020-2022 followed by heavy precipitation during the 2022-2023 winter raised concerns over potential increases in coccidioidomycosis cases in the fall of 2023, prompting California Department of Public Health (CDPH) to issue public health alerts. As anticipated, California saw a near record number of cases in 2023, with 9,054 provisional cases reported. During the 2023-2024 California wet season, precipitation was 115% the long-term average, furthering concerns about continued high coccidioidomycosis risk. We developed an ensemble model to forecast coccidioidomycosis cases in California in 2024-2025. Using this model, we predicted a total of 11,846 cases (90% PI: 10,056-14,094) in California between April 1, 2023, and March 31, 2024, encompassing the preliminary state report of 10,593. Our model forecasted 12,244 cases statewide between April 1, 2024, and March 31, 2025 - a 62% increase over the cases reported during the same period two years prior, and on par with the high incidence seen in 2023. The Southern San Joaquin Valley (5,398 cases, 90% PI: 4,556-6,442), Southern Coast (3,322, 90% PI: 2,694-3,961), and Central Coast (1,207 cases, 90% PI: 867-1,585) regions are expected to see the largest number of infections. Our model forecasts that disease incidence will exhibit pronounced seasonality, particularly in endemic regions, with cases rising in June and peaking in November at 1,411 (90% PI: 815-2,172) cases statewide - 98% higher than the peak two years prior (714) and nearly as high as the peak in 2023 (1,462). Near-term forecasts have the potential to inform public health messaging to enhance provider and patient awareness, encourage risk reduction practices, and improve recognition and management of coccidioidomycosis.
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Affiliation(s)
- Simon K. Camponuri
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Alexandra K. Heaney
- Herbert Wertheim School of Public Health and Human Longevity, University of California, San Diego, San Diego, CA, USA
| | | | - Duc J. Vugia
- Infectious Diseases Branch, California Department of Public Health, Richmond, CA, USA
| | - Seema Jain
- Infectious Diseases Branch, California Department of Public Health, Richmond, CA, USA
| | - Daniel L. Swain
- Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
- Capacity Center for Climate and Weather Extremes, NSF National Center for Atmospheric Research, Boulder, CO, USA
| | - John Balmes
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Justin V. Remais
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer R Head
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Institute of Global Change Biology, University of Michigan, Ann Arbor, MI, USA
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Bhunjun C, Chen Y, Phukhamsakda C, Boekhout T, Groenewald J, McKenzie E, Francisco E, Frisvad J, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie C, Bai F, Błaszkowski J, Braun U, de Souza F, de Queiroz M, Dutta A, Gonkhom D, Goto B, Guarnaccia V, Hagen F, Houbraken J, Lachance M, Li J, Luo K, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe D, Wang D, Wei D, Zhao C, Aiphuk W, Ajayi-Oyetunde O, Arantes T, Araujo J, Begerow D, Bakhshi M, Barbosa R, Behrens F, Bensch K, Bezerra J, Bilański P, Bradley C, Bubner B, Burgess T, Buyck B, Čadež N, Cai L, Calaça F, Campbell L, Chaverri P, Chen Y, Chethana K, Coetzee B, Costa M, Chen Q, Custódio F, Dai Y, Damm U, Santiago A, De Miccolis Angelini R, Dijksterhuis J, Dissanayake A, Doilom M, Dong W, Álvarez-Duarte E, Fischer M, Gajanayake A, Gené J, Gomdola D, Gomes A, Hausner G, He M, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena R, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin C, Liu J, Liu X, Loizides M, Luangharn T, Maharachchikumbura S, Mkhwanazi GM, Manawasinghe I, Marin-Felix Y, McTaggart A, Moreau P, Morozova O, Mostert L, Osiewacz H, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips A, Phonemany M, Promputtha I, Rathnayaka A, Rodrigues A, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe S, Scholler M, Scott P, Shivas R, Silar P, Silva-Filho A, Souza-Motta C, Spies C, Stchigel A, Sterflinger K, Summerbell R, Svetasheva T, Takamatsu S, Theelen B, Theodoro R, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang X, Wartchow F, Welti S, Wijesinghe S, Wu F, Xu R, Yang Z, Yilmaz N, Yurkov A, Zhao L, Zhao R, Zhou N, Hyde K, Crous P. What are the 100 most cited fungal genera? Stud Mycol 2024; 108:1-411. [PMID: 39100921 PMCID: PMC11293126 DOI: 10.3114/sim.2024.108.01] [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: 02/12/2024] [Accepted: 03/17/2024] [Indexed: 08/06/2024] Open
Abstract
The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.
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Affiliation(s)
- C.S. Bhunjun
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Y.J. Chen
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - C. Phukhamsakda
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- The Yeasts Foundation, Amsterdam, the Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - E.H.C. McKenzie
- Landcare Research Manaaki Whenua, Private Bag 92170, Auckland, New Zealand
| | - E.C. Francisco
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Laboratório Especial de Micologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - V. G. Hurdeal
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Luangsa-ard
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - G. Perrone
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), Via G. Amendola 122/O, 70126 Bari, Italy
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - F.Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - J. Błaszkowski
- Laboratory of Plant Protection, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, Słowackiego 17, PL-71434 Szczecin, Poland
| | - U. Braun
- Martin Luther University, Institute of Biology, Department of Geobotany and Botanical Garden, Neuwerk 21, 06099 Halle (Saale), Germany
| | - F.A. de Souza
- Núcleo de Biologia Aplicada, Embrapa Milho e Sorgo, Empresa Brasileira de Pesquisa Agropecuária, Rodovia MG 424 km 45, 35701–970, Sete Lagoas, MG, Brazil
| | - M.B. de Queiroz
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - A.K. Dutta
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - D. Gonkhom
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B.T. Goto
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - V. Guarnaccia
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Braccini 2, 10095 Grugliasco, TO, Italy
| | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - M.A. Lachance
- Department of Biology, University of Western Ontario London, Ontario, Canada N6A 5B7
| | - J.J. Li
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - K.Y. Luo
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - F. Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
| | - S. Mongkolsamrit
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - N. Roy
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - S. Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China
| | - D.N. Wanasinghe
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - D.Q. Wang
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - D.P. Wei
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
| | - C.L. Zhao
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - W. Aiphuk
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - O. Ajayi-Oyetunde
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
| | - T.D. Arantes
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - J.C. Araujo
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
| | - D. Begerow
- Organismic Botany and Mycology, Institute of Plant Sciences and Microbiology, Ohnhorststraße 18, 22609 Hamburg, Germany
| | - M. Bakhshi
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - R.N. Barbosa
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - F.H. Behrens
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - J.D.P. Bezerra
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - P. Bilański
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - C.A. Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, USA
| | - B. Bubner
- Johan Heinrich von Thünen-Institut, Bundesforschungsinstitut für Ländliche Räume, Wald und Fischerei, Institut für Forstgenetik, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany
| | - T.I. Burgess
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
| | - B. Buyck
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 39, 75231, Paris cedex 05, France
| | - N. Čadež
- University of Ljubljana, Biotechnical Faculty, Food Science and Technology Department Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.J.S. Calaça
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
- Laboratório de Pesquisa em Ensino de Ciências (LabPEC), Centro de Pesquisas e Educação Científica, Universidade Estadual de Goiás, Campus Central (CEPEC/UEG), Anápolis, GO, 75132-903, Brazil
| | - L.J. Campbell
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - P. Chaverri
- Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, U.S.A
| | - Y.Y. Chen
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - K.W.T. Chethana
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B. Coetzee
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- School for Data Sciences and Computational Thinking, University of Stellenbosch, South Africa
| | - M.M. Costa
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.A. Custódio
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Y.C. Dai
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - A.L.C.M.A. Santiago
- Post-graduate course in the Biology of Fungi, Department of Mycology, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, 50740-465, Recife, PE, Brazil
| | | | - J. Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - A.J. Dissanayake
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - M. Doilom
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - W. Dong
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - E. Álvarez-Duarte
- Mycology Unit, Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile, Chile
| | - M. Fischer
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - A.J. Gajanayake
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Gené
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - D. Gomdola
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.A.M. Gomes
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife-PE, Brazil
| | - G. Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 5N6
| | - M.Q. He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - L. Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - I. Iturrieta-González
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
- Department of Preclinic Sciences, Medicine Faculty, Laboratory of Infectology and Clinical Immunology, Center of Excellence in Translational Medicine-Scientific and Technological Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile
| | - F. Jami
- Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
| | - R. Jankowiak
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - R.S. Jayawardena
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, South Korea
| | - H. Kandemir
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - L. Kiss
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
- Centre for Research and Development, Eszterházy Károly Catholic University, H-3300 Eger, Hungary
| | - N. Kobmoo
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - T. Kowalski
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - L. Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - C.G. Lin
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - J.K. Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - X.B. Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Temesvári krt. 62, Szeged H-6726, Hungary
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | | | - T. Luangharn
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - S.S.N. Maharachchikumbura
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - G.J. Makhathini Mkhwanazi
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - I.S. Manawasinghe
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - Y. Marin-Felix
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - A.R. McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park 4102, Queensland, Australia
| | - P.A. Moreau
- Univ. Lille, ULR 4515 - LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000 Lille, France
| | - O.V. Morozova
- Komarov Botanical Institute of the Russian Academy of Sciences, 2, Prof. Popov Str., 197376 Saint Petersburg, Russia
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - H.D. Osiewacz
- Faculty for Biosciences, Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - D. Pem
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - R. Phookamsak
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - S. Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - A. Pordel
- Plant Protection Research Department, Baluchestan Agricultural and Natural Resources Research and Education Center, AREEO, Iranshahr, Iran
| | - C. Poyntner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - A.J.L. Phillips
- Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - M. Phonemany
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - I. Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - A.R. Rathnayaka
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - G. Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - L. Rothmann
- Plant Pathology, Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa
| | - C. Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), 10300 Baltimore Avenue, Beltsville MD, 20705, USA
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - S.J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS Université de Bordeaux, 1 rue Camille Saint Saëns, 33077 Bordeaux cedex, France
| | - M. Scholler
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstraße 13, 76133 Karlsruhe, Germany
| | - P. Scott
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, Perth WA 6000, Australia
| | - R.G. Shivas
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
| | - P. Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université de Paris Cité, 75205 Paris Cedex, France
| | - A.G.S. Silva-Filho
- IFungiLab, Departamento de Ciências e Matemática (DCM), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), São Paulo, BraziI
| | - C.M. Souza-Motta
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - C.F.J. Spies
- Agricultural Research Council - Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
| | - A.M. Stchigel
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - K. Sterflinger
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Augasse 2–6, 1090, Vienna, Austria
| | - R.C. Summerbell
- Sporometrics, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - T.Y. Svetasheva
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - S. Takamatsu
- Mie University, Graduate School, Department of Bioresources, 1577 Kurima-Machiya, Tsu 514-8507, Japan
| | - B. Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.C. Theodoro
- Laboratório de Micologia Médica, Instituto de Medicina Tropical do RN, Universidade Federal do Rio Grande do Norte, 59078-900, Natal, RN, Brazil
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt Am Main, Germany
| | - N. Thongklang
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - R. Torres
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Agrobiotech de Lleida, Parc de Gardeny, 25003, Lleida, Catalonia, Spain
| | - B. Turchetti
- Department of Agricultural, Food and Environmental Sciences and DBVPG Industrial Yeasts Collection, University of Perugia, Italy
| | - T. van den Brule
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- TIFN, P.O. Box 557, 6700 AN Wageningen, the Netherlands
| | - X.W. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F. Wartchow
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Paraiba, João Pessoa, Brazil
| | - S. Welti
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - S.N. Wijesinghe
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - F. Wu
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - R. Xu
- School of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
| | - Z.L. Yang
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - L. Zhao
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.L. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - N. Zhou
- Department of Biological Sciences and Biotechnology, Botswana University of Science and Technology, Private Bag, 16, Palapye, Botswana
| | - K.D. Hyde
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht
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3
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Homer C, Ochoa E, Voorhies M, Sil A. Optimizing in vitro spherulation cues in the fungal pathogen Coccidioides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597856. [PMID: 38895214 PMCID: PMC11185734 DOI: 10.1101/2024.06.06.597856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Coccidioides spp . are part of a group of thermally dimorphic fungal pathogens, which grow as filamentous cells (hyphae) in the soil and transform to a different morphology upon inhalation into the host. The Coccidioides host form, the spherule, is unique and highly under characterized due to both technical and biocontainment challenges. Each spherule arises from an environmental spore (arthroconidium), matures, and develops hundreds of internal endospores, which are released from the spherule upon rupture. Each endospore can then go on to form another spherule in a cycle called spherulation. One of the foremost technical challenges has been reliably growing spherules in culture without the formation of contaminating hyphae, and consistently inducing endospore release from spherules. Here, we present optimization of in vitro spherule growth and endospore release, by closely controlling starting cell density in the culture, using freshly-harvested arthroconidia, and decreasing the concentration of multiple salts in spherulation media. We developed a minimal media to test spherule growth on various carbon and nitrogen sources. We defined a critical role for the dispersant Tamol in both early spherule formation and prevention of the accumulation of a visible film around spherules. Finally, we examined how the conditions under which arthroconidia are generated influence their transcriptome and subsequent development into spherules, demonstrating that this is an important variable to control when designing spherulation experiments. Together, our data reveal multiple strategies to optimize in vitro spherulation growth, enabling characterization of this virulence-relevant morphology.
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Barker BM, Thompson GR, Ampel NM. Challenges to Implementing a Vaccine for Coccidioidomycosis. Open Forum Infect Dis 2024; 11:ofae095. [PMID: 38887487 PMCID: PMC11181188 DOI: 10.1093/ofid/ofae095] [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: 11/02/2023] [Accepted: 02/20/2024] [Indexed: 06/20/2024] Open
Abstract
A vaccine for coccidioidomycosis is likely to undergo trials in the near future. In this paper, we raise 4 questions that should be answered before its use and offer our solutions to these questions. These include defining the goals of vaccination, determining who should be vaccinated, how to measure vaccine immunity and protection, and how to address vaccine hesitancy and denial.
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Affiliation(s)
- Bridget M Barker
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - George R Thompson
- Department of Medical Microbiology and Immunology, University of California at Davis, Davis, California, USA
| | - Neil M Ampel
- Departments of Medicine and Immunobiology, University of Arizona, Tucson, Arizona, USA
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5
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Williams SL, Toda M, Chiller T, Brunkard JM, Litvintseva AP. Effects of climate change on fungal infections. PLoS Pathog 2024; 20:e1012219. [PMID: 38814855 PMCID: PMC11139277 DOI: 10.1371/journal.ppat.1012219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
Affiliation(s)
- Samantha L. Williams
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mitsuru Toda
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Joan M. Brunkard
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Anastasia P. Litvintseva
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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6
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Eulálio KD, Kollath DR, Martins LMS, Filho ADD, Cavalcanti MDAS, Moreira LM, Tenório BG, Alves LGDB, Yamauchi D, Barrozo LV, Thompson Iii GR, Nacher M, Stajich JE, Benard G, Bagagli E, Felipe MSS, Barker BM, Trilles L, Teixeira MDM. Epidemiological, clinical, and genomic landscape of coccidioidomycosis in northeastern Brazil. Nat Commun 2024; 15:3190. [PMID: 38609393 PMCID: PMC11014852 DOI: 10.1038/s41467-024-47388-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Coccidioidomycosis, listed as a priority mycosis by the WHO, is endemic in the United States but often overlooked in Central and South America. Employing a multi-institutional approach, we investigate how disease characteristics, pathogen genetic variation, and environmental factors impact coccidioidomycosis epidemiology and outcomes in South America. We identified 292 cases (1978-2021) and 42 outbreaks in Piauí and Maranhão states, Brazil, the largest series outside the US/Mexico epidemic zone. The male-to-female ratio was 57.4:1 and the most common activity was armadillo hunting (91.1%) 4 to 30 days before symptom onset. Most patients (92.8%) exhibited typical acute pulmonary disease, with cough (93%), fever (90%), and chest pain (77%) as predominant symptoms. The case fatality rate was 8%. Our negative binomial regression model indicates that reduced precipitation levels in the current (p = 0.015) and preceding year (p = 0.001) predict heightened incidence. Unlike other hotspots, acidic soil characterizes this region. Brazilian strains differ genomically from other C. posadasii lineages. Northeastern Brazil presents a distinctive coccidioidomycosis profile, with armadillo hunters facing elevated risks. Low annual rainfall emerges as a key factor in increasing cases. A unique C. posadasii lineage in Brazil suggests potential differences in environmental, virulence, and/or pathogenesis traits compared to other Coccidioides genotypes.
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Affiliation(s)
- Kelsen Dantas Eulálio
- Hospital de Doenças Infecto Contagiosas-HDIC, Federal University of Piauí-UFPI, Teresina, Piauí, Brazil
| | - Daniel R Kollath
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Antonio de Deus Filho
- Hospital de Doenças Infecto Contagiosas-HDIC, Federal University of Piauí-UFPI, Teresina, Piauí, Brazil
| | | | - Lucas Machado Moreira
- Evandro Chagas National Institute of Infectology, Fiocruz - RJ, Rio de Janeiro, Brazil
| | | | | | - Danielle Yamauchi
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista/UNESP, Botucatu, Brazil
| | - Ligia Vizeu Barrozo
- Department of Geography, Faculty of Philosophy, Languages and Literature, and Human Sciences, University of São Paulo, São Paulo, Brazil
| | - George R Thompson Iii
- Department of Internal Medicine, Division of Infectious Diseases and Department of Medical Microbiology and Immunology, UC-Davis, Sacramento, CA, USA
| | - Mathieu Nacher
- Centre d'Investigations Cliniques, INSERM 1424, Centre hospitalier de Cayenne - French Guiana, Cayenne, French Guiana
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology University of California-Riverside, Riverside, CA, USA
| | - Gil Benard
- Laboratório de Micologia Medica, Departamento de Dermatologia, Instituto de Medicina Tropical, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
| | - Eduardo Bagagli
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista/UNESP, Botucatu, Brazil
| | | | - Bridget M Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Luciana Trilles
- Evandro Chagas National Institute of Infectology, Fiocruz - RJ, Rio de Janeiro, Brazil
| | - Marcus de Melo Teixeira
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
- Faculty of Medicine, University of Brasília, Brasília, Federal District, Brazil.
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7
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Hallas-Mølle M, Burow M, Henrissat B, Johansen KS. Cryptococcus neoformans: plant-microbe interactions and ecology. Trends Microbiol 2024:S0966-842X(24)00059-3. [PMID: 38519353 DOI: 10.1016/j.tim.2024.03.002] [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: 01/23/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
While the opportunistic human pathogens Cryptococcus neoformans and Cryptococcus gattii are often isolated from plants and plant-related material, evidence suggests that these Cryptococcus species do not directly infect plants. Studies find that plants are important for Cryptococcus mating and dispersal. However, these studies have not provided enough detail about how plants and these fungi interact, especially in ways that could show the fungi are capable of causing disease. This review synthesizes recent findings from studies utilizing different plant models associated with the ecology of C. neoformans and C. gattii. Unanswered questions about their environmental role are highlighted. Overall, current research indicates that Cryptococcus utilizes plants as a substrate rather than harming them, arguing against Cryptococcus as a genuine plant pathogen. We hypothesize that plants represent reservoirs that aid dispersal, not hosts vulnerable to infection.
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Affiliation(s)
- Magnus Hallas-Mølle
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Meike Burow
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kgs, Lyngby, Denmark
| | - Katja Salomon Johansen
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark.
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8
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Porter WT, Gade L, Montfort P, Mihaljevic JR, Bowers JR, Willman A, Klimowski BA, LaFleur BJ, Sunenshine RH, Collins J, Adame G, Brady S, Komatsu KK, Williams S, Toda M, Chiller T, Litvintseva AP, Engelthaler DM. Understanding the exposure risk of aerosolized Coccidioides in a Valley fever endemic metropolis. Sci Rep 2024; 14:1311. [PMID: 38225347 PMCID: PMC10789871 DOI: 10.1038/s41598-024-51407-x] [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: 07/20/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Coccidioides is the fungal causative agent of Valley fever, a primarily pulmonary disease caused by inhalation of fungal arthroconidia, or spores. Although Coccidioides has been an established pathogen for 120 years and is responsible for hundreds of thousands of infections per year, little is known about when and where infectious Coccidioides arthroconidia are present within the ambient air in endemic regions. Long-term air sampling programs provide a means to investigate these characteristics across space and time. Here we present data from > 18 months of collections from 11 air sampling sites across the Phoenix, Arizona, metropolitan area. Overall, prevalence was highly variable across space and time with no obvious spatial or temporal correlations. Several high prevalence periods were identified at select sites, with no obvious spatial or temporal associations. Comparing these data with weather and environmental factor data, wind gusts and temperature were positively associated with Coccidioides detection, while soil moisture was negatively associated with Coccidioides detection. These results provide critical insights into the frequency and distribution of airborne arthroconidia and the associated risk of inhalation and potential disease that is present across space and time in a highly endemic locale.
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Affiliation(s)
- W Tanner Porter
- Pathogen & Microbiome Division, Translational Genomics Research Institute, Flagstaff, AZ, USA.
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Parker Montfort
- Pathogen & Microbiome Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Joseph R Mihaljevic
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Jolene R Bowers
- Pathogen & Microbiome Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | | | | | - Bonnie J LaFleur
- College of Pharmacy, The University of Arizona, Phoenix, AZ, USA
| | | | | | | | - Shane Brady
- Arizona Department of Health Services, Phoenix, AZ, USA
| | | | - Samantha Williams
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mitsuru Toda
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - David M Engelthaler
- Pathogen & Microbiome Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
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9
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Ferguson AJ, Thompson GR, Bruyette D, Sykes JE. The dog as a sentinel and animal model for coccidioidomycosis. Med Mycol 2024; 62:myad139. [PMID: 38148116 DOI: 10.1093/mmy/myad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2023] Open
Abstract
Coccidioidomycosis is a potentially fatal fungal disease of humans and animals that follows inhalation of Coccidioides spp. arthroconidia in the environment. The disease in dogs resembles that in people, and because dogs may be at increased risk of exposure due to their proximity to the ground and digging behavior, they are valuable models for the disease in humans. Dogs have been sentinels for identification of new regions of endemicity in Washington and Texas. Canine serosurveillance has also been used to predict variables associated with environmental presence of Coccidioides spp. Expansion of the endemic region of coccidioidomycosis with climate change-along with predicted population increases and increased development in the southwest United States-may result in 45.4 million additional people at risk of infection by 2090. Here we provide an overview of the value of dogs as sentinels for the disease and encourage the routine reporting of coccidioidomycosis cases in dogs to public health agencies. We also highlight the value of dogs as naturally occurring models for studying novel treatment options and preventatives, such as a novel live avirulent coccidioidomycosis vaccine.
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Affiliation(s)
- Adam J Ferguson
- Department of Biological Sciences, University of California-San Diego, La Jolla, USA
| | - George R Thompson
- Department of Internal Medicine - Division of Infectious Diseases, University of California-Davis, Davis, USA
| | | | - Jane E Sykes
- Department of Medicine & Epidemiology, University of California-Davis, Davis, USA
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10
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Chashchina MV, Sadovnikova SS, Chesalina YO, Briginevich VE, Bagirov MA. [Differential diagnosis of coccidioidomycosis manifested by peripheral pulmonary lesion]. Khirurgiia (Mosk) 2024:77-85. [PMID: 39140947 DOI: 10.17116/hirurgia202408177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
We present this clinical case as a demonstration of difficulties in differential diagnosis of pulmonary coccidioidomycosis. Differential diagnostics of peripheral pulmonary lesion performed using bronchoscopy with BAL and TBCB and video-assisted thoracic surgery (VATS) biopsy. Diagnostic specimens were tested using microbiological (luminescent microscopy, culture for M. tuberculosis (BACTEC MGIT960 and Lowenstein-Jensen Medium), RT-PCR, cytological and morphological (hematoxylin-eosin, Ziehl-Neelsen, PAS, Grocott methenamine silver (GMS) stainings) examinations. A diagnosis was verified correctly In Russia the country is not endemic for coccidioidomycosis and patient was treated accordingly. Diagnostics of peripheral pulmonary lesions requires of multidisciplinary approaches. Morphological examination, based on detection of only granulomatous inflammation in lung biopsy cannot be used for finally DS and requires microbiological confirmation for TB or other infections, and dynamic monitoring of the patient with concordance their anamnesis vitae and morbi.
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Affiliation(s)
| | - S S Sadovnikova
- Central TB Research Institute (CTRI), Moscow, Russia
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | | | | | - M A Bagirov
- Central TB Research Institute (CTRI), Moscow, Russia
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
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11
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Smith DJ, Gold JAW, Benedict K, Wu K, Lyman M, Jordan A, Medina N, Lockhart SR, Sexton DJ, Chow NA, Jackson BR, Litvintseva AP, Toda M, Chiller T. Public Health Research Priorities for Fungal Diseases: A Multidisciplinary Approach to Save Lives. J Fungi (Basel) 2023; 9:820. [PMID: 37623591 PMCID: PMC10455901 DOI: 10.3390/jof9080820] [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: 07/07/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023] Open
Abstract
Fungal infections can cause severe disease and death and impose a substantial economic burden on healthcare systems. Public health research requires a multidisciplinary approach and is essential to help save lives and prevent disability from fungal diseases. In this manuscript, we outline the main public health research priorities for fungal diseases, including the measurement of the fungal disease burden and distribution and the need for improved diagnostics, therapeutics, and vaccines. Characterizing the public health, economic, health system, and individual burden caused by fungal diseases can provide critical insights to promote better prevention and treatment. The development and validation of fungal diagnostic tests that are rapid, accurate, and cost-effective can improve testing practices. Understanding best practices for antifungal prophylaxis can optimize prevention in at-risk populations, while research on antifungal resistance can improve patient outcomes. Investment in vaccines may eliminate certain fungal diseases or lower incidence and mortality. Public health research priorities and approaches may vary by fungal pathogen.
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Affiliation(s)
- Dallas J. Smith
- Mycotic Diseases Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (J.A.W.G.); (K.B.); (K.W.); (M.L.); (A.J.); (N.M.); (S.R.L.); (D.J.S.); (N.A.C.); (B.R.J.); (A.P.L.); (M.T.)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Tom Chiller
- Mycotic Diseases Branch, Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (J.A.W.G.); (K.B.); (K.W.); (M.L.); (A.J.); (N.M.); (S.R.L.); (D.J.S.); (N.A.C.); (B.R.J.); (A.P.L.); (M.T.)
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12
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Phillips S, Jones I, Sondermyer-Cooksey G, Yu AT, Heaney AK, Zhou B, Bhattachan A, Weaver AK, Campo SK, Mgbara W, Wagner R, Taylor J, Lettenmaier D, Okin GS, Jain S, Vugia D, Remais JV, Head JR. Association between wildfires and coccidioidomycosis incidence in California, 2000-2018: a synthetic control analysis. Environ Epidemiol 2023; 7:e254. [PMID: 37545805 PMCID: PMC10402968 DOI: 10.1097/ee9.0000000000000254] [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: 02/03/2023] [Accepted: 05/04/2023] [Indexed: 08/08/2023] Open
Abstract
The frequency and severity of wildfires in the Western United States have increased over recent decades, motivating hypotheses that wildfires contribute to the incidence of coccidioidomycosis, an emerging fungal disease in the Western United States with sharp increases in incidence observed since 2000. While coccidioidomycosis outbreaks have occurred among wildland firefighters clearing brush, it remains unknown whether fires are associated with an increased incidence among the general population. Methods We identified 19 wildfires occurring within California's highly endemic San Joaquin Valley between 2003 and 2015. Using geolocated surveillance records, we applied a synthetic control approach to estimate the effect of each wildfire on the incidence of coccidioidomycosis among residents that lived within a hexagonal buffer of 20 km radii surrounding the fire. Results We did not detect excess cases due to wildfires in the 12 months (pooled estimated percent change in cases: 2.8%; 95% confidence interval [CI] = -29.0, 85.2), 13-24 months (7.9%; 95% CI = -27.3, 113.9), or 25-36 months (17.4%; 95% CI = -25.1, 157.1) following a wildfire. When examined individually, we detected significant increases in incidence following three of the 19 wildfires, all of which had relatively large adjacent populations, high transmission before the fire, and a burn area exceeding 5,000 acres. Discussion We find limited evidence that wildfires drive increases in coccidioidomycosis incidence among the general population. Nevertheless, our results raise concerns that large fires in regions with ongoing local transmission of Coccidioides may be associated with increases in incidence, underscoring the need for field studies examining Coccidioides spp. in soils and air pre- and post-wildfires.
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Affiliation(s)
- Sophie Phillips
- Department of Statistics, University of California, Los Angeles, Los Angeles, California
| | - Isabel Jones
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California
| | | | - Alexander T. Yu
- Infectious Diseases Branch, California Department of Public Health, Richmond, California
| | - Alexandra K. Heaney
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California
| | - Bo Zhou
- Department of Geography, University of California, Los Angeles, Los Angeles, California
| | | | - Amanda K. Weaver
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California
| | - Simon K. Campo
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California
| | - Whitney Mgbara
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California
| | - Robert Wagner
- Department of Plant and Microbial Biology, College of Natural Resources, University of California, Berkeley, Berkeley, California
| | - John Taylor
- Department of Plant and Microbial Biology, College of Natural Resources, University of California, Berkeley, Berkeley, California
| | - Dennis Lettenmaier
- Department of Geography, University of California, Los Angeles, Los Angeles, California
| | - Gregory S. Okin
- Department of Geography, University of California, Los Angeles, Los Angeles, California
| | - Seema Jain
- Infectious Diseases Branch, California Department of Public Health, Richmond, California
| | - Duc Vugia
- Infectious Diseases Branch, California Department of Public Health, Richmond, California
| | - Justin V. Remais
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California
| | - Jennifer R. Head
- Department of Statistics, University of California, Los Angeles, Los Angeles, California
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California
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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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Laux K, Teixeira MDM, Barker B. Love in the time of climate change: A review of sexual reproduction in the order Onygenales. Fungal Genet Biol 2023; 167:103797. [PMID: 37100376 DOI: 10.1016/j.fgb.2023.103797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 02/02/2023] [Accepted: 04/03/2023] [Indexed: 04/28/2023]
Abstract
Life-threatening infections caused by fungi in the order Onygenales have been rising over the last few decades. Increasing global temperature due to anthropogenic climate change is one potential abiotic selection pressure that may explain the increase in infections. The generation of genetically novel offspring with novel phenotypes through the process of sexual recombination could allow fungi to adapt to changing climate conditions. The basic structures associated with sexual reproduction have been identified in Histoplasma, Blastomyces, Malbranchea, and Brunneospora. However, for Coccidioides and Paracoccidioides, the actual structural identification of these processes has yet to be identified despite having genetic evidence that suggests sexual recombination is occurring in these organisms. This review highlights the importance of assessing sexual recombination in the order Onygenales as a means of understanding the mechanisms these organisms might employ to enhance fitness in the face of a changing climate and provides details regarding the known reproductive mechanisms in the Onygenales.
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Affiliation(s)
- Klaire Laux
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Bldg 56 Ste 210, Flagstaff, AZ 86011, USA.
| | - Marcus de Melo Teixeira
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Bldg 56 Ste 210, Flagstaff, AZ 86011, USA; Nùcleo de Medicina Tropical, University of Brasilia, Universitário Darcy Ribeiro, s/n -Asa Norte, Brasília, DF 70910-900, Brazil
| | - Bridget Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Bldg 56 Ste 210, Flagstaff, AZ 86011, USA.
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15
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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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16
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Abstract
Coccidioides immitis, a pathogenic environmental fungus that causes Valley fever (coccidioidomycosis) primarily in the American Southwest and parts of Central and South America, has emerged over the past 12 years in the Columbia River Basin region, near the confluence with the Yakima River, in southcentral Washington state, USA. An initial autochthonous Washington human case was found in 2010, stemming from a wound derived from soil contamination during an all-terrain vehicle crash. Subsequent analysis identified multiple positive soil samples from the park where the crash occurred (near the Columbia River in Kennewick, WA), and from another riverside location several kilometers upstream from the park location. Intensified disease surveillance identified several more cases of coccidioidomycosis in the region that lacked any relevant travel history to known endemic locales. Genomic analysis of both patient and soil isolates from the Washington cases determined that all samples from the region are phylogenetically closely related. Given the genomic and the epidemiological link between case and environment, C. immitis was declared to be a newly endemic fungus in the region, spawning many questions as to the scope of its presence, the causes of its recent emergence, and what it predicts about the changing landscape of this disease. Here, we review this discovery through a paleo-epidemiological lens in the context of what is known about C. immitis biology and pathogenesis and propose a novel hypothesis for the cause of the emergence in southcentral Washington. We also try to place it in the context of our evolving understanding of this regionally specific pathogenic fungus.
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17
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Dubin CA, Voorhies M, Sil A, Teixeira MM, Barker BM, Brem RB. Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii. J Fungi (Basel) 2022; 8:jof8121235. [PMID: 36547568 PMCID: PMC9782707 DOI: 10.3390/jof8121235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
The human fungal pathogen Coccidioides spp. causes valley fever, a treatment-refractory and sometimes deadly disease prevalent in arid regions of the western hemisphere. Fungal virulence in the mammalian host hinges on a switch between growth as hyphae and as large spherules containing infectious spores. How these virulence programs are encoded in the genome remains poorly understood. Drawing on Coccidioides genomic resources, we first discovered a new facet of genome organization in this system: spherule-gene islands, clusters of genes physically linked in the genome that exhibited specific mRNA induction in the spherule phase. Next, we surveyed copy-number variation genome-wide among strains of C. posadasii. Emerging from this catalog were spherule-gene islands with striking presence-absence differentiation between C. posadasii populations, a pattern expected from virulence factors subjected to different selective pressures across habitats. Finally, analyzing single-nucleotide differences across C. posadasii strains, we identified signatures of natural selection in spherule-expressed genes. Together, our data establish spherule-gene islands as candidate determinants of virulence and targets of selection in Coccidioides.
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Affiliation(s)
- Claire A. Dubin
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720-3102, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, UC San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Department of Microbiology and Immunology, UC San Francisco, San Francisco, CA 94143, USA
| | - Marcus M. Teixeira
- The Translational Genomics Research Institute (TGen)-Affiliate of City of Hope, Flagstaff, AZ 85004, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Bridget M. Barker
- The Translational Genomics Research Institute (TGen)-Affiliate of City of Hope, Flagstaff, AZ 85004, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Rachel B. Brem
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720-3102, USA
- Correspondence:
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18
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Head JR, Sondermeyer-Cooksey G, Heaney AK, Yu AT, Jones I, Bhattachan A, Campo SK, Wagner R, Mgbara W, Phillips S, Keeney N, Taylor J, Eisen E, Lettenmaier DP, Hubbard A, Okin GS, Vugia DJ, Jain S, Remais JV. Effects of precipitation, heat, and drought on incidence and expansion of coccidioidomycosis in western USA: a longitudinal surveillance study. Lancet Planet Health 2022; 6:e793-e803. [PMID: 36208642 PMCID: PMC10189771 DOI: 10.1016/s2542-5196(22)00202-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Drought is an understudied driver of infectious disease dynamics. Amidst the ongoing southwestern North American megadrought, California (USA) is having the driest multi-decadal period since 800 CE, exacerbated by anthropogenic warming. In this study, we aimed to examine the influence of drought on coccidioidomycosis, an emerging infectious disease in southwestern USA. METHODS We analysed California census tract-level surveillance data from 2000 to 2020 using generalised additive models and distributed monthly lags on precipitation and temperature. We then developed an ensemble prediction algorithm of incident cases of coccidioidomycosis per census tract to estimate the counterfactual incidence that would have occurred in the absence of drought. FINDINGS Between April 1, 2000, and March 31, 2020, there were 81 448 reported cases of coccidioidomycosis throughout California. An estimated 1467 excess cases of coccidioidomycosis were observed in California in the 2 years following the drought that occurred between 2007 and 2009, and an excess 2649 drought-attributable cases of coccidioidomycosis were observed in the 2 years following the drought that occurred between 2012 and 2015. These increased numbers of cases more than offset the declines in cases that occurred during drought. An IQR increase in summer temperatures was associated with 2·02 (95% CI 1·84-2·22) times higher incidence in the following autumn (September to November), and an IQR increase in precipitation in the winter was associated with 1·45 (1·36-1·55) times higher incidence in the autumn. The effect of winter precipitation was 36% (25-48) stronger when preceded by two dry, rather than average, winters. Incidence in arid counties was most sensitive to precipitation fluctuations, while incidence in wetter counties was most sensitive to temperature. INTERPRETATION In California, multi-year cycles of dry conditions followed by a wet winter increases transmission of coccidioidomycosis, especially in historically wetter areas. With anticipated increasing frequency of drought in southwestern USA, continued expansion of coccidioidomycosis, along with more intense seasons, is expected. Our results motivate the need for heightened precautions against coccidioidomycosis in seasons that follow major droughts. FUNDING National Institutes of Health.
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Affiliation(s)
- Jennifer R Head
- Division of Epidemiology, University of California, Berkeley, Berkeley, CA, USA; Division of Environmental Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Alexandra K Heaney
- Division of Environmental Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Alexander T Yu
- Infectious Disease Branch, California Department of Public Health, Richmond, CA, USA
| | - Isabel Jones
- Division of Environmental Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Simon K Campo
- Division of Environmental Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Robert Wagner
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Whitney Mgbara
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Sophie Phillips
- College of Letters and Science, University of California, Berkeley, Berkeley, CA, USA
| | - Nicole Keeney
- Division of Environmental Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - John Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ellen Eisen
- Division of Environmental Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Alan Hubbard
- Division of Biostatistics, University of California, Berkeley, Berkeley, CA, USA
| | - Gregory S Okin
- Department of Geography, University of California, Berkeley, Berkeley, CA, USA
| | - Duc J Vugia
- Infectious Disease Branch, California Department of Public Health, Richmond, CA, USA
| | - Seema Jain
- Infectious Disease Branch, California Department of Public Health, Richmond, CA, USA
| | - Justin V Remais
- Division of Environmental Health Sciences, University of California, Berkeley, Berkeley, CA, USA.
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Wagner R, Montoya L, Gao C, Head JR, Remais J, Taylor JW. The air mycobiome is decoupled from the soil mycobiome in the California San Joaquin Valley. Mol Ecol 2022; 31:4962-4978. [PMID: 35933707 PMCID: PMC9624177 DOI: 10.1111/mec.16640] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 07/21/2022] [Accepted: 08/01/2022] [Indexed: 01/07/2023]
Abstract
Dispersal is a key force in the assembly of fungal communities and the air is the dominant route of dispersal for most fungi. Understanding the dynamics of airborne fungi is important for determining their source and for helping to prevent fungal disease. This understanding is important in the San Joaquin Valley of California, which is home to 4.2 million people and where the airborne fungus Coccidioides is responsible for the most important fungal disease of otherwise healthy humans, coccidioidomycosis. The San Joaquin Valley is the most productive agricultural region in the United States, with the principal crops grown therein susceptible to fungal pathogens. Here, we characterize the fungal community in soil and air on undeveloped and agricultural land in the San Joaquin Valley using metabarcoding of the internal transcribed spacer 2 variable region of fungal rDNA. Using 1,002 individual samples, we report one of the most extensive studies of fungi sampled simultaneously from air and soil using modern sequencing techniques. We find that the air mycobiome in the San Joaquin Valley is distinct from the soil mycobiome, and that the assemblages of airborne fungi from sites as far apart as 160 km are far more similar to one another than to the fungal communities in nearby soils. Additionally, we present evidence that airborne fungi in the San Joaquin Valley are subject to dispersal limitation and cyclical intra-annual patterns of community composition. Our findings are broadly applicable to understanding the dispersal of airborne fungi and the taxonomic structure of airborne fungal assemblages.
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Affiliation(s)
- Robert Wagner
- Department of Plant & Microbial BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Liliam Montoya
- Department of Plant & Microbial BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Cheng Gao
- Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Jennifer R. Head
- Division of EpidemiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Justin Remais
- Division of Environmental Health SciencesUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - John W. Taylor
- Department of Plant & Microbial BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
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20
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Salazar-Hamm PS, Montoya KN, Montoya L, Cook K, Liphardt S, Taylor JW, Cook JA, Natvig DO. Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:996574. [PMID: 37746221 PMCID: PMC10512277 DOI: 10.3389/ffunb.2022.996574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/24/2022] [Indexed: 09/26/2023]
Abstract
Human lung mycobiome studies typically sample bronchoalveolar lavage or sputum, potentially overlooking fungi embedded in tissues. Employing ultra-frozen lung tissues from biorepositories, we obtained fungal ribosomal RNA ITS2 sequences from 199 small mammals across 39 species. We documented diverse fungi, including common environmental fungi such as Penicillium and Aspergillus, associates of the human mycobiome such as Malassezia and Candida, and others specifically adapted for lungs (Coccidioides, Blastomyces, and Pneumocystis). Pneumocystis sequences were detected in 83% of the samples and generally exhibited phylogenetic congruence with hosts. Among sequences from diverse opportunistic pathogens in the Onygenales, species of Coccidioides occurred in 12% of samples and species of Blastomyces in 85% of samples. Coccidioides sequences occurred in 14 mammalian species. The presence of neither Coccidioides nor Aspergillus fumigatus correlated with substantial shifts in the overall mycobiome, although there was some indication that fungal communities might be influenced by high levels of A. fumigatus. Although members of the Onygenales were common in lung samples (92%), they are not common in environmental surveys. Our results indicate that Pneumocystis and certain Onygenales are common commensal members of the lung mycobiome. These results provide new insights into the biology of lung-inhabiting fungi and flag small mammals as potential reservoirs for emerging fungal pathogens.
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Affiliation(s)
| | - Kyana N. Montoya
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Liliam Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Kel Cook
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Schuyler Liphardt
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Joseph A. Cook
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, United States
| | - Donald O. Natvig
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
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21
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Phylogenomic Placement of American Southwest-Associated Clinical and Veterinary Isolates Expands Evidence for Distinct Cryptococcus gattii VGVI. Microorganisms 2022; 10:microorganisms10081681. [PMID: 36014098 PMCID: PMC9412296 DOI: 10.3390/microorganisms10081681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Whole-genome sequencing has advanced our understanding of the population structure of the pathogenic species complex Cryptococcus gattii, which has allowed for the phylogenomic specification of previously described major molecular type groupings and novel lineages. Recently, isolates collected in Mexico in the 1960s were determined to be genetically distant from other known molecular types and were classified as VGVI. We sequenced four clinical isolates and one veterinary isolate collected in the southwestern United States and Argentina from 2012 to 2021. Phylogenomic analysis groups these genomes with those of the Mexican VGVI isolates, expanding VGVI into a clade and establishing this molecular type as a clinically important population. These findings also potentially expand the known Cryptococcus ecological range with a previously unrecognized endemic area.
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22
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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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Coccidioides Species: A Review of Basic Research: 2022. J Fungi (Basel) 2022; 8:jof8080859. [PMID: 36012847 PMCID: PMC9409882 DOI: 10.3390/jof8080859] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Coccidioides immitis and posadasii are closely related fungal species that cause coccidioidomycosis. These dimorphic organisms cause disease in immunocompetent as well as immunocompromised individuals and as much as 40% of the population is infected in the endemic area. Although most infections resolve spontaneously, the infection can be prolonged and, in some instances, fatal. Coccidioides has been studied for more than 100 years and many aspects of the organism and the disease it causes have been investigated. There are over 500 manuscripts concerning Coccidioides (excluding clinical articles) referenced in PubMed over the past 50 years, so there is a large body of evidence to review. We reviewed the most accurate and informative basic research studies of these fungi including some seminal older studies as well as an extensive review of current research. This is an attempt to gather the most important basic research studies about this fungus into one publication. To focus this review, we will discuss the mycology of the organism exclusively rather than the studies of the host response or clinical studies. We hope that this review will be a useful resource to those interested in Coccidioides and coccidioidomycosis.
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Coccidioidomycosis (Valley Fever), Soil Moisture, and El Nino Southern Oscillation in California and Arizona. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19127262. [PMID: 35742514 PMCID: PMC9223181 DOI: 10.3390/ijerph19127262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/03/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
The soil-borne fungal disease coccidioidomycosis (Valley fever) is prevalent across the southwestern United States (US). Previous studies have suggested that the occurrence of this infection is associated with anomalously wet or dry soil moisture states described by the "grow and blow" hypothesis. The growth of coccidioidomycosis is favored by moist conditions both at the surface and in the root zone. A statistical analysis identified two areas in Arizona and central California, with a moderate-to-high number of coccidioidomycosis cases. A Wavelet Transform Coherence (WTC) analysis between El Nino Southern Oscillation (ENSO), coccidioidomycosis cases, surface soil moisture (SSM; 0 to 5 cm) from European Space Agency-Climate Change Initiative (ESA-CCI), and shallow root zone soil moisture (RZSM; 0 to 40 cm depth) from Soil MERGE (SMERGE) was executed for twenty-four CA and AZ counties. In AZ, only SSM was modulated by ENSO. When case values were adjusted for overreporting between 2009 to 2012, a moderate but significant connection between ENSO and cases was observed at a short periodicity (2.1 years). In central CA, SSM, RZSM, and cases all had a significant link to ENSO at longer periodicities (5-to-7 years). This study provides an example of how oceanic-atmospheric teleconnections can impact human health.
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Boro R, Iyer PC, Walczak MA. Current Landscape of Coccidioidomycosis. J Fungi (Basel) 2022; 8:413. [PMID: 35448644 PMCID: PMC9027852 DOI: 10.3390/jof8040413] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/13/2022] [Indexed: 02/06/2023] Open
Abstract
Coccidioidomycosis, also known as Valley fever, is an endemic fungal infection commonly found in the southwestern parts of the United States. However, the disease has seen an increase in both in its area of residency and its prevalence. This review compiles some of the latest information on the epidemiology, current and in-development pharmaceutical approaches to treat the disease, trends and projections, diagnostic concerns, and the overlapping dynamics of coccidioidomycosis and COVID-19, including in special populations. This review provides an overview of the current diagnostic and therapeutic strategies and identifies areas of future development.
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Affiliation(s)
- Ryan Boro
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA;
| | - Prema C. Iyer
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA;
| | - Maciej A. Walczak
- Department of Chemistry, University of Colorado, Boulder, CO 80309, USA
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26
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Comrie AC. No Consistent Link Between Dust Storms and Valley Fever (Coccidioidomycosis). GEOHEALTH 2021; 5:e2021GH000504. [PMID: 34877441 PMCID: PMC8628988 DOI: 10.1029/2021gh000504] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/06/2021] [Accepted: 11/10/2021] [Indexed: 05/04/2023]
Abstract
Dust storms, such as those associated with haboobs and strong regional winds, are frequently assumed to cause increases in cases of Valley fever (coccidioidomycosis). The disease is caused by inhaling arthroconidia of Coccidioides fungi that, after being disturbed from semi-desert subsoil, have become airborne. Fungal arthroconidia can be transported in low-wind conditions as well as in individual dust events, but there is no reliable evidence that all or most dust storms consistently lead to subsequent increases in coccidioidomycosis cases. Following a review of the relevant literature, this study examines the relationship between dust storms and coccidioidomycosis cases to determine if there is a consistent and general association between them. All recorded dust storms from 2006 to 2020 in and near the Phoenix area of Maricopa County, Arizona and the Bakersfield area of Kern County, California were used in a compositing analysis (superposed epoch analysis) of subsequent coccidioidomycosis cases in each area. Analyses of monthly and weekly disease case data showed no statistical differences in the patterns of coccidioidomycosis cases following dust storms versus non-dust storm conditions, for the entire data set as well as for seasonal subsets of the data. This study thoroughly analyzes post-dust storm coccidioidomycosis cases for a large set of dust storms, and it confirms and expands upon previous literature, including a recent study that measured airborne arthroconidia and found no consistent links connecting wind and dust conditions to increases in coccidioidomycosis.
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Abstract
Coccidioides immitis and Coccidioides posadasii are causative agents of Valley fever, a serious fungal disease endemic to regions with hot, arid climate in the United States, Mexico, and Central and South America. The environmental niche of Coccidioides spp. is not well defined, and it remains unknown whether these fungi are primarily associated with rodents or grow as saprotrophs in soil. To better understand the environmental reservoir of these pathogens, we used a systematic soil sampling approach, quantitative PCR (qPCR), culture, whole-genome sequencing, and soil chemical analysis to identify factors associated with the presence of C. immitis at a known colonization site in Washington State linked to a human case in 2010. We found that the same strain colonized an area of over 46,000 m2 and persisted in soil for over 6 years. No association with rodent burrows was observed, as C. immitis DNA was as likely to be detected inside rodent holes as it was in the surrounding soil. In addition, the presence of C. immitis DNA in soil was correlated with elevated levels of boron, calcium, magnesium, sodium, and silicon in soil leachates. We also observed differences in the microbial communities between C. immitis-positive and -negative soils. Our artificial soil inoculation experiments demonstrated that C. immitis can use soil as a sole source of nutrients. Taken together, these results suggest that soil parameters need to be considered when modeling the distribution of this fungus in the environment. IMPORTANCE Coccidioidomycosis is considered a highly endemic disease for which geographic range is likely to expand from climate change. A better understanding of the ecological niche of Coccidioides spp. is essential for generating accurate distribution maps and predicting future changes in response to the changing environment. Our study used a systematic sampling strategy, advanced molecular detection methods, and soil chemical analysis to identify environmental factors associated with the presence of C. immitis in soil. Our results demonstrate the fungus can colonize the same areas for years and is associated with chemical and microbiological soil characteristics. Our results suggest that in addition to climate parameters, soil characteristics need to be considered when building habitat distribution models for this pathogen.
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28
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Carey A, Gorris ME, Chiller T, Jackson B, Beadles W, Webb BJ. Epidemiology, Clinical Features, and Outcomes of Coccidioidomycosis, Utah, 2006-2015. Emerg Infect Dis 2021; 27:2269-2277. [PMID: 34423764 PMCID: PMC8386810 DOI: 10.3201/eid2709.210751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
On the basis of a 1957 geographic Coccidioides seropositivity survey, 3 counties in southwestern Utah, USA, were considered coccidioidomycosis-endemic, but there has been a paucity of information on the disease burden in Utah since. We report findings from a recent clinical and epidemiologic study of coccidioidomycosis in Utah. To describe clinical characteristics, we identified all coccidioidomycosis cases in an integrated health system in the state during 2006-2015. For epidemiologic analysis, we used cases reported to the Utah Department of Health during 2009-2015. Mean state incidence was 1.83 cases/100,000 population/year. Washington County, in southwestern Utah, had the highest incidence, 17.2 cases/100,000 population/year. In a generalized linear model with time as a fixed effect, mean annual temperature, population, and new construction were associated with regional variations in incidence. Using these variables in a spatiotemporal model, we estimated the adjusted regional variation by county to predict areas where Coccidioides infections might increase.
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29
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Gorris ME, Caballero Van Dyke MC, Carey A, Hamm PS, Mead HL, Uehling JK. A Review of Coccidioides Research, Outstanding Questions in the Field, and Contributions by Women Scientists. CURRENT CLINICAL MICROBIOLOGY REPORTS 2021; 8:114-128. [PMID: 34367880 PMCID: PMC8327307 DOI: 10.1007/s40588-021-00173-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 12/19/2022]
Abstract
Purpose of Review Coccidioidomycosis is an infectious disease that gained clinical significance in the early 20th century. Many of the foundational contributions to coccidioidomycosis research, including the discovery of the fungal disease agent, Coccidioides spp., were made by women. We review recent progress in Coccidioides research and big questions remaining in the field, while highlighting some of the contributions from women. Recent Findings New molecular-based techniques provide a promising method for detecting Coccidioides, which can help determine the dominate reservoir host and ideal environmental conditions for growth. Genetic and genomic analyses have allowed an understanding of population structure, species level diversity, and evolutionary histories. We present a current, comprehensive genome list, where women contributed many of these entries. Several efforts to develop a coccidioidomycosis vaccine are underway. Summary Women continue to pioneer research on Coccidioides, including the relationships between the fungi and the environment, genetics, and clinical observations. Significant questions remain in the field of Coccidioides, including the main host reservoir, the relationships between genotypic and phenotypic variation, and the underlying cause for chronic clinical coccidioidomycosis cases.
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Affiliation(s)
- Morgan E Gorris
- Los Alamos National Laboratory, Information Systems and Modeling & Center for Nonlinear Studies, Los Alamos, NM USA
| | | | - Adrienne Carey
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Paris S Hamm
- Department of Biology, University of New Mexico, Albuquerque, NM USA
| | - Heather L Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ USA
| | - Jessie K Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR USA
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30
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Raza N, Nasrawi F, Heidari A, Kuran R, Amin N, Johnson R. Coccidioidal Hepatic Abscess in a Patient With Disseminated Coccidioidomycosis: A Case Report. J Investig Med High Impact Case Rep 2021; 9:23247096211033051. [PMID: 34311612 PMCID: PMC8320554 DOI: 10.1177/23247096211033051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Coccidioidomycosis is an infection caused by inhalation of arthroconidia of Coccidioides. Forty percent of patients will develop mild and self-limited respiratory infection, and a small fraction of these individuals will develop extrapulmonary disseminated disease. This is the case of a patient with a known history of disseminated coccidioidomycosis, who initially presented for symptoms of persistent pneumonia. On evaluation, the patient was found to have a hepatic abscess for which he underwent percutaneous drainage. Culture grew Coccidioides immitis, and the patient was treated with systemic antifungal. This is a rare case of disseminated coccidioidomycosis in the liver.
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Affiliation(s)
| | | | - Arash Heidari
- Kern Medical, Bakersfield, CA, USA.,Valley Fever Institute, Bakersfield, CA, USA
| | - Rasha Kuran
- Kern Medical, Bakersfield, CA, USA.,Valley Fever Institute, Bakersfield, CA, USA
| | | | - Royce Johnson
- Kern Medical, Bakersfield, CA, USA.,Valley Fever Institute, Bakersfield, CA, USA
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31
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de Melo Teixeira M, Lang BF, Matute DR, Stajich JE, Barker BM. Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii. G3 (BETHESDA, MD.) 2021; 11:jkab132. [PMID: 33871031 PMCID: PMC8496281 DOI: 10.1093/g3journal/jkab132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/25/2021] [Indexed: 12/25/2022]
Abstract
Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation in nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify 14 mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.
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Affiliation(s)
- Marcus de Melo Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Faculty of Medicine, University of Brasília-DF, Brasília, Federal District 70910-3300, Brazil
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Génomiques, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jason E Stajich
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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Using soil survey data to model potential Coccidioides soil habitat and inform Valley fever epidemiology. PLoS One 2021; 16:e0247263. [PMID: 33606807 PMCID: PMC7894876 DOI: 10.1371/journal.pone.0247263] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 11/19/2022] Open
Abstract
Coccidioidomycosis, also known as Valley fever, is a disease that can result in substantial illness and death. It is most common in the southwestern United States and areas of Latin America with arid climates, though reports increasingly suggest its range is wider than previously recognized. The natural habitat of the causative organisms, Coccidioides spp., have been associated with certain soil properties and climatic conditions. Current understanding of its geographic range is primarily defined by skin test studies and outbreak locations. We developed a fuzzy system model to predict suitable soil habitats for Coccidioides across the western United States based on parameters (electrical conductivity, organic matter content, pH, water holding capacity, temperature, and precipitation) from sites where soil sampling has confirmed the presence of Coccidioides. The model identified high coccidioidomycosis incidence areas as having high suitability and identified pockets of elevated suitability corresponding with outbreak locations outside the traditional range. By providing high-resolution estimates of Coccidioides suitability, including areas without public health surveillance for coccidioidomycosis, this model may be able to aid public health and clinical provider decision making. Awareness of possible Coccidioides soil habitats could help mitigate risk during soil-disturbing activities and help providers improve coccidioidomycosis diagnosis and treatment.
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33
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Endemic and Other Dimorphic Mycoses in The Americas. J Fungi (Basel) 2021; 7:jof7020151. [PMID: 33672469 PMCID: PMC7923431 DOI: 10.3390/jof7020151] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 12/14/2022] Open
Abstract
Endemic fungi are thermally dimorphic fungi that have a limited geographic range and can cause both primary disease and opportunistic infections. The Americas are home to more genera of endemic fungi than anywhere else on earth. These include Coccidioides, Histoplasma, Blastomyces, Paracoccidioides, and Sporothrix. Endemic fungi are found across the Americas and the Caribbean, from Blastomyces gilchristi, which extends into the northeast corners of North America, to Histoplasma capsulatum, which occurs all the way down in the southern regions of South America and into the Caribbean Islands. Symptoms of endemic fungal infection, when present, mimic those of many other diseases and are often diagnosed only after initial treatment for a bacterial or viral disease has failed. Endemic fungi place a significant medical burden on the populations they affect, especially in immunocompromised individuals and in resource-limited settings. This review summarizes the ecology, geographical range, epidemiology, and disease forms of the endemic fungi found in the Americas. An emphasis is placed on new and proposed taxonomic changes, including the assignment of new species names in Histoplasma, Blastomyces, and Paracoccidioides.
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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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Abstract
Coccidioidomycosis is a fungal infection of the Western hemisphere that is endemic to the soil in areas with limited rainfall. Human and animal infections result with inhalation of arthroconidia. Most often, this is an asymptomatic event. When illness occurs, it is primarily a pneumonic presentation. A small minority of infections eventuate in disseminated disease. Predominately, this presents as meningitis or osteoarticular or integumentary disease. Treatment may not be required for the mildest illness. Azoles are commonly prescribed. Severe infections may require amphotericin B.
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Affiliation(s)
- Royce H Johnson
- Infectious Diseases, Kern Medical Center, Bakersfield, California, USA.,Valley Fever Institute, Bakersfield, California, USA
| | - Rupam Sharma
- Infectious Diseases, Kern Medical Center, Bakersfield, California, USA.,Valley Fever Institute, Bakersfield, California, USA
| | - Rasha Kuran
- Infectious Diseases, Kern Medical Center, Bakersfield, California, USA.,Valley Fever Institute, Bakersfield, California, USA
| | - Isabel Fong
- Infectious Diseases, Kern Medical Center, Bakersfield, California, USA.,Valley Fever Institute, Bakersfield, California, USA
| | - Arash Heidari
- Infectious Diseases, Kern Medical Center, Bakersfield, California, USA .,Valley Fever Institute, Bakersfield, California, USA
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Danesi P, Falcaro C, Schmertmann LJ, de Miranda LHM, Krockenberger M, Malik R. Cryptococcus in Wildlife and Free-Living Mammals. J Fungi (Basel) 2021; 7:jof7010029. [PMID: 33419125 PMCID: PMC7825559 DOI: 10.3390/jof7010029] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/22/2020] [Accepted: 01/01/2021] [Indexed: 12/21/2022] Open
Abstract
Cryptococcosis is typically a sporadic disease that affects a broad range of animal species globally. Disease is a consequence of infection with members of the Cryptococcus neoformans or Cryptococcus gattii species complexes. Although cryptococcosis in many domestic animals has been relatively well-characterized, free-living wildlife animal species are often neglected in the literature outside of occasional case reports. This review summarizes the clinical presentation, pathological findings and potential underlying causes of cryptococcosis in various other animals, including terrestrial wildlife species and marine mammals. The evaluation of the available literature supports the hypothesis that anatomy (particularly of the respiratory tract), behavior and environmental exposures of animals play vital roles in the outcome of host–pathogen–environment interactions resulting in different clinical scenarios. Key examples range from koalas, which exhibit primarily C. gattii species complex disease presumably due to their behavior and environmental exposure to eucalypts, to cetaceans, which show predominantly pulmonary lesions due to their unique respiratory anatomy. Understanding the factors at play in each clinical scenario is a powerful investigative tool, as wildlife species may act as disease sentinels.
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Affiliation(s)
- Patrizia Danesi
- Laboratory of Parasitology, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padua, Italy;
- Correspondence:
| | - Christian Falcaro
- Laboratory of Parasitology, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padua, Italy;
| | - Laura J. Schmertmann
- Veterinary Pathology Diagnostic Services, Sydney School of Veterinary Science, The University of Sydney, Sydney 2006, Australia; (L.J.S.); (L.H.M.d.M.); (M.K.)
| | - Luisa Helena Monteiro de Miranda
- Veterinary Pathology Diagnostic Services, Sydney School of Veterinary Science, The University of Sydney, Sydney 2006, Australia; (L.J.S.); (L.H.M.d.M.); (M.K.)
| | - Mark Krockenberger
- Veterinary Pathology Diagnostic Services, Sydney School of Veterinary Science, The University of Sydney, Sydney 2006, Australia; (L.J.S.); (L.H.M.d.M.); (M.K.)
| | - Richard Malik
- Centre for Veterinary Education, The University of Sydney, Sydney 2006, Australia;
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Human Fungal Pathogens: Diversity, Genomics, and Preventions. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Mead HL, Hamm PS, Shaffer IN, Teixeira MDM, Wendel CS, Wiederhold NP, Thompson GR, Muñiz-Salazar R, Castañón-Olivares LR, Keim P, Plude C, Terriquez J, Galgiani JN, Orbach MJ, Barker BM. Differential Thermotolerance Adaptation between Species of Coccidioides. J Fungi (Basel) 2020; 6:E366. [PMID: 33327629 PMCID: PMC7765126 DOI: 10.3390/jof6040366] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/24/2020] [Accepted: 12/05/2020] [Indexed: 12/18/2022] Open
Abstract
Coccidioidomycosis, or Valley fever, is caused by two species of dimorphic fungi. Based on molecular phylogenetic evidence, the genus Coccidioides contains two reciprocally monophyletic species: C. immitis and C. posadasii. However, phenotypic variation between species has not been deeply investigated. We therefore explored differences in growth rate under various conditions. A collection of 39 C. posadasii and 46 C. immitis isolates, representing the full geographical range of the two species, was screened for mycelial growth rate at 37 °C and 28 °C on solid media. The radial growth rate was measured for 16 days on yeast extract agar. A linear mixed effect model was used to compare the growth rate of C. posadasii and C. immitis at 37 °C and 28 °C, respectively. C. posadasii grew significantly faster at 37 °C, when compared to C. immitis; whereas both species had similar growth rates at 28 °C. These results indicate thermotolerance differs between these two species. As the ecological niche has not been well-described for Coccidioides spp., and disease variability between species has not been shown, the evolutionary pressure underlying the adaptation is unclear. However, this research reveals the first significant phenotypic difference between the two species that directly applies to ecological research.
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Affiliation(s)
- Heather L. Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (H.L.M.); (P.K.)
| | - Paris S. Hamm
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Isaac N. Shaffer
- School of Informatics, Computers, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA;
| | | | | | - Nathan P. Wiederhold
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 77030, USA;
| | - George R. Thompson
- Departments of Internal Medicine Division of Infectious Diseases, and Medical Microbiology and Immunology, University of California-Davis, Sacramento, CA 95616, USA;
| | - Raquel Muñiz-Salazar
- Laboratorio de Epidemiología y Ecología Molecular, Escuela Ciencias de la Salud, Universidad Autónoma de Baja California, Unidad Valle Dorado, Ensenada 22890, Mexico;
| | - Laura Rosio Castañón-Olivares
- Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Mexico, Ciudad de México 04510, Mexico;
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (H.L.M.); (P.K.)
| | - Carmel Plude
- Northern Arizona Healthcare, Flagstaff, AZ 86001, USA; (C.P.); (J.T.)
| | - Joel Terriquez
- Northern Arizona Healthcare, Flagstaff, AZ 86001, USA; (C.P.); (J.T.)
| | - John N. Galgiani
- Valley Fever Center for Excellence, University of Arizona, Tucson, AZ 85721, USA; (J.N.G.); (M.J.O.)
| | - Marc J. Orbach
- Valley Fever Center for Excellence, University of Arizona, Tucson, AZ 85721, USA; (J.N.G.); (M.J.O.)
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (H.L.M.); (P.K.)
- Valley Fever Center for Excellence, University of Arizona, Tucson, AZ 85721, USA; (J.N.G.); (M.J.O.)
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Ampel NM. Coccidioidomycosis: Changing Concepts and Knowledge Gaps. J Fungi (Basel) 2020; 6:jof6040354. [PMID: 33321746 PMCID: PMC7770576 DOI: 10.3390/jof6040354] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Although first described more than 120 years ago, much remains unknown about coccidioidomycosis. In this review, new information that has led to changing concepts will be reviewed and remaining gaps in our knowledge will be discussed. In particular, new ideas regarding ecology and epidemiology, problems and promises of diagnosis, controversies over management, and the possibility of a vaccine will be covered.
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Affiliation(s)
- Neil M Ampel
- Department of Infectious Diseases, Medicine and Immunobiology University of Arizona, 1501 North Campbell Avenue, Tucson, AZ 85724, USA
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Ocampo-Chavira P, Eaton-Gonzalez R, Riquelme M. Of Mice and Fungi: Coccidioides spp. Distribution Models. J Fungi (Basel) 2020; 6:jof6040320. [PMID: 33261168 PMCID: PMC7712536 DOI: 10.3390/jof6040320] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 12/25/2022] Open
Abstract
The continuous increase of Coccidioidomycosis cases requires reliable detection methods of the causal agent, Coccidioides spp., in its natural environment. This has proven challenging because of our limited knowledge on the distribution of this soil-dwelling fungus. Knowing the pathogen’s geographic distribution and its relationship with the environment is crucial to identify potential areas of risk and to prevent disease outbreaks. The maximum entropy (Maxent) algorithm, Geographic Information System (GIS) and bioclimatic variables were combined to obtain current and future potential distribution models (DMs) of Coccidioides and its putative rodent reservoirs for Arizona, California and Baja California. We revealed that Coccidioides DMs constructed with presence records from one state are not well suited to predict distribution in another state, supporting the existence of distinct phylogeographic populations of Coccidioides. A great correlation between Coccidioides DMs and United States counties with high Coccidioidomycosis incidence was found. Remarkably, under future scenarios of climate change and high concentration of greenhouse gases, the probability of habitat suitability for Coccidioides increased. Overlap analysis between the DMs of rodents and Coccidioides, identified Neotoma lepida as one of the predominant co-occurring species in all three states. Considering rodents DMs would allow to implement better surveillance programs to monitor disease spread.
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Affiliation(s)
- Pamela Ocampo-Chavira
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, Baja California 22860, Mexico;
| | - Ricardo Eaton-Gonzalez
- Academic Unit of Ensenada, Universidad Tecnológica de Tijuana, Ctra. a la Bufadora KM. 1, Maneadero Parte Alta, Ensenada, Baja California 22790, Mexico;
| | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, Baja California 22860, Mexico;
- Correspondence:
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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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Mead HL, Van Dyke MCC, Barker BM. Proper Care and Feeding of Coccidioides: A Laboratorian's Guide to Cultivating the Dimorphic Stages of C. immitis and C. posadasii. CURRENT PROTOCOLS IN MICROBIOLOGY 2020; 58:e113. [PMID: 32894648 PMCID: PMC9976608 DOI: 10.1002/cpmc.113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Coccidioidomycosis ("Valley fever") is caused by Coccidioides immitis and C. posadasii. These fungi are thermally dimorphic, cycling between mycelia and arthroconidia in the environment and converting into spherules and endospores within a host. Coccidioides can cause a broad spectrum of disease that can be difficult to treat. There has been a steady increase in disease, with an estimated 350,000 new infections per year in the United States. With the increase in disease and difficulty in treatment, there is an unmet need to increase research in basic biology and identify new treatments, diagnostics, and vaccine candidates. Here, we describe protocols required in any Coccidioides laboratory, such as growing, harvesting, and storing the different stages of this dimorphic fungal pathogen. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Growth and harvest of liquid mycelia cultures for extractions Alternate Protocol 1: Large-volume growth and harvest of liquid mycelia cultures Basic Protocol 2: Mycelial growth on solid medium Alternate Protocol 2: Maintaining mycelial growth on solid medium Basic Protocol 3: Harvesting and quantification of arthroconidia Alternate Protocol 3: Long-term storage of arthroconidia Basic Protocol 4: Parasitic spherule growth and harvest Alternate Protocol 4: Obtaining endospores from spherules Basic Protocol 5: Intranasal infection of murine models.
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Affiliation(s)
- Heather L. Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | | | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona,Corresponding author:
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Hamm PS, Taylor JW, Cook JA, Natvig DO. Decades-old studies of fungi associated with mammalian lungs and modern DNA sequencing approaches help define the nature of the lung mycobiome. PLoS Pathog 2020; 16:e1008684. [PMID: 32730326 PMCID: PMC7392203 DOI: 10.1371/journal.ppat.1008684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Paris S. Hamm
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Joseph A. Cook
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Donald O. Natvig
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- * E-mail:
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Lauer A, Etyemezian V, Nikolich G, Kloock C, Arzate AF, Sadiq Batcha F, Kaur M, Garcia E, Mander J, Kayes Passaglia A. Valley Fever: Environmental Risk Factors and Exposure Pathways Deduced from Field Measurements in California. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17155285. [PMID: 32707996 PMCID: PMC7432779 DOI: 10.3390/ijerph17155285] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/16/2020] [Accepted: 07/19/2020] [Indexed: 12/28/2022]
Abstract
Coccidioidomycosis, also known as Valley fever, has been reported among military personnel in Coccidioides-endemic areas of the southwestern United States since World War II. In this study, the prevalence of Coccidioides was confirmed in different soil and dust samples collected near three military bases in California using DNA extraction and Polymerase Chain Reaction (PCR) methods. Analyses of physical and chemical parameters revealed no significant differences between Coccidioides-positive and -negative sites. Soil samples collected in the Mojave Desert (near Twentynine Palms MCAGCC) showed the highest percentage of Coccidioides-positive soil and dust samples. Samples from the San Joaquin Valley (near NAS Lemoore) showed the lowest percentage of positive samples and were restricted to remnants of semi-natural areas between agricultural fields. Our results suggest that soil disturbance around all three military bases investigated poses a potential Coccidioides exposure risk for military personnel and the public. We conclude that once lands have been severely disturbed from their original state, they become less suitable for Coccidioides growth. We propose a conceptual framework for understanding exposure where disturbance of soils that exhibit natural or remnants of native vegetation (Creosote and Salt Bush) generate a high risk of exposure to the pathogen, likely during dry periods. In contrast, Coccidioides-positive sites, when undisturbed, will not pose a high risk of exposure.
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Affiliation(s)
- Antje Lauer
- Department of Biology, California State University Bakersfield (CSUB), Bakersfield, CA 93311-1022, USA; (C.K.); (A.F.A.); (F.S.B.); (M.K.); (E.G.); (J.M.); (A.K.P.)
- Correspondence:
| | - Vicken Etyemezian
- Desert Research Institute (DRI), Las Vegas, NV 89119, USA; (V.E.); (G.N.)
| | - George Nikolich
- Desert Research Institute (DRI), Las Vegas, NV 89119, USA; (V.E.); (G.N.)
| | - Carl Kloock
- Department of Biology, California State University Bakersfield (CSUB), Bakersfield, CA 93311-1022, USA; (C.K.); (A.F.A.); (F.S.B.); (M.K.); (E.G.); (J.M.); (A.K.P.)
| | - Angel Franco Arzate
- Department of Biology, California State University Bakersfield (CSUB), Bakersfield, CA 93311-1022, USA; (C.K.); (A.F.A.); (F.S.B.); (M.K.); (E.G.); (J.M.); (A.K.P.)
| | - Fazalath Sadiq Batcha
- Department of Biology, California State University Bakersfield (CSUB), Bakersfield, CA 93311-1022, USA; (C.K.); (A.F.A.); (F.S.B.); (M.K.); (E.G.); (J.M.); (A.K.P.)
| | - Manpreet Kaur
- Department of Biology, California State University Bakersfield (CSUB), Bakersfield, CA 93311-1022, USA; (C.K.); (A.F.A.); (F.S.B.); (M.K.); (E.G.); (J.M.); (A.K.P.)
| | - Eduardo Garcia
- Department of Biology, California State University Bakersfield (CSUB), Bakersfield, CA 93311-1022, USA; (C.K.); (A.F.A.); (F.S.B.); (M.K.); (E.G.); (J.M.); (A.K.P.)
| | - Jasleen Mander
- Department of Biology, California State University Bakersfield (CSUB), Bakersfield, CA 93311-1022, USA; (C.K.); (A.F.A.); (F.S.B.); (M.K.); (E.G.); (J.M.); (A.K.P.)
| | - Alyce Kayes Passaglia
- Department of Biology, California State University Bakersfield (CSUB), Bakersfield, CA 93311-1022, USA; (C.K.); (A.F.A.); (F.S.B.); (M.K.); (E.G.); (J.M.); (A.K.P.)
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Lauer A, Lopez J, Abarca S, Bains J. Earthquake-Ridden Area in USA Contains Coccidioides, the Valley Fever Pathogen. ECOHEALTH 2020; 17:248-254. [PMID: 32666206 DOI: 10.1007/s10393-020-01485-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/15/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
Early July 2019, two major earthquakes occurred in the Mojave Desert of California near the city of Ridgecrest and the community of Trona and generated a large dust plume that lingered for days. The earthquakes hit an area endemic for Coccidioides, a soil-borne fungal pathogen that can become airborne when soil is disturbed and typically manifests as a pulmonary disease when inhaled. This study is the first to confirm the presence of Coccidioides in soils near Trona using a nested polymerase chain reaction (PCR) approach. First responders to earthquake events, the public, and physicians in the San Joaquin Valley and the Mojave Desert should be informed about the risk of pathogen exposure during and after the time of an earthquake, since there are many fault lines in addition to the large San Andreas Fault and future earthquakes in this region are expected to occur.
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Affiliation(s)
- Antje Lauer
- Department of Biology, California State University Bakersfield, 9001 Stockdale Highway, Bakersfield, CA, 93311-1022, USA.
| | - Jocelyne Lopez
- Department of Biology, California State University Bakersfield, 9001 Stockdale Highway, Bakersfield, CA, 93311-1022, USA
| | - Stephanie Abarca
- Department of Biology, California State University Bakersfield, 9001 Stockdale Highway, Bakersfield, CA, 93311-1022, USA
| | - Jasmeet Bains
- Omni Family Health Clinic, Taft Health Center, 4th Street, Taft, CA, 93268, 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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Coelho C, Farrer RA. Pathogen and host genetics underpinning cryptococcal disease. ADVANCES IN GENETICS 2020; 105:1-66. [PMID: 32560785 DOI: 10.1016/bs.adgen.2020.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cryptococcosis is a severe fungal disease causing 220,000 cases of cryptococcal meningitis yearly. The etiological agents of cryptococcosis are taxonomically grouped into at least two species complexes belonging to the genus Cryptococcus. All of these yeasts are environmentally ubiquitous fungi (often found in soil, leaves and decaying wood, tree hollows, and associated with bird feces especially pigeon guano). Infection in a range of animals including humans begins following inhalation of spores or aerosolized yeasts. Recent advances provide fundamental insights into the factors from both the pathogen and its hosts which influence pathogenesis and disease. The complex interactions leading to disease in mammalian hosts have also updated from the availability of better genomic tools and datasets. In this review, we discuss recent genetic research on Cryptococcus, covering the epidemiology, ecology, and evolution of Cryptococcus pathogenic species. We also discuss the insights into the host immune response obtained from the latest genetic modified host models as well as insights from monogenic disorders in humans. Finally we highlight outstanding questions that can be answered in the near future using bioinformatics and genomic tools.
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Affiliation(s)
- Carolina Coelho
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - Rhys A Farrer
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom.
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Van Dyke MCC, Teixeira MM, Barker BM. Fantastic yeasts and where to find them: the hidden diversity of dimorphic fungal pathogens. Curr Opin Microbiol 2019; 52:55-63. [PMID: 31181385 PMCID: PMC11227906 DOI: 10.1016/j.mib.2019.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 11/29/2022]
Abstract
Dimorphic fungal pathogens are a significant cause of human disease worldwide. Notably, the dimorphic fungal pathogens within the order Onygenales are considered primary pathogens, causing disease in healthy hosts. Current changes in taxonomy are underway due to advances in molecular phylogenetics, population genetics, and new emerging dimorphic fungal pathogens causing human disease. In this review, we highlight evolutionary relationships of dimorphic fungal pathogens that cause human disease within the order Onygenales and provide rationale to support increased investment in studies understanding the evolutionary relationships of these pathogens to improve rapid diagnostics, help identify mechanisms of antifungal resistance, understand adaptation to human host, and factors associated with virulence.
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Affiliation(s)
| | - Marcus M Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States; Faculty of Medicine, University of Brasília, Brasília-DF, Brazil
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States.
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Abstract
We discovered a new lineage of the globally important fungal pathogen Cryptococcus gattii on the basis of analysis of six isolates collected from three locations spanning the Central Miombo Woodlands of Zambia, Africa. All isolates were from environments (middens and tree holes) that are associated with a small mammal, the African hyrax. Phylogenetic and population genetic analyses confirmed that these isolates form a distinct, deeply divergent lineage, which we name VGV. VGV comprises two subclades (A and B) that are capable of causing mild lung infection with negligible neurotropism in mice. Comparing the VGV genome to previously identified lineages of C. gattii revealed a unique suite of genes together with gene loss and inversion events. However, standard URA5 restriction fragment length polymorphism (RFLP) analysis could not distinguish between VGV and VGIV isolates. We therefore developed a new URA5 RFLP method that can reliably identify the newly described lineage. Our work highlights how sampling understudied ecological regions alongside genomic and functional characterization can broaden our understanding of the evolution and ecology of major global pathogens.IMPORTANCE Cryptococcus gattii is an environmental pathogen that causes severe systemic infection in immunocompetent individuals more often than in immunocompromised humans. Over the past 2 decades, researchers have shown that C. gattii falls within four genetically distinct major lineages. By combining field work from an understudied ecological region (the Central Miombo Woodlands of Zambia, Africa), genome sequencing and assemblies, phylogenetic and population genetic analyses, and phenotypic characterization (morphology, histopathological, drug-sensitivity, survival experiments), we discovered a hitherto unknown lineage, which we name VGV (variety gattii five). The discovery of a new lineage from an understudied ecological region has far-reaching implications for the study and understanding of fungal pathogens and diseases they cause.
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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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