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10/2/2018 Endemic and Other Mycoses : Genetics, Evolutionary Biology, Environment John Taylor UC Berkeley [email protected] Endemic and Other Mycoses : Genetics, Evolutionary Biology, Environment John Taylor, Rachel Adams, Cheng Gao, Bridget Barker UC Berkeley, Northern Arizona University, TGen 1 10/2/2018 Where are the agents of endemic mycoses? Basidiomycota - Cryptococcus Ascomycota – Taphrinomycotina - Pneumocystis Ascomycota – Saccharomycotina - Candida Ascomycota – Pezizomycota – Eurotiomycetes Eurotiales - Aspergillus Ascomycota – Pezizomycota – Eurotiomycetes Onygenales – Endemic Mycoses Where are the agents of endemic mycoses? Basidiomycota - Cryptococcus Ascomycota – Taphrinomycotina - Pneumocystis Ascomycota – Saccharomycotina - Candida Ascomycota – Pezizomycota – Eurotiomycetes Eurotiales - Aspergillus Ascomycota – Pezizomycota – Eurotiomycetes Onygenales – Endemic Mycoses 2 10/2/2018 Muñoz et al. 2018. Scientific Reports Coccidioides DOI:10.1038/s41598-018-22816-6 Histoplasma Onygenales Blastomyces Paracoccidioides Coccidioides Aspergillus Muñoz et al. 2018. Scientific Reports Coccidioides DOI:10.1038/s41598-018-22816-6 Histoplasma Onygenales Blastomyces Paracoccidioides Coccidioides Aspergillus 3 10/2/2018 Muñoz et al. 2018. Scientific Reports Coccidioides DOI:10.1038/s41598-018-22816-6 Histoplasma Onygenales Blastomyces Paracoccidioides Coccidioides Aspergillus What is coccidioidomycosis? Healthy Infected www.emedicine.com 4 10/2/2018 What is coccidioidomycosis and why should we care? Distribution of Coccidioides species Hector and Laniado-Laborin 2005. PLoSMedicine What is coccidioidomycosis and why should we care? California Arizona https://www.cdc.gov/fungal/diseases/coccidioidomycosis/statistics.html 5 10/2/2018 What is coccidioidomycosis and why should we care? Cooksey et al. 2017 MMWR August 11, 2017 / 66(31);833–834 2016 California What is coccidioidomycosis and why should we care? https://www.cdph.ca.gov/Programs/CID/DCDC/CDPH%20Document%20Library/CocciEpiSummary2017.pdf 2017 6 10/2/2018 7 10/2/2018 Move from the patient to the environment. Move from the patient to the environment. Diagnostics. How dangerous is this job? Do I need a respirator? 8 10/2/2018 Move from the patient to the environment. Diagnostics. How dangerous is this job? Do I need a respirator? Pharmaceuticals. Is this area so dangerous that I need to take antifungals prophylactically? 9 10/2/2018 10 10/2/2018 Today’s Question: What is the role, if any, of native mammals in the life cycle of Coccidioides? 11 10/2/2018 Background Small mammals 1942 Chester W. Emmons 12 10/2/2018 Granuloma in mouse lung 1942 Ashburn and Emmons 1942. Archives of Pathology 34:791-800. 1942 Emmons and Ashburn, 1942 Pocket Mouse 13% 17% Kangaroo Rat 13 10/2/2018 1943 C. W. EMMONS . it may be primarily a disease of rodents . certain species of rodents constitute a natural reservoir of coccidioidomycosis and by their geographical distribution determine the areas of endemicity of the disease. / / / 14 10/2/2018 15 10/2/2018 Coccidioides immitis in the soil of the southern San Joaquin Valley. Roger O. Egeberg and Ann Frank Ely 1956 American Journal of the Medical Sciences, February 1956, 151-4 Coccidioides immitis in the soil of the southern San Joaquin Valley. Roger O. Egeberg and Ann Frank Ely 1956 American Journal of the Medical Sciences, February 1956, 151-4 16 10/2/2018 Growth patterns of Coccidioides immitis in the soil of an endemic area. Ann Frank Elconin, Roger O. Egeberg and Robert Lubarsky 1957 In: Ajello, L. et al. 1957. Proc. Symp. Coccidioidomycosis. Public Health Service Publication 575. Total 428 31 7.4% Growth patterns of Coccidioides immitis in the soil of an endemic area. Ann Frank Elconin, Roger O. Egeberg and Robert Lubarsky 1957 In: Ajello, L. et al. 1957. Proc. Symp. Coccidioidomycosis. Public Health Service Publication 575. 17 10/2/2018 Growth patterns of Coccidioides immitis in the soil of an endemic area. Ann Frank Elconin, Roger O. Egeberg and Robert Lubarsky 1957 In: Ajello, L. et al. 1957. Proc. Symp. Coccidioidomycosis. Public Health Service Publication 575. 18 10/2/2018 Ecological studies of Coccidioides immitis. Orda A. Plunkett and F. E. Swatek 1957 In: Ajello, L. et al. 1957. Proc. Symp. Coccidioidomycosis. Public Health Service Publication 575. May 1954, coccidioidomycosis found in 5 UCLA anthropology students excavating an Native American midden. Ecological studies of Coccidioides immitis. Orda A. Plunkett and F. E. Swatek 1957 In: Ajello, L. et al. 1957. Proc. Symp. Coccidioidomycosis. Public Health Service Publication 575. May 1954, coccidioidomycosis found in 5 UCLA anthropology students excavating an Native American midden. Soil Samples from the midden were positive. 19 10/2/2018 Ecological studies of Coccidioides immitis. Orda A. Plunkett and F. E. Swatek 1957 In: Ajello, L. et al. 1957. Proc. Symp. Coccidioidomycosis. Public Health Service Publication 575. May 1954, coccidioidomycosis found in 5 UCLA anthropology students excavating an Native American midden. Soil Samples from the midden were positive. 80 burrow samples taken near the midden – all negative. Ecological studies of Coccidioides immitis. Orda A. Plunkett and F. E. Swatek 1957 In: Ajello, L. et al. 1957. Proc. Symp. Coccidioidomycosis. Public Health Service Publication 575. May 1954, coccidioidomycosis found in 5 UCLA anthropology students excavating an Native American midden. Soil Samples from the midden were positive. 80 burrow samples taken near the midden – all negative. 440 pocket mice and kangaroo rats captured near the midden -- all negative. 20 10/2/2018 1957-2018 Studies of physical parameters. Climate: temperature, water and wind Soil Climate: California 2000 Morbidity caused by C. immitis was best explained by the interaction between two variables, the lengths of droughts and the amounts of rainfall preceding epidemics. Fisher MC et al. 2000 J. Clin Microbiol 38:807-813 21 10/2/2018 Climate: California Relative change 2000 in cocci morbidity Morbidity caused by C. immitis was best explained by the interaction between two variables, the lengths of droughts and the amounts of rainfall preceding epidemics. Fisher MC et al. 2000 J. Clin Microbiol 38:807-813 Climate: California Relative change 2000 in cocci morbidity Morbidity caused by Model based on length of drought and mean annual C. immitis was best rainfall in the preceding year explained by the interaction between two variables, the lengths of droughts and the amounts of rainfall preceding epidemics. Fisher MC et al. 2000 J. Clin Microbiol 38:807-813 22 10/2/2018 Climate: California & Arizona 2017 GeoHealth 1, 51–63 (2017) The results indicate that in both states, coccidioidomycosis incidence is related to soil moisture levels from previous summers and falls. Climate Coccidioides Soil 23 10/2/2018 Climate Coccidioides Soil Climate Coccidioides Soil Cocci has to eat. 24 10/2/2018 Background Fungal Nutrition de.wikipedia.org http://www.botanicalgarden.ubc.ca/potd/2007/07/xylaria_hypoxylon_tentative.php crampball.html /fungi/ siegelr /~ web.stanford.edu http:// Ascomycota, Pezizomycotina 25 10/2/2018 2009 Evolution of Gene Family Size Eurotiales Onygenales Sordariomycetes Sharpton, Stajich et al. 2009. Genome Research Gene Family Reductions: 2009 Genes coding enzymes that digest plants https://www.123rf.com/photo_27279678_dried-out-dead-plants-lying-in-a-dry-arid-desert-environment.html Sharpton, Stajich et al. 2009. Genome Research 26 10/2/2018 Keratin, hair, skin & connective tissue Rock Pocket Mouse http://www.snipview.com/q/Rock%20pocket%20mouse www.privemillenia.com Gene Family Reductions: 2009 Genes coding enzymes that digest animals Perognathus longimembris Sharpton, Stajich et al. 2009. Genome Research Jonah Evans, Texas. Parks and Wildlife Department, http://www.inaturalist.org/photos/407437 27 10/2/2018 de.wikipedia.org http://www.botanicalgarden.ubc.ca/potd/2007/07/xylaria_hypoxylon_tentative.php crampball.html /fungi/ siegelr /~ web.stanford.edu http:// Ascomycota, Pezizomycotina Ecology Many fungi are endophytes, they live in their plant hosts without causing apparent disease. When the leaf, stem or plant dies, the fungus becomes active, consumes the dead plant and reproduces. 28 10/2/2018 de.wikipedia.org http://www.botanicalgarden.ubc.ca/potd/2007/07/xylaria_hypoxylon_tentative.php crampball.html /fungi/ siegelr /~ web.stanford.edu http:// Ascomycota, Pezizomycotina Ecology Many fungi are endophytes, they live in their plant hosts without causing apparent disease. When the leaf, stem or plant dies, the fungus becomes active, consumes the dead plant and reproduces. Hypothesis, Coccidioides spp. are Endozoans, they live in their natural animal hosts without causing apparent disease. When the animal dies, the fungus becomes active, consumes the dead animal and reproduces. 29 10/2/2018 Climate Coccidioides Soil Cocci has to eat. Climate Coccidioides Soil Animal 30 10/2/2018 Climate Coccidioides Soil Animal Climate Coccidioides Soil Animals have to eat. Animal 31 10/2/2018 Climate Coccidioides Soil Plant Animal Climate Coccidioides Soil Plant Animal 32 10/2/2018 Climate Coccidioides Soil Plant Animal 33 10/2/2018 Avenal Maricopa California State Hwy 33 34 10/2/2018 California State Hwy 33 The CocciDx assay* Coccidioides-Specific PCR Assay Targeting a Transposable Element *CocciENV Assay. Bowers et al. 2018 Med Mycol doi: 10.1093/mmy/myy007 35 10/2/2018 Avenal Coccidioides detected in burrows at all sites Maricopa Avenal Coccidioides detected at surface at two sites Maricopa 36 10/2/2018
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  • Culture Inventory

    Culture Inventory

    For queries, contact the SFA leader: John Dunbar - [email protected] Fungal collection Putative ID Count Ascomycota Incertae sedis 4 Ascomycota Incertae sedis 3 Pseudogymnoascus 1 Basidiomycota Incertae sedis 1 Basidiomycota Incertae sedis 1 Capnodiales 29 Cladosporium 27 Mycosphaerella 1 Penidiella 1 Chaetothyriales 2 Exophiala 2 Coniochaetales 75 Coniochaeta 56 Lecythophora 19 Diaporthales 1 Prosthecium sp 1 Dothideales 16 Aureobasidium 16 Dothideomycetes incertae sedis 3 Dothideomycetes incertae sedis 3 Entylomatales 1 Entyloma 1 Eurotiales 393 Arthrinium 2 Aspergillus 172 Eladia 2 Emericella 5 Eurotiales 2 Neosartorya 1 Paecilomyces 13 Penicillium 176 Talaromyces 16 Thermomyces 4 Exobasidiomycetes incertae sedis 7 Tilletiopsis 7 Filobasidiales 53 Cryptococcus 53 Fungi incertae sedis 13 Fungi incertae sedis 12 Veroneae 1 Glomerellales 1 Glomerella 1 Helotiales 34 Geomyces 32 Helotiales 1 Phialocephala 1 Hypocreales 338 Acremonium 20 Bionectria 15 Cosmospora 1 Cylindrocarpon 2 Fusarium 45 Gibberella 1 Hypocrea 12 Ilyonectria 13 Lecanicillium 5 Myrothecium 9 Nectria 1 Pochonia 29 Purpureocillium 3 Sporothrix 1 Stachybotrys 3 Stanjemonium 2 Tolypocladium 1 Tolypocladium 2 Trichocladium 2 Trichoderma 171 Incertae sedis 20 Oidiodendron 20 Mortierellales 97 Massarineae 2 Mortierella 92 Mortierellales 3 Mortiererallales 2 Mortierella 2 Mucorales 109 Absidia 4 Backusella 1 Gongronella 1 Mucor 25 RhiZopus 13 Umbelopsis 60 Zygorhynchus 5 Myrmecridium 2 Myrmecridium 2 Onygenales 4 Auxarthron 3 Myceliophthora 1 Pezizales 2 PeZiZales 1 TerfeZia 1