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Tracking a Global Threat: a New Genotyping Method for Candida auris.

Cuomo CA, Alanio A.

mBio. 2020 Mar 10;11(2). pii: e00259-20. doi: 10.1128/mBio.00259-20.


Diversity and Complexity of the Large Surface Protein Family in the Compacted Genomes of Multiple Pneumocystis Species.

Ma L, Chen Z, Huang DW, Cissé OH, Rothenburger JL, Latinne A, Bishop L, Blair R, Brenchley JM, Chabé M, Deng X, Hirsch V, Keesler R, Kutty G, Liu Y, Margolis D, Morand S, Pahar B, Peng L, Van Rompay KKA, Song X, Song J, Sukura A, Thapar S, Wang H, Weissenbacher-Lang C, Xu J, Lee CH, Jardine C, Lempicki RA, Cushion MT, Cuomo CA, Kovacs JA.

mBio. 2020 Mar 3;11(2). pii: e02878-19. doi: 10.1128/mBio.02878-19.


Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase.

Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cooke S, Shea T, Gienger E, Lintner R, Yates JR 3rd, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD.

Cell. 2020 Feb 20;180(4):816. doi: 10.1016/j.cell.2020.02.006. No abstract available.


Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase.

Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cooke S, Shea T, Gienger E, Lintner R, Yates JR 3rd, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD.

Cell. 2020 Jan 23;180(2):263-277.e20. doi: 10.1016/j.cell.2019.12.012. Epub 2020 Jan 16. Erratum in: Cell. 2020 Feb 20;180(4):816.


Complete Genome Sequences for Two Talaromyces marneffei Clinical Isolates from Northern and Southern Vietnam.

Cuomo CA, Shea T, Nguyen T, Ashton P, Perfect J, Le T.

Microbiol Resour Announc. 2020 Jan 9;9(2). pii: e01367-19. doi: 10.1128/MRA.01367-19.


Human Blastomycosis in South Africa Caused by Blastomyces percursus and Blastomyces emzantsi sp. nov., 1967 to 2014.

Maphanga TG, Birkhead M, Muñoz JF, Allam M, Zulu TG, Cuomo CA, Schwartz IS, Ismail A, Naicker SD, Mpembe RS, Corcoran C, de Hoog S, Kenyon C, Borman AM, Frean JA, Govender NP.

J Clin Microbiol. 2020 Feb 24;58(3). pii: e01661-19. doi: 10.1128/JCM.01661-19. Print 2020 Feb 24.


Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses.

Yu CH, Chen Y, Desjardins CA, Tenor JL, Toffaletti DL, Giamberardino C, Litvintseva A, Perfect JR, Cuomo CA.

Microb Genom. 2020 Jan;6(1). doi: 10.1099/mgen.0.000319.


Cryptococcus neoformans Recovered From Olive Trees (Olea europaea) in Turkey Reveal Allopatry With African and South American Lineages.

Ergin Ç, Şengül M, Aksoy L, Döğen A, Sun S, Averette AF, Cuomo CA, Seyedmousavi S, Heitman J, Ilkit M.

Front Cell Infect Microbiol. 2019 Nov 8;9:384. doi: 10.3389/fcimb.2019.00384. eCollection 2019.


A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands.

Farrer RA, Chang M, Davis MJ, van Dorp L, Yang DH, Shea T, Sewell TR, Meyer W, Balloux F, Edwards HM, Chanda D, Kwenda G, Vanhove M, Chang YC, Cuomo CA, Fisher MC, Kwon-Chung KJ.

mBio. 2019 Nov 12;10(6). pii: e02306-19. doi: 10.1128/mBio.02306-19.


Emergomyces: The global rise of new dimorphic fungal pathogens.

Schwartz IS, Govender NP, Sigler L, Jiang Y, Maphanga TG, Toplis B, Botha A, Dukik K, Hoving JC, Muñoz JF, de Hoog S, Cuomo CA, Colebunders R, Kenyon C.

PLoS Pathog. 2019 Sep 19;15(9):e1007977. doi: 10.1371/journal.ppat.1007977. eCollection 2019 Sep. Review. No abstract available.


Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity.

Baltrus DA, Cuomo CA, Dennehy JJ, Dunning Hotopp JC, Maresca JA, Newton ILG, Rasko DA, Rokas A, Roux S, Stajich JE.

Microbiol Resour Announc. 2019 Sep 5;8(36). pii: e00954-19. doi: 10.1128/MRA.00954-19.


Identification of Candida auris by Use of the Updated Vitek 2 Yeast Identification System, Version 8.01: a Multilaboratory Evaluation Study.

Ambaraghassi G, Dufresne PJ, Dufresne SF, Vallières É, Muñoz JF, Cuomo CA, Berkow EL, Lockhart SR, Luong ML.

J Clin Microbiol. 2019 Oct 23;57(11). pii: e00884-19. doi: 10.1128/JCM.00884-19. Print 2019 Nov.


Genome Sequence for Candida albicans Clinical Oral Isolate 529L.

Cuomo CA, Fanning S, Gujja S, Zeng Q, Naglik JR, Filler SG, Mitchell AP.

Microbiol Resour Announc. 2019 Jun 20;8(25). pii: e00554-19. doi: 10.1128/MRA.00554-19.


Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to Cryptococcus Pathogens.

Passer AR, Coelho MA, Billmyre RB, Nowrousian M, Mittelbach M, Yurkov AM, Averette AF, Cuomo CA, Sun S, Heitman J.

mBio. 2019 Jun 11;10(3). pii: e00764-19. doi: 10.1128/mBio.00764-19.


Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single macrophages infected with Candida albicans.

Muñoz JF, Delorey T, Ford CB, Li BY, Thompson DA, Rao RP, Cuomo CA.

Nat Commun. 2019 Apr 8;10(1):1607. doi: 10.1038/s41467-019-09599-8.


Erratum for Kim et al., "Genetic Analysis of Candida auris Implicates Hsp90 in Morphogenesis and Azole Tolerance and Cdr1 in Azole Resistance".

Kim SH, Iyer KR, Pardeshi L, Muñoz JF, Robbins N, Cuomo CA, Wong KH, Cowen LE.

mBio. 2019 Mar 19;10(2). pii: e00346-19. doi: 10.1128/mBio.00346-19. No abstract available.


Genome Sequence of the Black Yeast Exophiala lecanii-corni.

Schultzhaus Z, Cuomo CA, Wang Z.

Microbiol Resour Announc. 2019 Mar 7;8(10). pii: e01709-18. doi: 10.1128/MRA.01709-18. eCollection 2019 Mar.


Genetic Analysis of Candida auris Implicates Hsp90 in Morphogenesis and Azole Tolerance and Cdr1 in Azole Resistance.

Kim SH, Iyer KR, Pardeshi L, Muñoz JF, Robbins N, Cuomo CA, Wong KH, Cowen LE.

mBio. 2019 Jan 29;10(1). pii: e02529-18. doi: 10.1128/mBio.02529-18. Erratum in: mBio. 2019 Mar 19;10(2):.


Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans.

Reddy KC, Dror T, Underwood RS, Osman GA, Elder CR, Desjardins CA, Cuomo CA, Barkoulas M, Troemel ER.

PLoS Pathog. 2019 Jan 14;15(1):e1007528. doi: 10.1371/journal.ppat.1007528. eCollection 2019 Jan.


Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species.

Muñoz JF, Gade L, Chow NA, Loparev VN, Juieng P, Berkow EL, Farrer RA, Litvintseva AP, Cuomo CA.

Nat Commun. 2018 Dec 17;9(1):5346. doi: 10.1038/s41467-018-07779-6.


Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways.

Farrer RA, Ford CB, Rhodes J, Delorey T, May RC, Fisher MC, Cloutman-Green E, Balloux F, Cuomo CA.

mSphere. 2018 Oct 24;3(5). pii: e00445-18. doi: 10.1128/mSphere.00445-18.


Phenotypic Variability Correlates with Clinical Outcome in Cryptococcus Isolates Obtained from Botswanan HIV/AIDS Patients.

Fernandes KE, Brockway A, Haverkamp M, Cuomo CA, van Ogtrop F, Perfect JR, Carter DA.

mBio. 2018 Oct 23;9(5). pii: e02016-18. doi: 10.1128/mBio.02016-18.


Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal Pathogen Rhizopus delemar.

Sephton-Clark PCS, Muñoz JF, Ballou ER, Cuomo CA, Voelz K.

mSphere. 2018 Sep 26;3(5). pii: e00403-18. doi: 10.1128/mSphere.00403-18.


Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen.

Ene IV, Farrer RA, Hirakawa MP, Agwamba K, Cuomo CA, Bennett RJ.

Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):E8688-E8697. doi: 10.1073/pnas.1806002115. Epub 2018 Aug 27.


Author Correction: Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris.

Rhodes J, Abdolrasouli A, Farrer RA, Cuomo CA, Aanensen DM, Armstrong-James D, Fisher MC, Schelenz S.

Emerg Microbes Infect. 2018 May 31;7(1):104. doi: 10.1038/s41426-018-0098-x.


Genomic characterization of recurrent mold infections in thoracic transplant recipients.

Messina JA, Wolfe CR, Hemmersbach-Miller M, Milano C, Todd JL, Reynolds J, Alexander BD, Schell WA, Cuomo CA, Perfect JR.

Transpl Infect Dis. 2018 Oct;20(5):e12935. doi: 10.1111/tid.12935. Epub 2018 Jun 19.


Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators.

Hommel B, Mukaremera L, Cordero RJB, Coelho C, Desjardins CA, Sturny-Leclère A, Janbon G, Perfect JR, Fraser JA, Casadevall A, Cuomo CA, Dromer F, Nielsen K, Alanio A.

PLoS Pathog. 2018 May 18;14(5):e1006982. doi: 10.1371/journal.ppat.1006982. eCollection 2018 May.


Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis.

Cissé OH, Ma L, Wei Huang D, Khil PP, Dekker JP, Kutty G, Bishop L, Liu Y, Deng X, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, Kovacs JA.

mBio. 2018 May 8;9(3). pii: e00381-18. doi: 10.1128/mBio.00381-18.


Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris.

Rhodes J, Abdolrasouli A, Farrer RA, Cuomo CA, Aanensen DM, Armstrong-James D, Fisher MC, Schelenz S.

Emerg Microbes Infect. 2018 Mar 29;7(1):43. doi: 10.1038/s41426-018-0045-x. Erratum in: Emerg Microbes Infect. 2018 May 31;7(1):104.


Genome analysis reveals evolutionary mechanisms of adaptation in systemic dimorphic fungi.

Muñoz JF, McEwen JG, Clay OK, Cuomo CA.

Sci Rep. 2018 Mar 14;8(1):4473. doi: 10.1038/s41598-018-22816-6.


Advances in Cryptococcus genomics: insights into the evolution of pathogenesis.

Cuomo CA, Rhodes J, Desjardins CA.

Mem Inst Oswaldo Cruz. 2018;113(7):e170473. doi: 10.1590/0074-02760170473. Epub 2018 Feb 19. Review.


RNAi is a critical determinant of centromere evolution in closely related fungi.

Yadav V, Sun S, Billmyre RB, Thimmappa BC, Shea T, Lintner R, Bakkeren G, Cuomo CA, Heitman J, Sanyal K.

Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):3108-3113. doi: 10.1073/pnas.1713725115. Epub 2018 Mar 5.


Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum.

Persinoti GF, Martinez DA, Li W, Döğen A, Billmyre RB, Averette A, Goldberg JM, Shea T, Young S, Zeng Q, Oliver BG, Barton R, Metin B, Hilmioğlu-Polat S, Ilkit M, Gräser Y, Martinez-Rossi NM, White TC, Heitman J, Cuomo CA.

Genetics. 2018 Apr;208(4):1657-1669. doi: 10.1534/genetics.117.300573. Epub 2018 Feb 21.


Genomic Understanding of an Infectious Brain Disease from the Desert.

Moreno LF, Ahmed AAO, Brankovics B, Cuomo CA, Menken SBJ, Taj-Aldeen SJ, Faidah H, Stielow JB, Teixeira MM, Prenafeta-Boldú FX, Vicente VA, de Hoog S.

G3 (Bethesda). 2018 Mar 2;8(3):909-922. doi: 10.1534/g3.117.300421.


Pas de deux: An Intricate Dance of Anther Smut and Its Host.

San Toh S, Chen Z, Rouchka EC, Schultz DJ, Cuomo CA, Perlin MH.

G3 (Bethesda). 2018 Feb 2;8(2):505-518. doi: 10.1534/g3.117.300318.


Harnessing Whole Genome Sequencing in Medical Mycology.

Cuomo CA.

Curr Fungal Infect Rep. 2017;11(2):52-59. doi: 10.1007/s12281-017-0276-7. Epub 2017 Jun 9. Review.


Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination.

Sun S, Yadav V, Billmyre RB, Cuomo CA, Nowrousian M, Wang L, Souciet JL, Boekhout T, Porcel B, Wincker P, Granek JA, Sanyal K, Heitman J.

PLoS Biol. 2017 Aug 11;15(8):e2002527. doi: 10.1371/journal.pbio.2002527. eCollection 2017 Aug.


Whole Genome Sequence of the Heterozygous Clinical Isolate Candida krusei 81-B-5.

Cuomo CA, Shea T, Yang B, Rao R, Forche A.

G3 (Bethesda). 2017 Sep 7;7(9):2883-2889. doi: 10.1534/g3.117.043547.


Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level.

Rhodes J, Desjardins CA, Sykes SM, Beale MA, Vanhove M, Sakthikumar S, Chen Y, Gujja S, Saif S, Chowdhary A, Lawson DJ, Ponzio V, Colombo AL, Meyer W, Engelthaler DM, Hagen F, Illnait-Zaragozi MT, Alanio A, Vreulink JM, Heitman J, Perfect JR, Litvintseva AP, Bicanic T, Harrison TS, Fisher MC, Cuomo CA.

Genetics. 2017 Sep;207(1):327-346. doi: 10.1534/genetics.117.203836. Epub 2017 Jul 5.


Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans.

Desjardins CA, Giamberardino C, Sykes SM, Yu CH, Tenor JL, Chen Y, Yang T, Jones AM, Sun S, Haverkamp MR, Heitman J, Litvintseva AP, Perfect JR, Cuomo CA.

Genome Res. 2017 Jul;27(7):1207-1219. doi: 10.1101/gr.218727.116.


Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota).

Teixeira MM, Moreno LF, Stielow BJ, Muszewska A, Hainaut M, Gonzaga L, Abouelleil A, Patané JS, Priest M, Souza R, Young S, Ferreira KS, Zeng Q, da Cunha MM, Gladki A, Barker B, Vicente VA, de Souza EM, Almeida S, Henrissat B, Vasconcelos AT, Deng S, Voglmayr H, Moussa TA, Gorbushina A, Felipe MS, Cuomo CA, de Hoog GS.

Stud Mycol. 2017 Mar;86:1-28. doi: 10.1016/j.simyco.2017.01.001. Epub 2017 Jan 27.


Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi.

Farrer RA, Martel A, Verbrugghe E, Abouelleil A, Ducatelle R, Longcore JE, James TY, Pasmans F, Fisher MC, Cuomo CA.

Nat Commun. 2017 Mar 21;8:14742. doi: 10.1038/ncomms14742.


Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii.

Chen Y, Farrer RA, Giamberardino C, Sakthikumar S, Jones A, Yang T, Tenor JL, Wagih O, Van Wyk M, Govender NP, Mitchell TG, Litvintseva AP, Cuomo CA, Perfect JR.

mBio. 2017 Mar 7;8(2). pii: e00166-17. doi: 10.1128/mBio.00166-17.


Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia.

Wu JQ, Sakthikumar S, Dong C, Zhang P, Cuomo CA, Park RF.

Front Plant Sci. 2017 Feb 9;8:148. doi: 10.3389/fpls.2017.00148. eCollection 2017.


Novel taxa of thermally dimorphic systemic pathogens in the Ajellomycetaceae (Onygenales).

Dukik K, Muñoz JF, Jiang Y, Feng P, Sigler L, Stielow JB, Freeke J, Jamalian A, Gerrits van den Ende B, McEwen JG, Clay OK, Schwartz IS, Govender NP, Maphanga TG, Cuomo CA, Moreno LF, Kenyon C, Borman AM, de Hoog S.

Mycoses. 2017 May;60(5):296-309. doi: 10.1111/myc.12601. Epub 2017 Feb 7.


The Case for Adopting the "Species Complex" Nomenclature for the Etiologic Agents of Cryptococcosis.

Kwon-Chung KJ, Bennett JE, Wickes BL, Meyer W, Cuomo CA, Wollenburg KR, Bicanic TA, Castañeda E, Chang YC, Chen J, Cogliati M, Dromer F, Ellis D, Filler SG, Fisher MC, Harrison TS, Holland SM, Kohno S, Kronstad JW, Lazera M, Levitz SM, Lionakis MS, May RC, Ngamskulrongroj P, Pappas PG, Perfect JR, Rickerts V, Sorrell TC, Walsh TJ, Williamson PR, Xu J, Zelazny AM, Casadevall A.

mSphere. 2017 Jan 11;2(1). pii: e00357-16. doi: 10.1128/mSphere.00357-16. eCollection 2017 Jan-Feb.


Transcriptional analysis of mating and pre-infection stages of the anther smut, Microbotryum lychnidis-dioicae.

Toh SS, Chen Z, Schultz DJ, Cuomo CA, Perlin MH.

Microbiology. 2017 Mar;163(3):410-420. doi: 10.1099/mic.0.000421.


Paracoccidioides spp. catalases and their role in antioxidant defense against host defense responses.

Tamayo D, Muñoz JF, Almeida AJ, Puerta JD, Restrepo Á, Cuomo CA, McEwen JG, Hernández O.

Fungal Genet Biol. 2017 Mar;100:22-32. doi: 10.1016/j.fgb.2017.01.005. Epub 2017 Jan 16.


Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii.

Farrer RA, Voelz K, Henk DA, Johnston SA, Fisher MC, May RC, Cuomo CA.

Philos Trans R Soc Lond B Biol Sci. 2016 Dec 5;371(1709). pii: 20160021. doi: 10.1098/rstb.2016.0021.


Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses.

Lockhart SR, Etienne KA, Vallabhaneni S, Farooqi J, Chowdhary A, Govender NP, Colombo AL, Calvo B, Cuomo CA, Desjardins CA, Berkow EL, Castanheira M, Magobo RE, Jabeen K, Asghar RJ, Meis JF, Jackson B, Chiller T, Litvintseva AP.

Clin Infect Dis. 2017 Jan 15;64(2):134-140. doi: 10.1093/cid/ciw691. Epub 2016 Oct 20. Erratum in: Clin Infect Dis. 2018 Aug 31;67(6):987.

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