{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T09:02:14Z","timestamp":1790413334692,"version":"4.1.0"},"reference-count":43,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2021,10,15]],"date-time":"2021-10-15T00:00:00Z","timestamp":1634256000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004586","name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro","doi-asserted-by":"publisher","award":["E-26\/203.076\/2016"],"award-info":[{"award-number":["E-26\/203.076\/2016"]}],"id":[{"id":"10.13039\/501100004586","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004586","name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro","doi-asserted-by":"publisher","award":["FAPERJ E-26\/202.527\/2019"],"award-info":[{"award-number":["FAPERJ E-26\/202.527\/2019"]}],"id":[{"id":"10.13039\/501100004586","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004586","name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro","doi-asserted-by":"publisher","award":["FAPERJ E-26\/202.696\/2018"],"award-info":[{"award-number":["FAPERJ E-26\/202.696\/2018"]}],"id":[{"id":"10.13039\/501100004586","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["CNPq 302796\/2017-7"],"award-info":[{"award-number":["CNPq 302796\/2017-7"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["43460\/2018-2"],"award-info":[{"award-number":["43460\/2018-2"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["311470\/2018-1"],"award-info":[{"award-number":["311470\/2018-1"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015691","name":"Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R21AI28536, ADHS17-0007403, and ADHS16-162415"],"award-info":[{"award-number":["R21AI28536, ADHS17-0007403, and ADHS16-162415"]}],"id":[{"id":"10.13039\/100015691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI153523"],"award-info":[{"award-number":["R01AI153523"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoF"],"abstract":"<jats:p>Histoplasmosis is a severe mycotic disease affecting thousands of immunocompetent and immunocompromised individuals with high incidence in Latin America, where the disease agents are Histoplasma capsulatum and Histoplasma suramericanum. In this work, we used whole-genome sequencing to infer the species diversity and the population structure of H. suramericanum in South America. We find evidence for strong population structure and little admixture within the species. Genome-level phylogenetic trees indicate the existence of at least three different discrete populations. We recovered the existence of a previously identified population, LAmB, and confirm that it is highly differentiated along the whole genome. We also find that H. suramericanum is composed of two populations, one in Northern South America, and another in the southern portion of the continent. Moreover, one of the lineages from the southern population is endemic to Rio de Janeiro and there was no association with clinical data and species isolated from patients with histoplasmosis. Our results point out the need to characterize the symptomatology of histoplasmosis caused by different species and lineages of Histoplasma spp.<\/jats:p>","DOI":"10.3390\/jof7100865","type":"journal-article","created":{"date-parts":[[2021,10,15]],"date-time":"2021-10-15T13:35:47Z","timestamp":1634304947000},"page":"865","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Genomic Diversity Analysis Reveals a Strong Population Structure in Histoplasma capsulatum LAmA (Histoplasma suramericanum)"],"prefix":"10.3390","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7378-1990","authenticated-orcid":false,"given":"Fernando","family":"Almeida-Silva","sequence":"first","affiliation":[{"name":"Laborat\u00f3rio de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Funda\u00e7\u00e3o Oswaldo Cruz-INI\/Fiocruz, Rio de Janeiro 21040-360, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1763-3464","authenticated-orcid":false,"given":"Marcus","family":"de Melo Teixeira","sequence":"additional","affiliation":[{"name":"Faculdade de Medicina, Universidadede Bras\u00edlia, Bras\u00edlia 70910-900, Brazil"},{"name":"Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel R.","family":"Matute","sequence":"additional","affiliation":[{"name":"Biology Department, University of North Carolina, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcela","family":"de Faria Ferreira","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Funda\u00e7\u00e3o Oswaldo Cruz-INI\/Fiocruz, Rio de Janeiro 21040-360, Brazil"},{"name":"Servi\u00e7o Ambulatorial do Instituto Nacional de Infectologia Evandro Chagas, Funda\u00e7\u00e3o Oswaldo Cruz-INI\/Fiocruz, Rio de Janeiro 21040-360, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3439-4517","authenticated-orcid":false,"given":"Bridget M.","family":"Barker","sequence":"additional","affiliation":[{"name":"Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6639-6058","authenticated-orcid":false,"given":"Rodrigo","family":"Almeida-Paes","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Funda\u00e7\u00e3o Oswaldo Cruz-INI\/Fiocruz, Rio de Janeiro 21040-360, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2856-9667","authenticated-orcid":false,"given":"Allan J.","family":"Guimar\u00e3es","sequence":"additional","affiliation":[{"name":"Departamento de Microbiologia e Parasitologia, Instituto Biom\u00e9dico, Universidade Federal Fluminense, Niter\u00f3i, Rio de Janeiro 24210-130, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosely M.","family":"Zancop\u00e9-Oliveira","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Funda\u00e7\u00e3o Oswaldo Cruz-INI\/Fiocruz, Rio de Janeiro 21040-360, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,10,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.idcr.2017.12.005","article-title":"Oropharyngeal histoplasmosis: The diagnosis lies in the biopsy","volume":"11","author":"Miranda","year":"2018","journal-title":"IDCases"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1016\/S1473-3099(18)30354-2","article-title":"Burden of HIV-associated histoplasmosis compared with tuberculosis in Latin America: A modelling study","volume":"18","author":"Adenis","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Deepe, G.S. (2018). Outbreaks of histoplasmosis: The spores set sail. PLoS Pathog, 14.","DOI":"10.1371\/journal.ppat.1007213"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1016\/j.rmed.2012.02.004","article-title":"Endemic mycoses: Overlooked causes of community acquired pneumonia","volume":"106","author":"Hage","year":"2012","journal-title":"Respir. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.ijid.2019.07.009","article-title":"The occurrence of histoplasmosis in Brazil: A systematic review","volume":"86","author":"Almeida","year":"2019","journal-title":"Int. J. Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.idc.2015.10.009","article-title":"Histoplasmosis","volume":"30","author":"Wheat","year":"2016","journal-title":"Infect. Dis Clin. North. Am."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1590\/0037-8682-0124-2013","article-title":"Histoplasmosis in immunocompetent individuals living in an endemic area in the Brazilian Southeast","volume":"46","author":"Faiolla","year":"2013","journal-title":"Rev. Soc. Bras. Med. Trop."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1590\/S0074-02761945000600004","article-title":"Histoplasmose","volume":"43","author":"Duarte","year":"1945","journal-title":"Mem Inst. Oswaldo Cruz"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1590\/S1806-37132009001100013","article-title":"Chapter 4\u2013Histoplasmosis","volume":"35","year":"2009","journal-title":"J Bras Pneumol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1590\/S0036-46651998000300005","article-title":"Epidemiologic Surveys of Histoplasmin and Paracoccidioidin Sensitivity in Brazil","volume":"40","author":"Fava","year":"1998","journal-title":"Rev. Inst. Med. Trop. S. Paulo"},{"key":"ref_11","first-page":"881","article-title":"Histoplasmosis in Brazil: Lessons to learn about preventing exposure","volume":"185","author":"Guerra","year":"2020","journal-title":"Mycopathologia"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1111\/myc.12877","article-title":"Role of western blot assay for the diagnosis of histoplasmosis in AIDS patients from a National Institute of Infectious Diseases in Rio de Janeiro, Brazil","volume":"62","author":"Almeida","year":"2019","journal-title":"Mycoses"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/S1130-1406(05)70027-9","article-title":"Histoplasmosis in a Brazilian center: Clinical forms and laboratory tests","volume":"22","author":"Leimann","year":"2005","journal-title":"Rev. Iberoam Micol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3383","DOI":"10.1046\/j.1365-294X.2003.01995.x","article-title":"Phylogeography of the fungal pathogen Histoplasma capsulatum","volume":"12","author":"Kasuga","year":"2003","journal-title":"Mol. Ecol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e01339-17","DOI":"10.1128\/mBio.01339-17","article-title":"Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum","volume":"8","author":"Sepulveda","year":"2017","journal-title":"MBio"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Teixeira Mde, M., Patane, J.S., Taylor, M.L., Gomez, B.L., Theodoro, R.C., de Hoog, S., Engelthaler, D.M., Zancope-Oliveira, R.M., Felipe, M.S., and Barker, B.M. (2016). Worldwide Phylogenetic Distributions and Population Dynamics of the Genus Histoplasma. PLoS Negl. Trop. Dis., 10.","DOI":"10.1371\/journal.pntd.0004732"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"11789","DOI":"10.1038\/s41598-019-48111-6","article-title":"Novel clinical and dual infection by Histoplasma capsulatum genotypes in HIV patients from Northeastern, Brazil","volume":"9","author":"Damasceno","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_18","unstructured":"Andrews, S. (2019, May 23). FastQC: A Quality Control Tool for High Throughput Sequence Data. Available online: http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"ref_23","first-page":"e000074","article-title":"NASP: An accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats","volume":"2","author":"Sahl","year":"2016","journal-title":"Microb. Genom."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1093\/molbev\/mst024","article-title":"Ultrafast approximation for phylogenetic bootstrap","volume":"30","author":"Minh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"3070","DOI":"10.1093\/bioinformatics\/btr521","article-title":"Adegenet 1.3-1: New tools for the analysis of genome-wide SNP data","volume":"27","author":"Jombart","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res."},{"key":"ref_30","unstructured":"Team, R.C. (2013). R: A Language and Environment for Statistical Computing, R Core Team."},{"key":"ref_31","unstructured":"Champely, S., Ekstrom, C., Dalgaard, P., Gill, J., Weibelzahl, S., Anandkumar, A., Ford, C., Volcic, R., and De Rosario, H. (2021, July 25). Basic Functions for Power Analysis, Package \u2018pwr\u2019. Available online: https:\/\/cran.r-project.org\/web\/packages\/pwr\/."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.3389\/fmicb.2019.01052","article-title":"Dissecting the Heterogeneous Population Genetic Structure of Candida albicans: Limitations and Constraints of the Multilocus Sequence Typing Scheme","volume":"10","author":"Munoz","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1128\/jb.165.3.813-818.1986","article-title":"Classification of Histoplasma capsulatum isolates by restriction fragment polymorphisms","volume":"165","author":"Vincent","year":"1986","journal-title":"J. Bacteriol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1128\/JCM.37.3.653-663.1999","article-title":"Phylogenetic relationships of varieties and geographical groups of the human pathogenic fungus Histoplasma capsulatum Darling","volume":"37","author":"Kasuga","year":"1999","journal-title":"J. Clin. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1038\/s41467-018-04787-4","article-title":"Gene flow contributes to diversification of the major fungal pathogen Candida albicans","volume":"9","author":"Ropars","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1002\/evl3.59","article-title":"Recent admixture between species of the fungal pathogen Histoplasma","volume":"2","author":"Maxwell","year":"2018","journal-title":"Evol. Lett."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e01376-01314","DOI":"10.1128\/mBio.01376-14","article-title":"Comparison of phylogenetically distinct Histoplasma strains reveals evolutionarily divergent virulence strategies","volume":"5","author":"Sepulveda","year":"2014","journal-title":"MBio"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"e00742-20","DOI":"10.1128\/mSphere.00742-20","article-title":"Biodiverse Histoplasma Species Elicit Distinct Patterns of Pulmonary Inflammation following Sublethal Infection","volume":"5","author":"Jones","year":"2020","journal-title":"mSphere"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1016\/j.ympev.2011.08.026","article-title":"Molecular evidence of cryptic speciation, historical range expansion, and recent intraspecific hybridization in the Neotropical seasonal forest tree Cedrela fissilis (Meliaceae)","volume":"61","author":"Garcia","year":"2011","journal-title":"Mol. Phylogenet Evol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1038\/s41437-019-0234-y","article-title":"Historical climate changes and hybridization shaped the evolution of Atlantic Forest spinetails (Aves: Furnariidae)","volume":"123","author":"Miyaki","year":"2019","journal-title":"Heredity"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"492","DOI":"10.4257\/oeco.2016.2004.08","article-title":"A Survey of Small Mammals in the Atlantic Forest Of the Northwestern Region Of Rio De Janeiro State","volume":"20","author":"Teixeira","year":"2016","journal-title":"Oecologia Aust."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"103249","DOI":"10.1016\/j.fgb.2019.103249","article-title":"Fungal species boundaries in the genomics era","volume":"131","author":"Matute","year":"2019","journal-title":"Fungal Genet. Biol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"e02084","DOI":"10.1016\/j.heliyon.2019.e02084","article-title":"Molecular epidemiology of Colombian Histoplasma capsulatum isolates obtained from human and chicken manure samples","volume":"5","author":"Gomez","year":"2019","journal-title":"Heliyon"}],"container-title":["Journal of Fungi"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2309-608X\/7\/10\/865\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:15:07Z","timestamp":1760166907000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2309-608X\/7\/10\/865"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,15]]},"references-count":43,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2021,10]]}},"alternative-id":["jof7100865"],"URL":"https:\/\/doi.org\/10.3390\/jof7100865","relation":{},"ISSN":["2309-608X"],"issn-type":[{"value":"2309-608X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,10,15]]}}}