{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T18:24:00Z","timestamp":1792607040213,"version":"4.5.0"},"reference-count":99,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,7,5]],"date-time":"2017-07-05T00:00:00Z","timestamp":1499212800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically human immunodeficiency virus\/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterize the major subdivisions, their relative diversity, and the level of genetic exchange between them. While most isolates of C. neoformans var. grubii belong to one of three major lineages (VNI, VNII, and VNB), some haploid isolates show hybrid ancestry including some that appear to have recently interbred, based on the detection of large blocks of each ancestry across each chromosome. Many isolates display evidence of aneuploidy, which was detected for all chromosomes. In diploid isolates of C. neoformans var. grubii (serotype AA) and of hybrids with C. neoformans var. neoformans (serotype AD) such aneuploidies have resulted in loss of heterozygosity, where a chromosomal region is represented by the genotype of only one parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil reveal that the previously \u201cAfrican\u201d VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America prior to its diversification, supported by finding ancestral recombination events between isolates from different lineages and regions. The results provide evidence of substantial population structure, with all lineages showing multi-continental distributions; demonstrating the highly dispersive nature of this pathogen.<\/jats:p>","DOI":"10.1534\/genetics.117.203836","type":"journal-article","created":{"date-parts":[[2017,7,5]],"date-time":"2017-07-05T21:10:36Z","timestamp":1499289036000},"page":"327-346","source":"Crossref","is-referenced-by-count":105,"title":["Tracing Genetic Exchange and Biogeography of\n                    <i>Cryptococcus neoformans<\/i>\n                    var.\n                    <i>grubii<\/i>\n                    at the Global Population Level"],"prefix":"10.1093","volume":"207","author":[{"given":"Johanna","family":"Rhodes","sequence":"first","affiliation":[{"name":"Department of Infectious Disease Epidemiology , Imperial College London, W2 1PG, United Kingdom"},{"name":"Department of Infectious Disease Epidemiology , Imperial College London, W2 1PG, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher A","family":"Desjardins","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program , Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142"},{"name":"Department of Infectious Disease Epidemiology , Imperial College London, W2 1PG, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean M","family":"Sykes","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program , Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathew A","family":"Beale","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease Epidemiology , Imperial College London, W2 1PG, United Kingdom"},{"name":"Institute of Infection and Immunity , St. George\u2019s University London, WC1E 6BT, United Kingdom"},{"name":"Infection Genomics , Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathieu","family":"Vanhove","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease Epidemiology , Imperial College London, W2 1PG, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharadha","family":"Sakthikumar","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program , Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Chen","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases , Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharvari","family":"Gujja","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program , Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sakina","family":"Saif","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program , Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anuradha","family":"Chowdhary","sequence":"additional","affiliation":[{"name":"Department of Medical Mycology , Vallabhbhai Patel Chest Institute, University of Delhi, 110007, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel John","family":"Lawson","sequence":"additional","affiliation":[{"name":"Integrative Epidemiology Unit , School of Social and Community Medicine, University of Bristol, BS8 1TH, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vinicius","family":"Ponzio","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases , Federal University of S\u00e3o Paulo, 04039-032, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnaldo Lopes","family":"Colombo","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases , Federal University of S\u00e3o Paulo, 04039-032, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wieland","family":"Meyer","sequence":"additional","affiliation":[{"name":"Molecular Mycology Research Laboratory , Centre for Infectious Diseases and Microbiology, Sydney Medical School\u2013Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead Institute for Medical Research, 2145, Australia"},{"name":"Mycology Laboratory , Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, 21040-360, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M","family":"Engelthaler","sequence":"additional","affiliation":[{"name":"TGen North , Translational Genomics Research Institute, Flagstaff, Arizona 86005"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ferry","family":"Hagen","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Infectious Diseases , Canisius-Wilhelmina Hospital, 6532SZ Nijmegen, The Netherlands"},{"name":"Centre of Expertise in Mycology , Radboudumc\/Canisius-Wilhelmina Hospital, 6532SZ Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Teresa","family":"Illnait-Zaragozi","sequence":"additional","affiliation":[{"name":"Departamento Bacteriolog\u00eda-Micologia , Centro de Investigaci\u00f3n, Diagn\u00f3stico y Referencia, Instituto de Medicina Tropical Pedro Kour\u00ed, La Habana, 601, Cuba"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandre","family":"Alanio","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie-Mycologie , Assistance Publique\u2013H\u00f4pitaux de Paris, Groupe Hospitalier Saint-Louis-Lariboisi\u00e8re-Fernand-Widal Paris, 75010, France; Universit\u00e9 Paris Diderot, Sorbonne Paris Cit\u00e9, 75010, Paris, France; Unit\u00e9 de Mycologie Mol\u00e9culaire, Institut Pasteur, Centre National de la Recherche Scientifique, Centre National de R\u00e9f\u00e9rence Mycoses Invasives et Antifongiques, URA3012, 75015, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo-Marie","family":"Vreulink","sequence":"additional","affiliation":[{"name":"Department of Microbiology , Stellenbosch University, 7600, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph","family":"Heitman","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology , Duke University Medical Center, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John R","family":"Perfect","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases , Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasia P","family":"Litvintseva","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology , Duke University Medical Center, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tihana","family":"Bicanic","sequence":"additional","affiliation":[{"name":"Institute of Infection and Immunity , St. George\u2019s University London, WC1E 6BT, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas S","family":"Harrison","sequence":"additional","affiliation":[{"name":"Institute of Infection and Immunity , St. George\u2019s University London, WC1E 6BT, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew C","family":"Fisher","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease Epidemiology , Imperial College London, W2 1PG, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina A","family":"Cuomo","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program , Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,7,5]]},"reference":[{"key":"2022110414541151100_bib1","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.tim.2014.01.001","article-title":"A neglected epidemic: fungal infections in HIV\/AIDS.","volume":"22","author":"Armstrong-James","year":"2014","journal-title":"Trends Microbiol."},{"key":"2022110414541151100_bib2","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. 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