{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T21:32:28Z","timestamp":1780695148556,"version":"3.54.1"},"reference-count":40,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T00:00:00Z","timestamp":1619481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Health Laboratory Service Research Trust","award":["94712"],"award-info":[{"award-number":["94712"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoF"],"abstract":"<jats:p>In South Africa, Cryptococcus neoformans is the most common cause of adult meningitis. We performed multi locus sequence typing and fluconazole susceptibility testing of clinical C. neoformans isolates collected from 251 South African patients with cryptococcosis through national surveillance from 2005 to 2009. We examined the association between clinical characteristics of patients and genotype, and the effect of genotype on in-hospital mortality. We performed whole genome phylogenetic analysis of fifteen C. neoformans isolates with the molecular type VNB and tested their virulence in a Galleria mellonella model. Most isolates had the molecular type VNI (206\/251, 82%), followed by VNII (25\/251, 10%), VNB (15\/251, 6%), and VNIV (5\/251, 2%); 67 sequence types were identified. There were no differences in fluconazole minimum inhibitory concentration (MIC) values among molecular types and the majority of strains had low MIC values (MIC50 of 1 \u00b5g\/mL and MIC90 of 4 \u00b5g\/mL). Males were almost twice as likely of being infected with a non-VNI genotype (adjusted odds ratio [OR]: 1.65, 95% confidence interval [CI]: 0.25\u201310.99; p = 0.61). Compared to patients infected with a VNI genotype, those with a non-VNI genotype had a 50% reduced adjusted odds of dying in hospital (95% CI: 0.03\u20137.57; p = 0.62). However, for both these analyses, our estimates had wide confidence intervals spanning 1 with large p-values. Fifteen VNB strains were not as virulent in a G. mellonella larval model as the H99 reference strain. A majority of these VNB strains belonged to the VNBII clade and were very closely related by phylogenetic analysis.<\/jats:p>","DOI":"10.3390\/jof7050338","type":"journal-article","created":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T21:18:20Z","timestamp":1619558300000},"page":"338","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005\u20132009"],"prefix":"10.3390","volume":"7","author":[{"given":"Serisha D.","family":"Naicker","sequence":"first","affiliation":[{"name":"Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa"},{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rindidzani E.","family":"Magobo","sequence":"additional","affiliation":[{"name":"Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsidiso G.","family":"Maphanga","sequence":"additional","affiliation":[{"name":"Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7547-5172","authenticated-orcid":false,"given":"Carolina","family":"Firacative","sequence":"additional","affiliation":[{"name":"Studies in Translational Microbiology and Emerging Diseases (MICROS) Research Group, School of Medicine and Health Sciences, Universidad del Rosario, 111611 Bogota, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erika","family":"van Schalkwyk","sequence":"additional","affiliation":[{"name":"Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8692-1286","authenticated-orcid":false,"given":"Juan","family":"Monroy-Nieto","sequence":"additional","affiliation":[{"name":"Pathogen and Microbiome Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jolene","family":"Bowers","sequence":"additional","affiliation":[{"name":"Pathogen and Microbiome Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M.","family":"Engelthaler","sequence":"additional","affiliation":[{"name":"Pathogen and Microbiome Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liliwe","family":"Shuping","sequence":"additional","affiliation":[{"name":"Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9933-8340","authenticated-orcid":false,"given":"Wieland","family":"Meyer","sequence":"additional","affiliation":[{"name":"Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia"},{"name":"Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW 2006, Australia"},{"name":"Westmead Institute for Medical Research, Westmead, NSW 2145, Australia"},{"name":"Research and Educational Network, Westmead Hospital, Western Sydney Local Health District, Westmead, NSW 2145, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7869-9462","authenticated-orcid":false,"given":"Nelesh P.","family":"Govender","sequence":"additional","affiliation":[{"name":"Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa"},{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa"},{"name":"Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town 7701, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,4,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Britz, E., Perovic, O., von Mollendorf, C., von Gottberg, A., Iyaloo, S., Quan, V., Chetty, V., Sriruttan, C., Ismail, N.A., and Nanoo, A. (2016). The Epidemiology of Meningitis among Adults in a South African Province with a High HIV Prevalence, 2009-2012. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0163036"},{"key":"ref_2","first-page":"61","article-title":"Cryptococcal infections in non-HIV-infected patients","volume":"124","author":"Pappas","year":"2013","journal-title":"Trans. Am. Clin. Climatol. Assoc."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1128\/JCM.43.2.556-564.2005","article-title":"Comparative analysis of environmental and clinical populations of Cryptococcus neoformans","volume":"43","author":"Litvintseva","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4102\/sajhivmed.v20i1.1030","article-title":"Southern African HIV Clinicians Society guideline for the prevention, diagnosis and management of cryptococcal disease among HIV-infected persons: 2019 update","volume":"20","author":"Govender","year":"2019","journal-title":"S. Afr. J. HIV Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1921","DOI":"10.1128\/JCM.03177-13","article-title":"Multilocus sequence typing of serially collected isolates of Cryptococcus from HIV-infected patients in South Africa","volume":"52","author":"Govender","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1080\/13693780902953886","article-title":"Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii","volume":"47","author":"Meyer","year":"2009","journal-title":"Med. Mycol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.fgb.2015.02.009","article-title":"Recognition of seven species in the Cryptococcus gattii\/Cryptococcus neoformans species complex","volume":"78","author":"Hagen","year":"2015","journal-title":"Fungal Genet. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Kwon-Chung, K.J., Bennett, J.E., Wickes, B.L., Meyer, W., Cuomo, C.A., Wollenburg, K.R., Bicanic, T.A., Castaneda, E., Chang, Y.C., and Chen, J. (2017). The Case for Adopting the \u201cSpecies Complex\u201d Nomenclature for the Etiologic Agents of Cryptococcosis. mSphere, 2.","DOI":"10.1128\/mSphere.00357-16"},{"key":"ref_9","first-page":"675213","article-title":"Global Molecular Epidemiology of Cryptococcus neoformans and Cryptococcus gattii: An Atlas of the Molecular Types","volume":"2013","author":"Cogliati","year":"2013","journal-title":"Sci. Cairo"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Andrade-Silva, L.E., Ferreira-Paim, K., Ferreira, T.B., Vilas-Boas, A., Mora, D.J., Manzato, V.M., Fonseca, F.M., Buosi, K., Andrade-Silva, J., and Prudente, B.d.S. (2018). Genotypic analysis of clinical and environmental Cryptococcus neoformans isolates from Brazil reveals the presence of VNB isolates and a correlation with biological factors. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0193237"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1080\/22221751.2018.1562849","article-title":"Genotypic diversity and clinical outcome of cryptococcosis in renal transplant recipients in Brazil","volume":"8","author":"Ponzio","year":"2019","journal-title":"Emerg. Microbes Infect."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Litvintseva, A.P., Carbone, I., Rossouw, J., Thakur, R., Govender, N.P., and Mitchell, T.G. (2011). Evidence that the Human Pathogenic Fungus Cryptococcus neoformans var. grubii May Have Evolved in Africa. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0019688"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1111\/mec.13260","article-title":"Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana","volume":"24","author":"Chen","year":"2015","journal-title":"Mol. Ecol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1991","DOI":"10.1111\/mec.13891","article-title":"Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV\/AIDS cohort","volume":"26","author":"Vanhove","year":"2017","journal-title":"Mol. Ecol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1534\/genetics.117.203836","article-title":"Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level","volume":"207","author":"Rhodes","year":"2017","journal-title":"Genetics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1101\/gr.218727.116","article-title":"Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans","volume":"27","author":"Desjardins","year":"2017","journal-title":"Genome Res."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Beale, M.A., Sabiiti, W., Robertson, E.J., Fuentes-Cabrejo, K.M., O\u2019Hanlon, S.J., Jarvis, J.N., Loyse, A., Meintjes, G., Harrison, T.S., and May, R.C. (2015). Genotypic Diversity Is Associated with Clinical Outcome and Phenotype in Cryptococcal Meningitis across Southern Africa. PLoS Negl. Trop. Dis., 9.","DOI":"10.1371\/journal.pntd.0003847"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2307","DOI":"10.1097\/QAD.0b013e3283570567","article-title":"A comparison of cases of paediatric-onset and adult-onset cryptococcosis detected through population-based surveillance, 2005-2007","volume":"26","author":"Meiring","year":"2012","journal-title":"AIDS Lond. Engl."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Firacative, C., Roe, C.C., Malik, R., Ferreira-Paim, K., Escandon, P., Sykes, J.E., Castanon-Olivares, L.R., Contreras-Peres, C., Samayoa, B., and Sorrell, T.C. (2016). MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors. PLoS Negl. Trop. Dis., 10.","DOI":"10.1371\/journal.pntd.0004861"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1128\/EC.4.8.1403-1409.2005","article-title":"Clonality and recombination in genetically differentiated subgroups of Cryptococcus gattii","volume":"4","author":"Campbell","year":"2005","journal-title":"Eukaryot. Cell"},{"key":"ref_21","unstructured":"Clinical and Laboratory Standards Institute (2008). Reference Method for Broth Dilution Antifungal Susceptibility Testing of Yeasts, CLSI. Approved Standard\u2014Third Edition M27-A3."},{"key":"ref_22","unstructured":"Clinical and Laboratory Standards Institute (2017). Performance Standards for Antifungal Susceptibility Testing of Yeasts\u2014First Edition M60, CLSI."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Naicker, S.D., Mpembe, R.S., Maphanga, T.G., Zulu, T.G., Desanto, D., Wadula, J., Mvelase, N., Maluleka, C., Reddy, K., and Dawood, H. (2020). Decreasing fluconazole susceptibility of clinical South African Cryptococcus neoformans isolates over a decade. PLoS Negl. Trop. Dis., 14.","DOI":"10.1371\/journal.pntd.0008137"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"5898","DOI":"10.1128\/AAC.01115-12","article-title":"Cryptococcus neoformans-Cryptococcus gattii species complex: An international study of wild-type susceptibility endpoint distributions and epidemiological cutoff values for fluconazole, itraconazole, posaconazole, and voriconazole","volume":"56","author":"Aller","year":"2012","journal-title":"Antimicrob. Agents Chemother"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3842","DOI":"10.1128\/IAI.73.7.3842-3850.2005","article-title":"Galleria mellonella as a model system to study Cryptococcus neoformans pathogenesis","volume":"73","author":"Mylonakis","year":"2005","journal-title":"Infect. Immun."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Firacative, C., Duan, S., and Meyer, W. (2014). Galleria mellonella model identifies highly virulent strains among all major molecular types of Cryptococcus gattii. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0105076"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"dos Santos, R.A.C., Steenwyk, J.L., Rivero-Menendez, O., Mead, M.E., Silva, L.P., Bastos, R.W., Alastruey-Izquierdo, A., Goldman, G.H., and Rokas, A. (2020). Genomic and Phenotypic Heterogeneity of Clinical Isolates of the Human Pathogens Aspergillus fumigatus, Aspergillus lentulus, and Aspergillus fumigatiaffinis. Front. Genet., 11.","DOI":"10.3389\/fgene.2020.00459"},{"key":"ref_28","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_29","doi-asserted-by":"crossref","first-page":"e00196-12","DOI":"10.1128\/mBio.00196-12","article-title":"Cryptococcal genotype influences immunologic response and human clinical outcome after meningitis","volume":"3","author":"Wiesner","year":"2012","journal-title":"MBio"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1534\/g3.116.037499","article-title":"A Population Genomics Approach to Assessing the Genetic Basis of Within-Host Microevolution Underlying Recurrent Cryptococcal Meningitis Infection","volume":"7","author":"Rhodes","year":"2017","journal-title":"G3 Bethesda Md."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Chen, Y., Farrer, R.A., Giamberardino, C., Sakthikumar, S., Jones, A., Yang, T., Tenor, J.L., Wagih, O., Van Wyk, M., and Govender, N.P. (2017). Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii. MBio, 8.","DOI":"10.1128\/mBio.00166-17"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1099\/jmm.0.000265","article-title":"Cryptococcus neoformans isolates from Yaound\u00e9 human immunodeficiency virus-infected patients exhibited intra-individual genetic diversity and variation in antifungal susceptibility profiles between isolates from the same patient","volume":"65","author":"Ngouana","year":"2016","journal-title":"J. Med Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1111\/myc.12411","article-title":"Molecular types of Cryptococcus gattii\/Cryptococcus neoformans species complex from clinical and environmental sources in Nairobi, Kenya","volume":"58","author":"Kangogo","year":"2015","journal-title":"Mycoses"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1111\/myc.12539","article-title":"Molecular epidemiology reveals genetic diversity among 363 isolates of the Cryptococcus neoformans and Cryptococcus gattii species complex in 61 Ivorian HIV-positive patients","volume":"59","author":"Kassi","year":"2016","journal-title":"Mycoses"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/j.diagmicrobio.2016.08.004","article-title":"In vitro antifungal susceptibility profiles of Cryptococcus species isolated from HIV-associated cryptococcal meningitis patients in Zimbabwe","volume":"86","author":"Nyazika","year":"2016","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1128\/JCM.01277-10","article-title":"Analyses of pediatric isolates of Cryptococcus neoformans from South Africa","volume":"49","author":"Miglia","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Ferreira-Paim, K., Andrade-Silva, L., Fonseca, F.M., Ferreira, T.B., Mora, D.J., Andrade-Silva, J., Khan, A., Dao, A., Reis, E.C., and Almeida, M.T. (2017). MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil. PLoS Negl. Trop. Dis., 11.","DOI":"10.1371\/journal.pntd.0005223"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1093\/mmy\/myy161","article-title":"Molecular types of Cryptococcus neoformans and Cryptococcus gattii in Western Australia and correlation with antifungal susceptibility","volume":"57","author":"Lee","year":"2019","journal-title":"Med. Mycol."},{"key":"ref_39","unstructured":"Cogliati, M., D\u2019Amicis, R., Zani, A., Montagna, M.T., Caggiano, G., De Giglio, O., Balbino, S., De Donno, A., Serio, F., and Susever, S. (2016). Environmental distribution of Cryptococcus neoformans and C. gattii around the Mediterranean basin. FEMS Yeast Res., 16."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Khayhan, K., Hagen, F., Pan, W., Simwami, S., Fisher, M.C., Wahyuningsih, R., Chakrabarti, A., Chowdhary, A., Ikeda, R., and Taj-Aldeen, S.J. (2013). Geographically structured populations of Cryptococcus neoformans variety grubii in Asia correlate with HIV status and show a clonal population structure. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0072222"}],"container-title":["Journal of Fungi"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2309-608X\/7\/5\/338\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:53:35Z","timestamp":1760162015000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2309-608X\/7\/5\/338"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,27]]},"references-count":40,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2021,5]]}},"alternative-id":["jof7050338"],"URL":"https:\/\/doi.org\/10.3390\/jof7050338","relation":{},"ISSN":["2309-608X"],"issn-type":[{"value":"2309-608X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,27]]}}}