{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T02:22:34Z","timestamp":1790389354157,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pntd.0013778","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T00:00:00Z","timestamp":1767139200000}}],"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T00:00:00Z","timestamp":1766361600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["Fogarty International Center Global Infectious Disease research training grant"],"award-info":[{"award-number":["Fogarty International Center Global Infectious Disease research training grant"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute for Communicable Diseases","award":["D43TW011255"],"award-info":[{"award-number":["D43TW011255"]}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health and Care Research","doi-asserted-by":"publisher","award":["NIHR134342 and NIHR303140"],"award-info":[{"award-number":["NIHR134342 and NIHR303140"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Histoplasma capsulatum<\/jats:italic>\n                      naturally occurs in cave soil enriched by bat guano. South African caves are documented as probable sources of exposure for speleologists, casual visitors, or guano miners with several outbreaks of acute pulmonary histoplasmosis reported since 1977. Sporadic cases of disseminated histoplasmosis occur in South Africans living with advanced HIV disease. However, detection from the environment has not been confirmed. We used molecular assays to detect and confirm the presence of\n                      <jats:italic>H. capsulatum<\/jats:italic>\n                      in regularly-explored caves.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Environmental samples were collected by a speleologist from seven South African caves from December 2020 to September 2021 in the Gauteng, Northern Cape and Western Cape provinces of South Africa and stored at 2\u20138\n                      <jats:sup>\u00b0<\/jats:sup>\n                      C. DNA was extracted directly from the samples using DNeasy PowerSoil Pro Kit. In-house internal transcribed spacer (\n                      <jats:italic>ITS<\/jats:italic>\n                      ) panfungal polymerase chain reaction (PCR), pan-dimorphic reverse transcriptase-quantitative (RT-q) PCR and nested Hc100 PCR assays were used to detect\n                      <jats:italic>H. capsulatum<\/jats:italic>\n                      . Sequence identity was confirmed using the National Centre for Biotechnology Information (NCBI) BLAST tool following Sanger sequencing of the Hc100 nested-PCR product.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      <jats:italic>H. capsulatum<\/jats:italic>\n                      was detected in five of the seven caves. Of 56 samples tested, 18 (32%) were positive from three caves in Gauteng Province [cave 1 (3\/10); cave 2 (7\/10); cave 3 (5\/10)], one cave in the Western Cape Province [cave 4 (2\/5)] and one cave in the Northern Cape Province [cave 6 (1\/10)]. These samples were positive either by RT-qPCR or Hc100 PCR assays. Both RT-qPCR and Hc100 PCR assays were positive in 21% (12\/56) samples. Seven percent (4\/56) of samples were only RT-qPCR assay-positive and 4% (2\/56) only Hc100 PCR-positive. Phylogenetic analysis of the Hc100 gene product from 10 samples (with good-quality sequences) identified four groups. Group 1 consisted of three samples from caves 1, 3, and 6 (Gauteng\/ Northern Cape); Group 2 included four samples from caves 1, 2, and 3 (Gauteng); Group 3 had one sample from cave 4 (Western Cape); and Group 4 included two samples from caves 1 and 3 (Gauteng). None of the 56 samples tested positive with the\n                      <jats:italic>ITS<\/jats:italic>\n                      PCR assay.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      <jats:italic>H. capsulatum<\/jats:italic>\n                      is probably present in several regularly-explored caves with bat populations. This finding should be confirmed by culture. The RT-qPCR and the Hc100 PCR assays could be useful tools for wider environmental surveillance.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pntd.0013778","type":"journal-article","created":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T18:31:27Z","timestamp":1766428287000},"page":"e0013778","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Molecular detection of Histoplasma capsulatum in environmental samples collected from South African caves"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6117-4309","authenticated-orcid":true,"given":"Tsidiso G.","family":"Maphanga","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rutendo E.","family":"Mapengo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oresti","family":"Ventouras","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serisha D.","family":"Naicker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nelesh P.","family":"Govender","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,12,22]]},"reference":[{"issue":"1","key":"pntd.0013778.ref001","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0006046","article-title":"Histoplasmosis in Africa: An emerging or a neglected disease?","volume":"12","author":"RO Oladele","year":"2018","journal-title":"PLoS Negl Trop Dis"},{"issue":"5","key":"pntd.0013778.ref002","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1007\/s11046-020-00431-2","article-title":"Re-drawing the Maps for Endemic Mycoses","volume":"185","author":"N Ashraf","year":"2020","journal-title":"Mycopathologia"},{"issue":"9","key":"pntd.0013778.ref003","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.00564-25","article-title":"Genomic epidemiology of Histoplasma in Africa","volume":"16","author":"RE Mapengo","year":"2025","journal-title":"mBio"},{"key":"pntd.0013778.ref004","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1002\/path.1700540303","article-title":"Histoplasmosis: report of a case","volume":"54","author":"FW Simson","year":"1942","journal-title":"J Path Bact"},{"issue":"9","key":"pntd.0013778.ref005","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0010737","article-title":"Endemic mycoses in South Africa, 2010-2020: A decade-long description of laboratory-diagnosed cases and prospects for the future","volume":"16","author":"RE Mapengo","year":"2022","journal-title":"PLoS Negl Trop Dis"},{"key":"pntd.0013778.ref006","first-page":"89","article-title":"Histoplasmosis in the Cape Province","volume":"55","author":"SA Craven","year":"1979","journal-title":"S Afr Med J"},{"issue":"4","key":"pntd.0013778.ref007","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1006\/mcpr.1999.0247","article-title":"Direct detection of Histoplasma capsulatum in soil suspensions by two-stage PCR","volume":"13","author":"TM Reid","year":"1999","journal-title":"Mol Cell Probes"},{"issue":"8","key":"pntd.0013778.ref008","doi-asserted-by":"crossref","first-page":"930","DOI":"10.2105\/AJPH.42.8.930","article-title":"Isolation of histoplasma capsulatum from soil","volume":"42","author":"LD Zeidberg","year":"1952","journal-title":"Am J Public Health Nations Health"},{"issue":"7","key":"pntd.0013778.ref009","first-page":"1020","article-title":"Histoplasma capsulatum in the soil of Gangetic Plain in India","volume":"63","author":"M Sanyal","year":"1975","journal-title":"Indian J Med Res"},{"issue":"7","key":"pntd.0013778.ref010","doi-asserted-by":"crossref","DOI":"10.1128\/aem.02010-21","article-title":"Considerations about the Geographic Distribution of Histoplasma Species","volume":"88","author":"ML Taylor","year":"2022","journal-title":"Appl Environ Microbiol"},{"issue":"6","key":"pntd.0013778.ref011","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1136\/thx.49.6.598","article-title":"Tropical respiratory medicine. 3. 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