{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T05:50:02Z","timestamp":1762926602491,"version":"3.37.3"},"reference-count":26,"publisher":"Microbiology Society","issue":"3","license":[{"start":{"date-parts":[[2021,3,1]],"date-time":"2021-03-01T00:00:00Z","timestamp":1614556800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Medical Research Council","award":["MR\/N006364\/2"],"award-info":[{"award-number":["MR\/N006364\/2"]}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"crossref","award":["U19AI110818"],"award-info":[{"award-number":["U19AI110818"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["215239\/Z\/19\/Z"],"award-info":[{"award-number":["215239\/Z\/19\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Medical Research Council","award":["MR\/R015600\/1"],"award-info":[{"award-number":["MR\/R015600\/1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,3,1]]},"abstract":"<jats:p>In 2018, a cluster of two cases of cryptococcosis occurred at the Queen Elizabeth University Hospital (QEUH) in Glasgow, Scotland (UK). It was postulated that these cases may have been linked to pigeon droppings found on the hospital site, given there have been previous reports of <jats:italic>Cryptococcus neoformans<\/jats:italic> associated with pigeon guano. Although some samples of pigeon guano taken from the site yielded culturable yeast from genera related to <jats:italic>Cryptococcus<\/jats:italic>, they have since been classified as <jats:italic>Naganishia<\/jats:italic> or <jats:italic>Papiliotrema<\/jats:italic> spp., and no isolates of <jats:italic>C. neoformans<\/jats:italic> were recovered from either the guano or subsequent widespread air sampling. In an attempt to further elucidate any possible shared source of the clinical isolates, we used whole-genome sequencing and phylogenetic analysis to examine the relationship of the two <jats:italic>Cryptococcus<\/jats:italic> isolates from the QEUH cases, along with two isolates from sporadic cases treated at a different Glasgow hospital earlier in 2018. Our work demonstrated that these four clinical isolates were not clonally related; while all isolates were from the VNI global lineage and of the same mating type (MAT\u03b1), the genotypes of the two QEUH isolates were separated by 1885 base changes and belonged to different sub-lineages, recently described as the intercontinental sub-clades VNIa-93 and VNIa-5. In contrast, one of the two sporadic 2018 clinical isolates was determined to belong to the VNIb sub-lineage and the other classified as a VNIV\/VNI hybrid. Our work demonstrated that the two 2018 QEUH isolates and the two prior <jats:italic>C. neoformans<\/jats:italic> clinical isolates were all genetically distinct. It was not possible to determine whether the QEUH genotypes stemmed from independent sources or from the same source, i.e. pigeons carrying different genotypes, but it should be noted that whilst members of allied genera within the <jats:italic>Tremellomycetes<\/jats:italic> were isolated from the hospital environment, there were no environmental isolations of <jats:italic>C. neoformans<\/jats:italic>.<\/jats:p>","DOI":"10.1099\/mgen.0.000537","type":"journal-article","created":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T16:31:50Z","timestamp":1614097910000},"source":"Crossref","is-referenced-by-count":3,"title":["Genomic epidemiology of a Cryptococcus neoformans case cluster in Glasgow, Scotland, 2018"],"prefix":"10.1099","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8456-7458","authenticated-orcid":false,"given":"Rhys A.","family":"Farrer","sequence":"first","affiliation":[{"name":"Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4PY, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0585-5721","authenticated-orcid":false,"given":"Andrew M.","family":"Borman","sequence":"additional","affiliation":[{"name":"Public Health England National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK"},{"name":"Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4PY, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teresa","family":"Inkster","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Queen Elizabeth University Hospital, Glasgow, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1862-6402","authenticated-orcid":false,"given":"Matthew C.","family":"Fisher","sequence":"additional","affiliation":[{"name":"Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3100-6969","authenticated-orcid":false,"given":"Elizabeth M.","family":"Johnson","sequence":"additional","affiliation":[{"name":"Public Health England National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK"},{"name":"Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4PY, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5778-960X","authenticated-orcid":false,"given":"Christina A.","family":"Cuomo","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1016\/bs.adgen.2020.02.001"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-280X.1999.00241.x"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(17)30243-8"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1128\/EC.00097-07"},{"key":"R5","article-title":"Isolation and detection of Cryptococcus neoformans from pigeon droppings: Isfahan and it\u2019s suburbs province pigeon towers","volume":"6","author":"Isfahani","year":"2001","journal-title":"J Res Med Sci"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1080\/00362178385380241"},{"volume":"45","volume-title":"Center for Food Security and Public Health Tech Factsheets","year":"2013","key":"R7"},{"key":"R8","first-page":"429","volume-title":"Cryptococcus: from Human Pathogen to Model Yeast","author":"Dromer","year":"2010"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.37.10.3204-3209.1999"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1172\/JCI136223"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004261"},{"key":"R12","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013","journal-title":"arXiv"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1101\/gr.218727.116"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp077"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0093766"},{"year":"2019","key":"R19","article-title":"Two dead after pigeon dropping infection. BBC News, 19 January 2019 (https:\/\/www.bbc.com\/news\/uk-scotland-glasgow-west-46931028);"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10092-5"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0019688"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1128\/EC.2.6.1162-1168.2003"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.117.203836"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000848"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.3201\/eid2110.150249"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.32.5.1188-1192.1994"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000537?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T00:25:46Z","timestamp":1702599946000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000537"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,3,1]]},"references-count":26,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,3,1]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000537","relation":{},"ISSN":["2057-5858"],"issn-type":[{"type":"electronic","value":"2057-5858"}],"subject":[],"published":{"date-parts":[[2021,3,1]]}}}