{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,28]],"date-time":"2026-06-28T07:17:42Z","timestamp":1782631062973,"version":"3.54.5"},"reference-count":105,"publisher":"Microbiology Society","issue":"1","license":[{"start":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T00:00:00Z","timestamp":1705363200000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,16]]},"abstract":"<jats:p>\n                  <jats:italic>Candida glabrata<\/jats:italic> is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common <jats:italic>Candida<\/jats:italic> pathogen causing bloodstream infections. Although there are many studies on the epidemiology of <jats:italic>C. glabrata<\/jats:italic> infections, the fine- and large-scale geographical nature of <jats:italic>C. glabrata<\/jats:italic> remain incompletely understood. Here we investigated both the fine- and large-scale population structure of <jats:italic>C. glabrata<\/jats:italic> through genome sequencing of 80 clinical isolates obtained from six tertiary hospitals in Qatar and by comparing with global collections. Our fine-scale analyses revealed high genetic diversity within the Qatari population of <jats:italic>C. glabrata<\/jats:italic> and identified signatures of recombination, inbreeding and clonal expansion within and between hospitals, including evidence for nosocomial transmission among coronavirus disease 2019 (COVID-19) patients. In addition to signatures of recombination at the population level, both MATa and MAT\u03b1 alleles were detected in most hospitals, indicating the potential for sexual reproduction in clinical environments. Comparisons with global samples showed that the Qatari <jats:italic>C. glabrata<\/jats:italic> population was very similar to those from other parts of the world, consistent with the significant role of recent anthropogenic activities in shaping its population structure. Genome-wide association studies identified both known and novel genomic variants associated with reduced susceptibilities to fluconazole, 5-flucytosine and echinocandins. Together, our genomic analyses revealed the diversity, transmission patterns and antifungal drug resistance mechanisms of <jats:italic>C. glabrata<\/jats:italic> in Qatar as well as the relationships between Qatari isolates and those from other parts of the world.<\/jats:p>","DOI":"10.1099\/mgen.0.001179","type":"journal-article","created":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T15:16:48Z","timestamp":1705418208000},"source":"Crossref","is-referenced-by-count":13,"title":["Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections"],"prefix":"10.1099","volume":"10","author":[{"given":"Yue","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Biology, McMaster University, Hamilton, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianping","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Biology, McMaster University, Hamilton, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatma","family":"Ben Abid","sequence":"additional","affiliation":[{"name":"Communicable Disease Centre, Hamad Medical Corporation, Doha, Qatar"},{"name":"Weill Cornell Medicine-Qatar, Doha, Qatar"},{"name":"Department of Medicine, Division of Infectious Diseases, Hamad Medical Corporation, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Husam","family":"Salah","sequence":"additional","affiliation":[{"name":"Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sathyavathi","family":"Sundararaju","sequence":"additional","affiliation":[{"name":"Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khalil","family":"Al Ismail","sequence":"additional","affiliation":[{"name":"Communicable Disease Centre, Hamad Medical Corporation, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kun","family":"Wang","sequence":"additional","affiliation":[{"name":"Research Department, Sidra Medicine, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Sara Matthew","sequence":"additional","affiliation":[{"name":"Research Department, Sidra Medicine, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saad","family":"Taj-Aldeen","sequence":"additional","affiliation":[{"name":"Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emad B.","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Tang","sequence":"additional","affiliation":[{"name":"Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar"},{"name":"Weill Cornell Medicine-Qatar, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andres","family":"Perez-Lopez","sequence":"additional","affiliation":[{"name":"Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar"},{"name":"Weill Cornell Medicine-Qatar, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5129-1037","authenticated-orcid":false,"given":"Clement K. M.","family":"Tsui","sequence":"additional","affiliation":[{"name":"Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar"},{"name":"Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada"},{"name":"Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore"},{"name":"Infectious Diseases Research Laboratory, National Center for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.12.1.80"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1002\/mlf2.12036"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1111\/1567-1364.12145"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1111\/1469-0691.12539"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0101510"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1111\/myc.12531"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1080\/13693780701218689"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1534\/g3.118.200182"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1016\/j.idc.2015.10.013"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00029-06"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2011.02.016"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1111\/j.1470-9465.2004.t01-1-00844.x"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.3760\/cma.j.cn112137-20200302-00555"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1007\/s11046-017-0228-3"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejogrb.2022.07.012"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.4103\/0377-4929.68266"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-023-00861-x"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.37.12.3835-3843.1999"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2020.571069"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.4172\/1989-8436.100086"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1093\/mmy\/myx030"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02946"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.808890"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1016\/j.simyco.2021.100133"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms11128"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1128\/EC.00299-07"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01827-22"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/iyac031"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkw422"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1093\/mmy\/myv114"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofy358"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2022.05.004"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1002\/jcla.23226"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1007\/s11046-019-00388-x"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.3201\/eid2703.203482"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1009582"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1009005"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2013.07.013"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.49.2.668-679.2005"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01924-17"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1080\/14787210.2020.1792773"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00423-08"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2019.00352"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2017.10.044"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1038\/nrdp.2018.26"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1097\/QCO.0000000000000411"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-63240-z"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2019.03.028"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1093\/femsyr\/fov110"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.1128\/EC.2.2.328-340.2003"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1093\/femsyr\/fow082"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.71.12.7109-7118.2003"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0140990"},{"key":"R54","article-title":"Statistics Site"},{"key":"R55","article-title":"Population of Qatar by nationality","year":"2019"},{"key":"R56","doi-asserted-by":"publisher","DOI":"10.1007\/s15010-013-0570-4"},{"key":"R57","article-title":"CLSI M60-Ed1 - Performance Standards for Antifungal Susceptibility Testing of Yeasts - 1st Edition"},{"key":"R58","article-title":"CLSI M59-Ed3 - Epidemiological Cutoff Values for Antifungal Susceptibility Testing - 3rd Edition"},{"key":"R59","article-title":"FastQC: a quality control tool for high throughput sequence data \u2013 ScienceOpen"},{"key":"R60","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R61","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013","journal-title":"ArXiv"},{"key":"R62","article-title":"Haplotype-based variant detection from short-read sequencing","author":"Garrison","year":"2012"},{"key":"R63","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490"},{"key":"R64","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab301"},{"key":"R65","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2017.11.027"},{"key":"R66","doi-asserted-by":"publisher","DOI":"10.1186\/s13742-015-0047-8"},{"key":"R67","doi-asserted-by":"publisher","DOI":"10.1101\/gr.094052.109"},{"key":"R68","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"R69","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"R70","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"R71","doi-asserted-by":"publisher","DOI":"10.1109\/MCSE.2007.55"},{"key":"R72","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2649-2"},{"key":"R73","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"R74","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.27256-0"},{"key":"R75","doi-asserted-by":"publisher","DOI":"10.1016\/j.fgb.2010.11.001"},{"key":"R76","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005767"},{"key":"R77","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2021.08.005"},{"key":"R78","doi-asserted-by":"publisher","DOI":"10.3390\/jof7080667"},{"key":"R79","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw924"},{"key":"R80","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.030072-0"},{"key":"R81","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.911322"},{"key":"R82","doi-asserted-by":"publisher","DOI":"10.1007\/s00284-022-02824-6"},{"key":"R83","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00065-15"},{"key":"R84","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0052871"},{"key":"R85","doi-asserted-by":"publisher","DOI":"10.3390\/genes13010019"},{"key":"R86","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2022.06.030"},{"key":"R87","doi-asserted-by":"publisher","DOI":"10.1128\/JB.181.4.1369-1373.1999"},{"key":"R88","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00900"},{"key":"R89","doi-asserted-by":"publisher","DOI":"10.3390\/genes13112045"},{"key":"R90","doi-asserted-by":"publisher","DOI":"10.3390\/jof9020276"},{"key":"R91","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-018-3381-5"},{"key":"R92","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2019.05.001"},{"key":"R93","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msj008"},{"key":"R94","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1011704"},{"key":"R95","doi-asserted-by":"publisher","DOI":"10.3390\/genes11010101"},{"key":"R96","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2019.06.073"},{"key":"R97","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkac110"},{"key":"R98","doi-asserted-by":"publisher","DOI":"10.18869\/acadpub.cmm.2.4.24"},{"key":"R99","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-143-2-405"},{"key":"R100","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00074-13"},{"key":"R101","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000268"},{"key":"R102","doi-asserted-by":"publisher","DOI":"10.1111\/myc.13104"},{"key":"R103","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkl221"},{"key":"R104","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-022-00720-1"},{"key":"R105","doi-asserted-by":"publisher","DOI":"10.3390\/jof7100860"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001179?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,22]],"date-time":"2024-01-22T14:17:34Z","timestamp":1705933054000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001179"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,16]]},"references-count":105,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,1,16]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001179","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,16]]}}}