{"id":"https://openalex.org/W4416634436","doi":"https://doi.org/10.1183/13993003.congress-2025.pa1725","title":"Respiratory tract mycobiota profiles and bacterial-fungal co-occurrence after severe COVID-19 are associated with lung function","display_name":"Respiratory tract mycobiota profiles and bacterial-fungal co-occurrence after severe COVID-19 are associated with lung function","publication_year":2025,"publication_date":"2025-09-27","ids":{"openalex":"https://openalex.org/W4416634436","doi":"https://doi.org/10.1183/13993003.congress-2025.pa1725"},"language":null,"primary_location":{"id":"doi:10.1183/13993003.congress-2025.pa1725","doi":"https://doi.org/10.1183/13993003.congress-2025.pa1725","is_oa":false,"landing_page_url":"https://doi.org/10.1183/13993003.congress-2025.pa1725","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Respiratory infections and bronchiectasis","raw_type":"proceedings-article"},"volume":null,"type":"conference-abstract","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067774408","display_name":"Sabine V. Stadler","orcid":"https://orcid.org/0009-0001-9581-2153","observed_orcids":["https://orcid.org/0009-0001-9581-2153"]},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"Centre Hospitalier Universitaire Vaudois","ror":"https://ror.org/05a353079","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Sabine Stadler","raw_affiliation_strings":["1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114539851","display_name":"Luca Stickley","orcid":"https://orcid.org/0000-0001-6344-3122","observed_orcids":["https://orcid.org/0000-0001-6344-3122"]},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"Centre Hospitalier Universitaire Vaudois","ror":"https://ror.org/05a353079","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Luca Stickley","raw_affiliation_strings":["1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014639963","display_name":"Eric Bernasconi","orcid":"https://orcid.org/0000-0002-4641-1409","observed_orcids":["https://orcid.org/0000-0002-4641-1409"]},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"Centre Hospitalier Universitaire Vaudois","ror":"https://ror.org/05a353079","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Eric Bernasconi","raw_affiliation_strings":["1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114539852","display_name":"Seher Guney","orcid":"https://orcid.org/0009-0004-6490-3724","observed_orcids":["https://orcid.org/0009-0004-6490-3724"]},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"Centre Hospitalier Universitaire Vaudois","ror":"https://ror.org/05a353079","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Seher Guney","raw_affiliation_strings":["1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061922083","display_name":"Louis Mercier","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"Centre Hospitalier Universitaire Vaudois","ror":"https://ror.org/05a353079","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Louis Mercier","raw_affiliation_strings":["1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044531408","display_name":"Berra Erko\u015far","orcid":"https://orcid.org/0000-0003-1152-6772","observed_orcids":["https://orcid.org/0000-0003-1152-6772"]},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"Centre Hospitalier Universitaire Vaudois","ror":"https://ror.org/05a353079","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Berra Erkosar","raw_affiliation_strings":["1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034045334","display_name":"Manuela Funke-Chambour","orcid":"https://orcid.org/0000-0003-3417-5872","observed_orcids":["https://orcid.org/0000-0003-3417-5872"]},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]},{"id":"https://openalex.org/I2801112126","display_name":"University Hospital of Bern","ror":"https://ror.org/01q9sj412","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I2801112126"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Manuela Funke-Chambour","raw_affiliation_strings":["2Department of Pulmonary Medicine, Allergology and Clinical Immunology, Inselspital, Bern University Hospital, University of Bern and Department for BioMedical Research DBMR, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2Department of Pulmonary Medicine, Allergology and Clinical Immunology, Inselspital, Bern University Hospital, University of Bern and Department for BioMedical Research DBMR, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535","https://openalex.org/I2801112126"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089959402","display_name":"Christophe von Garnier","orcid":"https://orcid.org/0000-0003-3585-9176","observed_orcids":["https://orcid.org/0000-0003-3585-9176"]},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"Centre Hospitalier Universitaire Vaudois","ror":"https://ror.org/05a353079","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Christophe Von Garnier","raw_affiliation_strings":["1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882","https://openalex.org/I97565354"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038328550","display_name":"Niki D. J. Ubags","orcid":"https://orcid.org/0000-0002-0177-4134","observed_orcids":["https://orcid.org/0000-0002-0177-4134"]},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"Centre Hospitalier Universitaire Vaudois","ror":"https://ror.org/05a353079","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Niki Ubags","raw_affiliation_strings":["1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882","https://openalex.org/I97565354"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"PA1725","last_page":"PA1725"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11368","display_name":"Long-Term Effects of COVID-19","score":0.42719998955726624,"subfield":{"id":"https://openalex.org/subfields/2728","display_name":"Neurology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11368","display_name":"Long-Term Effects of COVID-19","score":0.42719998955726624,"subfield":{"id":"https://openalex.org/subfields/2728","display_name":"Neurology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10150","display_name":"Antifungal resistance and susceptibility","score":0.20100000500679016,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10041","display_name":"COVID-19 Clinical Research Studies","score":0.11909999698400497,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/severe-covid-19","display_name":"severe COVID-19","score":0.9390000104904175},{"id":"https://openalex.org/keywords/sars-cov-2","display_name":"SARS-CoV-2","score":0.9390000104904175},{"id":"https://openalex.org/keywords/lung-function-recovery","display_name":"lung function recovery","score":0.8489999771118164},{"id":"https://openalex.org/keywords/oropharyngeal-microbiota","display_name":"oropharyngeal microbiota","score":0.9440000057220459},{"id":"https://openalex.org/keywords/candida","display_name":"Candida","score":0.8190000057220459},{"id":"https://openalex.org/keywords/cladosporium","display_name":"Cladosporium","score":0.8519999980926514},{"id":"https://openalex.org/keywords/saccharomyces","display_name":"Saccharomyces","score":0.9150000214576721},{"id":"https://openalex.org/keywords/rothia","display_name":"Rothia","score":0.9919999837875366},{"id":"https://openalex.org/keywords/streptococcus","display_name":"Streptococcus","score":0.8600000143051147},{"id":"https://openalex.org/keywords/neisseria","display_name":"Neisseria","score":0.8040000200271606},{"id":"https://openalex.org/keywords/veillonella","display_name":"Veillonella","score":0.9929999709129333},{"id":"https://openalex.org/keywords/predictive-biomarkers","display_name":"predictive biomarkers","score":0.6209999918937683}],"concepts":[{"id":"https://openalex.org/C2777649605","wikidata":"https://www.wikidata.org/wiki/Q1474267","display_name":"Mycobiota","level":2,"score":0.916700005531311},{"id":"https://openalex.org/C2779644171","wikidata":"https://www.wikidata.org/wiki/Q13400765","display_name":"Respiratory tract","level":3,"score":0.5946000218391418},{"id":"https://openalex.org/C2777714996","wikidata":"https://www.wikidata.org/wiki/Q7886","display_name":"Lung","level":2,"score":0.5083000063896179},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4846999943256378},{"id":"https://openalex.org/C3018587741","wikidata":"https://www.wikidata.org/wiki/Q7886","display_name":"Lung function","level":3,"score":0.4440999925136566},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.4194999933242798},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3937999904155731},{"id":"https://openalex.org/C2776012195","wikidata":"https://www.wikidata.org/wiki/Q754447","display_name":"Respiratory tract infections","level":3,"score":0.3806999921798706},{"id":"https://openalex.org/C2777165150","wikidata":"https://www.wikidata.org/wiki/Q269334","display_name":"Dysbiosis","level":3,"score":0.36820000410079956},{"id":"https://openalex.org/C534529494","wikidata":"https://www.wikidata.org/wiki/Q7891","display_name":"Respiratory system","level":2,"score":0.36149999499320984},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.3490999937057495},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.32089999318122864},{"id":"https://openalex.org/C155794727","wikidata":"https://www.wikidata.org/wiki/Q2306414","display_name":"Internal transcribed spacer","level":4,"score":0.3131999969482422},{"id":"https://openalex.org/C151437367","wikidata":"https://www.wikidata.org/wiki/Q7884646","display_name":"UniFrac","level":4,"score":0.3027999997138977},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.30230000615119934},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.29159998893737793},{"id":"https://openalex.org/C2776178081","wikidata":"https://www.wikidata.org/wiki/Q3286546","display_name":"Respiratory disease","level":3,"score":0.2879999876022339},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.27790001034736633},{"id":"https://openalex.org/C90924648","wikidata":"https://www.wikidata.org/wiki/Q120569","display_name":"Gastroenterology","level":1,"score":0.26489999890327454}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1183/13993003.congress-2025.pa1725","doi":"https://doi.org/10.1183/13993003.congress-2025.pa1725","is_oa":false,"landing_page_url":"https://doi.org/10.1183/13993003.congress-2025.pa1725","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Respiratory infections and bronchiectasis","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":1.0}],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Introduction:":[0],"Severe":[1],"SARS-CoV-2":[2,69,193],"infection":[3,70],"disrupts":[4],"the":[5,24,117,122,126,176],"respiratory":[6],"tract":[7],"microenvironment.":[8],"Such":[9],"dysbiosis":[10],"may":[11],"persist":[12],"and":[13,28,30,45,59,93,110,146,163,175,180],"contribute":[14],"to":[15,88],"post-acute":[16],"pulmonary":[17,202],"sequelae.":[18],"This":[19],"one-year":[20],"follow-up":[21,79],"study":[22],"investigated":[23],"oropharyngeal":[25],"(OP)":[26],"micro-":[27,92],"mycobiota":[29,94,101],"their":[31,196],"association":[32],"with":[33,67,91,148,153,187],"lung":[34,83,160,188],"function":[35,84,161,189],"recovery":[36,190,203],"after":[37,191],"severe":[38,68,192],"COVID-19.":[39],"Methods:":[40],"Internal":[41],"Transcribed":[42],"Spacer":[43],"(ITS)":[44],"16S":[46],"rRNA":[47],"amplicon":[48],"sequencing":[49],"were":[50,86,133],"performed":[51],"on":[52],"OP":[53],"swabs":[54],"collected":[55],"at":[56],"3,":[57],"6":[58],"12":[60],"months":[61],"post-hospitalisation":[62],"from":[63],"83":[64],"ICU-admitted":[65],"patients":[66],"(Swiss":[71],"COVIDlung":[72],"study,":[73],"NCT":[74],"04581135).":[75],"Participants":[76],"attended":[77],"1-3":[78],"visits,":[80],"during":[81],"which":[82],"tests":[85],"conducted":[87],"assess":[89],"correlations":[90],"composition.":[95,139],"Results:":[96],"Unsupervised":[97],"clustering":[98],"identified":[99],"three":[100],"profiles":[102],"dominated":[103],"by":[104,136,169],"Saccharomyces":[105],"(cluster":[106],"1),":[107],"Candida":[108,174],"(2)":[109],"Cladosporium":[111],"(3).":[112],"The":[113],"Cladosporium-dominated":[114],"cluster":[115,124],"exhibited":[116],"lowest":[118,127],"ITS":[119,131],"load,":[120],"while":[121],"Candida-dominated":[123],"had":[125],"fungal":[128],"diversity.":[129],"These":[130],"clusters":[132],"also":[134],"characterised":[135],"distinct":[137],"bacterial":[138],"Cluster":[140],"2":[141],"subjects":[142],"showed":[143],"increased":[144],"Rothia":[145,149],"Streptococcus,":[147],"abundance":[150],"positively":[151],"correlating":[152],"FVC":[154],"(p=0.047).":[155],"Mixed-effect":[156],"models":[157],"demonstrated":[158],"that":[159],"(FVC":[162],"FEV1)":[164],"could":[165],"be":[166],"significantly":[167],"predicted":[168],"bacterial-fungal":[170],"co-occurrence,":[171],"particularly":[172],"between":[173],"bacteria":[177],"Neisseria,":[178],"Veillonella":[179],"Rothia.":[181],"Conclusion:":[182],"Bacterial-fungal":[183],"interactions":[184],"are":[185],"associated":[186],"infection,":[194],"highlighting":[195],"potential":[197],"as":[198],"predictive":[199],"biomarkers":[200],"for":[201],"in":[204],"affected":[205],"patients.":[206]},"counts_by_year":[],"updated_date":"2026-09-22T06:50:58.402377","created_date":"2025-11-25T00:00:00"}