Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and on recovery. We performed deep shotg...
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| Veröffentlicht in: | Gastroenterology (New York, N.Y. 1943) N.Y. 1943), 2020-10, Vol.159 (4), p.1302-1310.e5 |
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| creator | Zuo, Tao Zhan, Hui Zhang, Fen Liu, Qin Tso, Eugene Y.K. Lui, Grace C.Y. Chen, Nan Li, Amy Lu, Wenqi Chan, Francis K.L. Chan, Paul K.S. Ng, Siew C. |
| description | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and on recovery.
We performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 patients with coronavirus disease 2019 (COVID-19) in Hong Kong, from February 5 through May 12, 2020. Fecal samples were collected 2 to 3 times per week from time of hospitalization until discharge. We compared fecal mycobiome compositions of patients with COVID-19 with those from 9 subjects with community-acquired pneumonia and 30 healthy individuals (controls). We assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples.
Patients with COVID-19 had significant alterations in their fecal mycobiomes compared with controls, characterized by enrichment of Candia albicans and a highly heterogeneous mycobiome configuration, at time of hospitalization. Although fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from those of controls during times of hospitalization, 8 of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition, through the last sample collected. The diversity of the fecal mycobiome of the last sample collected from patients with COVID-19 was 2.5-fold higher than that of controls (P < .05). Samples collected at all timepoints from patients with COVID-19 had increased proportions of opportunistic fungal pathogens, Candida albicans, Candida auris, and Aspergillus flavus compared with controls. Two respiratory-associated fungal pathogens, A. flavus and Aspergillus niger, were detected in fecal samples from a subset of patients with COVID-19, even after clearance of SARS-CoV-2 from nasopharyngeal samples and resolution of respiratory symptoms.
In a pilot study, we found heterogeneous configurations of the fecal mycobiome, with enrichment of fungal pathogens from the genera Candida and Aspergillus, during hospitalization of 30 patients with COVID-19 compared with controls. Unstable gut mycobiomes and prolonged dysbiosis persisted in a subset of patients with COVID-19 up to 12 days after nasopharyngeal clearance of SARS-CoV-2. Studies are needed to determine whether alterations in intestinal fungi contribute to or result from SARS-CoV-2 infection, and the effects of the |
| doi_str_mv | 10.1053/j.gastro.2020.06.048 |
| format | Article |
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We performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 patients with coronavirus disease 2019 (COVID-19) in Hong Kong, from February 5 through May 12, 2020. Fecal samples were collected 2 to 3 times per week from time of hospitalization until discharge. We compared fecal mycobiome compositions of patients with COVID-19 with those from 9 subjects with community-acquired pneumonia and 30 healthy individuals (controls). We assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples.
Patients with COVID-19 had significant alterations in their fecal mycobiomes compared with controls, characterized by enrichment of Candia albicans and a highly heterogeneous mycobiome configuration, at time of hospitalization. Although fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from those of controls during times of hospitalization, 8 of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition, through the last sample collected. The diversity of the fecal mycobiome of the last sample collected from patients with COVID-19 was 2.5-fold higher than that of controls (P < .05). Samples collected at all timepoints from patients with COVID-19 had increased proportions of opportunistic fungal pathogens, Candida albicans, Candida auris, and Aspergillus flavus compared with controls. Two respiratory-associated fungal pathogens, A. flavus and Aspergillus niger, were detected in fecal samples from a subset of patients with COVID-19, even after clearance of SARS-CoV-2 from nasopharyngeal samples and resolution of respiratory symptoms.
In a pilot study, we found heterogeneous configurations of the fecal mycobiome, with enrichment of fungal pathogens from the genera Candida and Aspergillus, during hospitalization of 30 patients with COVID-19 compared with controls. Unstable gut mycobiomes and prolonged dysbiosis persisted in a subset of patients with COVID-19 up to 12 days after nasopharyngeal clearance of SARS-CoV-2. Studies are needed to determine whether alterations in intestinal fungi contribute to or result from SARS-CoV-2 infection, and the effects of these changes in disease progression.
[Display omitted]</description><identifier>ISSN: 0016-5085</identifier><identifier>EISSN: 1528-0012</identifier><identifier>DOI: 10.1053/j.gastro.2020.06.048</identifier><identifier>PMID: 32598884</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Adult ; Aged ; Aspergillus flavus - genetics ; Aspergillus flavus - isolation & purification ; Aspergillus niger - genetics ; Aspergillus niger - isolation & purification ; Betacoronavirus ; Candida - genetics ; Candida - isolation & purification ; Candida albicans - genetics ; Candida albicans - isolation & purification ; Case-Control Studies ; Community-Acquired Infections - microbiology ; Coronavirus Infections - microbiology ; Coronovirus ; COVID-19 ; DNA, Fungal - analysis ; Feces - microbiology ; Female ; Fungi - genetics ; Fungi - isolation & purification ; Gastrointestinal Microbiome ; Humans ; Intestine ; Male ; Metagenomics ; Microbe ; Middle Aged ; Mycobiome ; Nasopharynx - virology ; Original Research ; Pandemics ; Patient Discharge ; Pneumonia - microbiology ; Pneumonia, Viral - microbiology ; SARS-CoV-2 ; Time Factors ; Yeast ; Young Adult</subject><ispartof>Gastroenterology (New York, N.Y. 1943), 2020-10, Vol.159 (4), p.1302-1310.e5</ispartof><rights>2020 The Authors</rights><rights>Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.</rights><rights>2020 The Authors 2020</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c463t-e3359807d9bd53bf28040364d8242874ee8e74b5eb5fbe28696e238e51684b1a3</citedby><cites>FETCH-LOGICAL-c463t-e3359807d9bd53bf28040364d8242874ee8e74b5eb5fbe28696e238e51684b1a3</cites><orcidid>0000-0002-6850-4454</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1053/j.gastro.2020.06.048$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,315,781,785,886,3551,27925,27926,45996</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32598884$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zuo, Tao</creatorcontrib><creatorcontrib>Zhan, Hui</creatorcontrib><creatorcontrib>Zhang, Fen</creatorcontrib><creatorcontrib>Liu, Qin</creatorcontrib><creatorcontrib>Tso, Eugene Y.K.</creatorcontrib><creatorcontrib>Lui, Grace C.Y.</creatorcontrib><creatorcontrib>Chen, Nan</creatorcontrib><creatorcontrib>Li, Amy</creatorcontrib><creatorcontrib>Lu, Wenqi</creatorcontrib><creatorcontrib>Chan, Francis K.L.</creatorcontrib><creatorcontrib>Chan, Paul K.S.</creatorcontrib><creatorcontrib>Ng, Siew C.</creatorcontrib><title>Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge</title><title>Gastroenterology (New York, N.Y. 1943)</title><addtitle>Gastroenterology</addtitle><description>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and on recovery.
We performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 patients with coronavirus disease 2019 (COVID-19) in Hong Kong, from February 5 through May 12, 2020. Fecal samples were collected 2 to 3 times per week from time of hospitalization until discharge. We compared fecal mycobiome compositions of patients with COVID-19 with those from 9 subjects with community-acquired pneumonia and 30 healthy individuals (controls). We assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples.
Patients with COVID-19 had significant alterations in their fecal mycobiomes compared with controls, characterized by enrichment of Candia albicans and a highly heterogeneous mycobiome configuration, at time of hospitalization. Although fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from those of controls during times of hospitalization, 8 of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition, through the last sample collected. The diversity of the fecal mycobiome of the last sample collected from patients with COVID-19 was 2.5-fold higher than that of controls (P < .05). Samples collected at all timepoints from patients with COVID-19 had increased proportions of opportunistic fungal pathogens, Candida albicans, Candida auris, and Aspergillus flavus compared with controls. Two respiratory-associated fungal pathogens, A. flavus and Aspergillus niger, were detected in fecal samples from a subset of patients with COVID-19, even after clearance of SARS-CoV-2 from nasopharyngeal samples and resolution of respiratory symptoms.
In a pilot study, we found heterogeneous configurations of the fecal mycobiome, with enrichment of fungal pathogens from the genera Candida and Aspergillus, during hospitalization of 30 patients with COVID-19 compared with controls. Unstable gut mycobiomes and prolonged dysbiosis persisted in a subset of patients with COVID-19 up to 12 days after nasopharyngeal clearance of SARS-CoV-2. Studies are needed to determine whether alterations in intestinal fungi contribute to or result from SARS-CoV-2 infection, and the effects of these changes in disease progression.
[Display omitted]</description><subject>Adult</subject><subject>Aged</subject><subject>Aspergillus flavus - genetics</subject><subject>Aspergillus flavus - isolation & purification</subject><subject>Aspergillus niger - genetics</subject><subject>Aspergillus niger - isolation & purification</subject><subject>Betacoronavirus</subject><subject>Candida - genetics</subject><subject>Candida - isolation & purification</subject><subject>Candida albicans - genetics</subject><subject>Candida albicans - isolation & purification</subject><subject>Case-Control Studies</subject><subject>Community-Acquired Infections - microbiology</subject><subject>Coronavirus Infections - microbiology</subject><subject>Coronovirus</subject><subject>COVID-19</subject><subject>DNA, Fungal - analysis</subject><subject>Feces - microbiology</subject><subject>Female</subject><subject>Fungi - genetics</subject><subject>Fungi - isolation & purification</subject><subject>Gastrointestinal Microbiome</subject><subject>Humans</subject><subject>Intestine</subject><subject>Male</subject><subject>Metagenomics</subject><subject>Microbe</subject><subject>Middle Aged</subject><subject>Mycobiome</subject><subject>Nasopharynx - virology</subject><subject>Original Research</subject><subject>Pandemics</subject><subject>Patient Discharge</subject><subject>Pneumonia - microbiology</subject><subject>Pneumonia, Viral - microbiology</subject><subject>SARS-CoV-2</subject><subject>Time Factors</subject><subject>Yeast</subject><subject>Young Adult</subject><issn>0016-5085</issn><issn>1528-0012</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9UU1v1DAUtBCILoV_gJCPXBKev7LOBana7baVisqhwNFykpesV9l4sZ1K8OvrsqXAhdMc3rx582YIecugZKDEh1052JiCLzlwKKEqQepnZMEU1wUA48_JIkNVKNDqhLyKcQcAtdDsJTkRXNVaa7kg_mxMGGxyforUTXSDrR3pZp6GDJ9cG3zj_B6p7-nnzMIpRfrNpS1d3Xy9Whespus5uGmgt-7IuvTx4JId3c9fonSekhvp2sV2a8OAr8mL3o4R3zziKfmyOb9dXRbXNxdXq7PropWVSAUKkR3CsqubTomm5xokiEp2mkuulxJR41I2ChvVN8h1VVfIhUbFKi0bZsUp-XjUPczNHrs2Gw92NIfg9jb8MN468-9kclsz-DuzFEzXHLLA-0eB4L_PGJPZ5x9wHO2Efo6GS1bnOFVdZ6o8UnNaMQbsn84wMA9dmZ05dmUeujJQmdxVXnv3t8Wnpd_l_PkBc1B3DoOJbW6gxc4FbJPpvPv_hXtIb6g4</recordid><startdate>20201001</startdate><enddate>20201001</enddate><creator>Zuo, Tao</creator><creator>Zhan, Hui</creator><creator>Zhang, Fen</creator><creator>Liu, Qin</creator><creator>Tso, Eugene Y.K.</creator><creator>Lui, Grace C.Y.</creator><creator>Chen, Nan</creator><creator>Li, Amy</creator><creator>Lu, Wenqi</creator><creator>Chan, Francis K.L.</creator><creator>Chan, Paul K.S.</creator><creator>Ng, Siew C.</creator><general>Elsevier Inc</general><general>by the AGA Institute. Published by Elsevier Inc</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-6850-4454</orcidid></search><sort><creationdate>20201001</creationdate><title>Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge</title><author>Zuo, Tao ; Zhan, Hui ; Zhang, Fen ; Liu, Qin ; Tso, Eugene Y.K. ; Lui, Grace C.Y. ; Chen, Nan ; Li, Amy ; Lu, Wenqi ; Chan, Francis K.L. ; Chan, Paul K.S. ; Ng, Siew C.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c463t-e3359807d9bd53bf28040364d8242874ee8e74b5eb5fbe28696e238e51684b1a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Adult</topic><topic>Aged</topic><topic>Aspergillus flavus - genetics</topic><topic>Aspergillus flavus - isolation & purification</topic><topic>Aspergillus niger - genetics</topic><topic>Aspergillus niger - isolation & purification</topic><topic>Betacoronavirus</topic><topic>Candida - genetics</topic><topic>Candida - isolation & purification</topic><topic>Candida albicans - genetics</topic><topic>Candida albicans - isolation & purification</topic><topic>Case-Control Studies</topic><topic>Community-Acquired Infections - microbiology</topic><topic>Coronavirus Infections - microbiology</topic><topic>Coronovirus</topic><topic>COVID-19</topic><topic>DNA, Fungal - analysis</topic><topic>Feces - microbiology</topic><topic>Female</topic><topic>Fungi - genetics</topic><topic>Fungi - isolation & purification</topic><topic>Gastrointestinal Microbiome</topic><topic>Humans</topic><topic>Intestine</topic><topic>Male</topic><topic>Metagenomics</topic><topic>Microbe</topic><topic>Middle Aged</topic><topic>Mycobiome</topic><topic>Nasopharynx - virology</topic><topic>Original Research</topic><topic>Pandemics</topic><topic>Patient Discharge</topic><topic>Pneumonia - microbiology</topic><topic>Pneumonia, Viral - microbiology</topic><topic>SARS-CoV-2</topic><topic>Time Factors</topic><topic>Yeast</topic><topic>Young Adult</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zuo, Tao</creatorcontrib><creatorcontrib>Zhan, Hui</creatorcontrib><creatorcontrib>Zhang, Fen</creatorcontrib><creatorcontrib>Liu, Qin</creatorcontrib><creatorcontrib>Tso, Eugene Y.K.</creatorcontrib><creatorcontrib>Lui, Grace C.Y.</creatorcontrib><creatorcontrib>Chen, Nan</creatorcontrib><creatorcontrib>Li, Amy</creatorcontrib><creatorcontrib>Lu, Wenqi</creatorcontrib><creatorcontrib>Chan, Francis K.L.</creatorcontrib><creatorcontrib>Chan, Paul K.S.</creatorcontrib><creatorcontrib>Ng, Siew C.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Gastroenterology (New York, N.Y. 1943)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zuo, Tao</au><au>Zhan, Hui</au><au>Zhang, Fen</au><au>Liu, Qin</au><au>Tso, Eugene Y.K.</au><au>Lui, Grace C.Y.</au><au>Chen, Nan</au><au>Li, Amy</au><au>Lu, Wenqi</au><au>Chan, Francis K.L.</au><au>Chan, Paul K.S.</au><au>Ng, Siew C.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge</atitle><jtitle>Gastroenterology (New York, N.Y. 1943)</jtitle><addtitle>Gastroenterology</addtitle><date>2020-10-01</date><risdate>2020</risdate><volume>159</volume><issue>4</issue><spage>1302</spage><epage>1310.e5</epage><pages>1302-1310.e5</pages><issn>0016-5085</issn><eissn>1528-0012</eissn><abstract>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and on recovery.
We performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 patients with coronavirus disease 2019 (COVID-19) in Hong Kong, from February 5 through May 12, 2020. Fecal samples were collected 2 to 3 times per week from time of hospitalization until discharge. We compared fecal mycobiome compositions of patients with COVID-19 with those from 9 subjects with community-acquired pneumonia and 30 healthy individuals (controls). We assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples.
Patients with COVID-19 had significant alterations in their fecal mycobiomes compared with controls, characterized by enrichment of Candia albicans and a highly heterogeneous mycobiome configuration, at time of hospitalization. Although fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from those of controls during times of hospitalization, 8 of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition, through the last sample collected. The diversity of the fecal mycobiome of the last sample collected from patients with COVID-19 was 2.5-fold higher than that of controls (P < .05). Samples collected at all timepoints from patients with COVID-19 had increased proportions of opportunistic fungal pathogens, Candida albicans, Candida auris, and Aspergillus flavus compared with controls. Two respiratory-associated fungal pathogens, A. flavus and Aspergillus niger, were detected in fecal samples from a subset of patients with COVID-19, even after clearance of SARS-CoV-2 from nasopharyngeal samples and resolution of respiratory symptoms.
In a pilot study, we found heterogeneous configurations of the fecal mycobiome, with enrichment of fungal pathogens from the genera Candida and Aspergillus, during hospitalization of 30 patients with COVID-19 compared with controls. Unstable gut mycobiomes and prolonged dysbiosis persisted in a subset of patients with COVID-19 up to 12 days after nasopharyngeal clearance of SARS-CoV-2. Studies are needed to determine whether alterations in intestinal fungi contribute to or result from SARS-CoV-2 infection, and the effects of these changes in disease progression.
[Display omitted]</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>32598884</pmid><doi>10.1053/j.gastro.2020.06.048</doi><orcidid>https://orcid.org/0000-0002-6850-4454</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Adult Aged Aspergillus flavus - genetics Aspergillus flavus - isolation & purification Aspergillus niger - genetics Aspergillus niger - isolation & purification Betacoronavirus Candida - genetics Candida - isolation & purification Candida albicans - genetics Candida albicans - isolation & purification Case-Control Studies Community-Acquired Infections - microbiology Coronavirus Infections - microbiology Coronovirus COVID-19 DNA, Fungal - analysis Feces - microbiology Female Fungi - genetics Fungi - isolation & purification Gastrointestinal Microbiome Humans Intestine Male Metagenomics Microbe Middle Aged Mycobiome Nasopharynx - virology Original Research Pandemics Patient Discharge Pneumonia - microbiology Pneumonia, Viral - microbiology SARS-CoV-2 Time Factors Yeast Young Adult |
| title | Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge |
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