{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T00:26:51Z","timestamp":1787012811996,"version":"build-2736575974"},"reference-count":34,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T00:00:00Z","timestamp":1761091200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology, Taiwan","doi-asserted-by":"publisher","award":["NSTC 112-2320-B-039-053"],"award-info":[{"award-number":["NSTC 112-2320-B-039-053"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004391","name":"China Medical University Hospital","doi-asserted-by":"publisher","award":["C1110812016"],"award-info":[{"award-number":["C1110812016"]}],"id":[{"id":"10.13039\/501100004391","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004391","name":"China Medical University Hospital","doi-asserted-by":"publisher","award":["DMR-112-169"],"award-info":[{"award-number":["DMR-112-169"]}],"id":[{"id":"10.13039\/501100004391","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004391","name":"China Medical University Hospital","doi-asserted-by":"publisher","award":["DMR-113-213"],"award-info":[{"award-number":["DMR-113-213"]}],"id":[{"id":"10.13039\/501100004391","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","ijidonline.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["International Journal of Infectious Diseases"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1016\/j.ijid.2025.108153","type":"journal-article","created":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T01:38:22Z","timestamp":1761356302000},"page":"108153","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"special_numbering":"C","title":["An integrative viro-bacterial signature based on viral load and high-resolution microbiome profiling predicts COVID-19 mortality"],"prefix":"10.1016","volume":"161","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6984-9083","authenticated-orcid":false,"given":"Zi-Lun","family":"Lai","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang-Di","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Yao","family":"Hsu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan-Hua","family":"Hung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan-Yu","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-An","family":"Tai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsiu-Hsien","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hung-Chieh","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong-Mo","family":"Shih","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mao-Wang","family":"Ho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Der-Yang","family":"Cho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Po-Ren","family":"Hsueh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"6","key":"10.1016\/j.ijid.2025.108153_bib0001","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/s41577-020-0311-8","article-title":"The trinity of COVID-19: immunity, inflammation and intervention","volume":"20","author":"Tay","year":"2020","journal-title":"Nat Rev Immunol"},{"issue":"1","key":"10.1016\/j.ijid.2025.108153_bib0002","doi-asserted-by":"crossref","first-page":"4375","DOI":"10.1038\/s41467-022-32096-4","article-title":"Dynamics of competing SARS-CoV-2 variants during the omicron epidemic in England","volume":"13","author":"Eales","year":"2022","journal-title":"Nat Commun"},{"issue":"1","key":"10.1016\/j.ijid.2025.108153_bib0003","doi-asserted-by":"crossref","first-page":"20","DOI":"10.37796\/2211-8039.1429","article-title":"Impact and prevalence of comorbidities and complications on the severity of COVID-19 in association with age, gender, obesity, and pre-existing smoking: a meta-analysis","volume":"14","author":"Djorw\u00e9","year":"2024","journal-title":"BioMedicine"},{"issue":"11","key":"10.1016\/j.ijid.2025.108153_bib0004","doi-asserted-by":"crossref","first-page":"e4197","DOI":"10.1093\/cid\/ciaa851","article-title":"Impact of severe acute respiratory syndrome coronavirus 2 viral load on risk of intubation and mortality among hospitalized patients with coronavirus disease 2019","volume":"73","author":"Magleby","year":"2021","journal-title":"Clin Infect Dis"},{"issue":"1","key":"10.1016\/j.ijid.2025.108153_bib0005","doi-asserted-by":"crossref","first-page":"5493","DOI":"10.1038\/s41467-020-19057-5","article-title":"SARS-CoV-2 viral load is associated with increased disease severity and mortality","volume":"11","author":"Fajnzylber","year":"2020","journal-title":"Nat Commun"},{"issue":"1","key":"10.1016\/j.ijid.2025.108153_bib0006","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-73857-9","article-title":"Lacticaseibacillus casei AMBR2 modulates the epithelial barrier function and immune response in a donor-derived nasal microbiota manner","volume":"10","author":"De Rudder","year":"2020","journal-title":"Sci Rep"},{"issue":"5","key":"10.1016\/j.ijid.2025.108153_bib0007","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nrmicro.2017.14","article-title":"The microbiota of the respiratory tract: gatekeeper to respiratory health","volume":"15","author":"Man","year":"2017","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"10.1016\/j.ijid.2025.108153_bib0008","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12915-019-0703-z","article-title":"The microbiome of the upper respiratory tract in health and disease","volume":"17","author":"Kumpitsch","year":"2019","journal-title":"BMC Biol"},{"key":"10.1016\/j.ijid.2025.108153_bib0009","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-021-03245-4","article-title":"SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts","volume":"11","author":"Hoque","year":"2021","journal-title":"Sci Rep"},{"key":"10.1016\/j.ijid.2025.108153_bib0010","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.jinf.2023.06.017","article-title":"Genomic characteristics of SARS-CoV-2 variants and their clinical impact on patients with COVID-19 in Taiwan","volume":"87","author":"Su","year":"2023","journal-title":"J Infect"},{"key":"10.1016\/j.ijid.2025.108153_bib0011","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.ijid.2025.108153_bib0012","doi-asserted-by":"crossref","first-page":"W310","DOI":"10.1093\/nar\/gkad407","article-title":"MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data","volume":"51","author":"Lu","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"10.1016\/j.ijid.2025.108153_bib0013","doi-asserted-by":"crossref","first-page":"e70","DOI":"10.1016\/S2213-2600(20)30354-4","article-title":"SARS-CoV-2 viral load predicts COVID-19 mortality","volume":"8","author":"Pujadas","year":"2020","journal-title":"Lancet Respir Med"},{"issue":"5","key":"10.1016\/j.ijid.2025.108153_bib0014","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/j.ccell.2020.09.007","article-title":"SARS-CoV-2 viral load predicts mortality in patients with and without cancer who are hospitalized with COVID-19","volume":"38","author":"Westblade","year":"2020","journal-title":"Cancer Cell"},{"issue":"9","key":"10.1016\/j.ijid.2025.108153_bib0015","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1080\/23744235.2025.2485274","article-title":"Influence of viral load on severity and mortality in COVID-19","volume":"57","author":"Ringlander","year":"2025","journal-title":"Infect Dis (Lond)"},{"key":"10.1016\/j.ijid.2025.108153_bib0016","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.3390\/v13081630","article-title":"Exacerbation of influenza a virus disease severity by respiratory syncytial virus co-infection in a mouse model","volume":"13","author":"George","year":"2021","journal-title":"Viruses"},{"key":"10.1016\/j.ijid.2025.108153_bib0017","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2025.1631198","article-title":"Identification of nasopharyngeal microbial dysbiosis in COVID-19 patients by 16S rRNA gene sequencing","volume":"16","author":"Kardaras","year":"2025","journal-title":"Front Microbiol"},{"issue":"1","key":"10.1016\/j.ijid.2025.108153_bib0018","doi-asserted-by":"crossref","DOI":"10.1080\/22221751.2023.2165970","article-title":"The nasopharyngeal microbiome in COVID-19","volume":"12","author":"Candel","year":"2023","journal-title":"Emerg Microbes Infect"},{"issue":"1","key":"10.1016\/j.ijid.2025.108153_bib0019","doi-asserted-by":"crossref","first-page":"5029","DOI":"10.1038\/s41467-019-13036-1","article-title":"Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis","volume":"10","author":"Johnson","year":"2019","journal-title":"Nat Commun"},{"key":"10.1016\/j.ijid.2025.108153_bib0020","doi-asserted-by":"crossref","DOI":"10.1016\/j.anaerobe.2020.102230","article-title":"Porphyromonas: a neglected potential key genus in human microbiomes","volume":"68","author":"Guilloux","year":"2021","journal-title":"Anaerobe"},{"key":"10.1016\/j.ijid.2025.108153_bib0021","doi-asserted-by":"crossref","DOI":"10.1016\/j.ebiom.2021.103500","article-title":"SARS-CoV-2 activates lung epithelia cell proinflammatory signaling and leads to immune dysregulation in COVID-19 patients by single-cell sequencing","volume":"70","author":"Chen","year":"2021","journal-title":"EBioMedicine"},{"issue":"6137","key":"10.1016\/j.ijid.2025.108153_bib0022","doi-asserted-by":"crossref","first-page":"1230","DOI":"10.1126\/science.1233632","article-title":"Role of tissue protection in lethal respiratory viral-bacterial coinfection","volume":"340","author":"Jamieson","year":"2013","journal-title":"Science"},{"issue":"12","key":"10.1016\/j.ijid.2025.108153_bib0023","doi-asserted-by":"crossref","first-page":"2007","DOI":"10.1007\/s00134-012-2699-5","article-title":"Pathophysiology of Escherichia coli ventilator-associated pneumonia: implication of highly virulent extraintestinal pathogenic strains","volume":"38","author":"Messika","year":"2012","journal-title":"Intensive Care Med"},{"key":"10.1016\/j.ijid.2025.108153_bib0024","article-title":"Pulmonary microbial composition in sepsis-induced acute respiratory distress syndrome","volume":"9","author":"Zhang","year":"2022","journal-title":"Front Mol Biosci"},{"issue":"2","key":"10.1016\/j.ijid.2025.108153_bib0025","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1590\/1806-9282.20210745","article-title":"Secondary bacterial infections in patients with coronavirus disease 2019-associated pneumonia","volume":"68","author":"Aydemir","year":"2022","journal-title":"Rev Assoc Med Bras (1992)"},{"key":"10.1016\/j.ijid.2025.108153_bib0026","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2022.1026457","article-title":"Association between Porphyromonas Gingivalis and systemic diseases: focus on T cells-mediated adaptive immunity","volume":"12","author":"Li","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"key":"10.1016\/j.ijid.2025.108153_bib0027","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.3389\/fimmu.2020.01446","article-title":"The COVID-19 cytokine storm; what we know so far","volume":"11","author":"Ragab","year":"2020","journal-title":"Front Immunol"},{"issue":"23","key":"10.1016\/j.ijid.2025.108153_bib0028","doi-asserted-by":"crossref","first-page":"2255","DOI":"10.1056\/NEJMra2026131","article-title":"Cytokine storm","volume":"383","author":"Fajgenbaum","year":"2020","journal-title":"N Engl J Med"},{"key":"10.1016\/j.ijid.2025.108153_bib0029","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.698169","article-title":"Long COVID or post-acute sequelae of COVID-19 (PASC): an overview of biological factors that may contribute to persistent symptoms","volume":"12","author":"Proal","year":"2021","journal-title":"Front Microbiol"},{"issue":"20","key":"10.1016\/j.ijid.2025.108153_bib0030","doi-asserted-by":"crossref","DOI":"10.1172\/jci.insight.152346","article-title":"Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long COVID","volume":"6","author":"Haran","year":"2021","journal-title":"JCI Insight"},{"issue":"4","key":"10.1016\/j.ijid.2025.108153_bib0031","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1136\/gutjnl-2020-323020","article-title":"Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19","volume":"70","author":"Yeoh","year":"2021","journal-title":"Gut"},{"issue":"1","key":"10.1016\/j.ijid.2025.108153_bib0032","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s40168-016-0227-5","article-title":"Host genetic variation in mucosal immunity pathways influences the upper airway microbiome","volume":"5","author":"Igartua","year":"2017","journal-title":"Microbiome"},{"issue":"1","key":"10.1016\/j.ijid.2025.108153_bib0033","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1186\/s13059-015-0759-1","article-title":"Host genetic variation impacts microbiome composition across human body sites","volume":"16","author":"Blekhman","year":"2015","journal-title":"Genome Biol"},{"issue":"1","key":"10.1016\/j.ijid.2025.108153_bib0034","first-page":"793","article-title":"Dexamethasone therapy and rates of secondary pulmonary and bloodstream infections in critically ill COVID-19 patients","volume":"33","author":"Rothe","year":"2021","journal-title":"Multidiscip Respir Med"}],"container-title":["International Journal of Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1201971225003753?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1201971225003753?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T13:06:05Z","timestamp":1780664765000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1201971225003753"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12]]},"references-count":34,"alternative-id":["S1201971225003753"],"URL":"https:\/\/doi.org\/10.1016\/j.ijid.2025.108153","relation":{},"ISSN":["1201-9712"],"issn-type":[{"value":"1201-9712","type":"print"}],"subject":[],"published":{"date-parts":[[2025,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"An integrative viro-bacterial signature based on viral load and high-resolution microbiome profiling predicts COVID-19 mortality","name":"articletitle","label":"Article Title"},{"value":"International Journal of Infectious Diseases","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ijid.2025.108153","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.","name":"copyright","label":"Copyright"}],"article-number":"108153"}}