{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T03:38:32Z","timestamp":1793331512668,"version":"4.5.0"},"reference-count":47,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,8,9]],"date-time":"2025-08-09T00:00:00Z","timestamp":1754697600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004587","name":"Carlos III Health Institute","doi-asserted-by":"publisher","award":["PI19\/01875"],"award-info":[{"award-number":["PI19\/01875"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","journalofinfection.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Infection"],"published-print":{"date-parts":[[2025,9]]},"DOI":"10.1016\/j.jinf.2025.106589","type":"journal-article","created":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T06:39:26Z","timestamp":1755153566000},"page":"106589","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":5,"title":["Differential nasopharyngeal microbiota patterns: A comparative study of pneumococcal pneumonia, COVID-19, and healthy adults"],"prefix":"10.1016","volume":"91","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6011-6986","authenticated-orcid":false,"given":"Beatriz","family":"Dietl","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Desir\u00e9e","family":"Henares","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"Cuch\u00ed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miguel","family":"Blanco-Fuertes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4650-3357","authenticated-orcid":false,"given":"Mireia","family":"Rajadell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2399-7320","authenticated-orcid":false,"given":"Pedro","family":"Brotons","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleix","family":"Lluans\u00ed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luc\u00eda","family":"Boix-Palop","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7750-5347","authenticated-orcid":false,"given":"Esther","family":"Calbo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5586-404X","authenticated-orcid":false,"given":"Carmen","family":"Mu\u00f1oz-Almagro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jinf.2025.106589_bib1","unstructured":"World Health\u00a0Organization. The top 10 causes of death World Health Organization website 2020 [updated 9\/12\/2020]. Available from: \u3008https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/the-top-10-causes-of-death\u3009."},{"issue":"4","key":"10.1016\/j.jinf.2025.106589_bib2","doi-asserted-by":"crossref","DOI":"10.1128\/cmr.00015-22","article-title":"The microbial etiology of community-acquired pneumonia in adults: from classical bacteriology to host transcriptional signatures","volume":"35","author":"Gadsby","year":"2022","journal-title":"Clin Microbiol Rev"},{"issue":"5","key":"10.1016\/j.jinf.2025.106589_bib3","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1183\/09031936.02.01942001","article-title":"Factors associated with unknown aetiology in patients with community-acquired pneumonia","volume":"20","author":"Ewig","year":"2002","journal-title":"Eur Respir J"},{"issue":"15","key":"10.1016\/j.jinf.2025.106589_bib4","doi-asserted-by":"crossref","first-page":"1282","DOI":"10.1001\/jama.2024.14796","article-title":"Community-acquired pneumonia: a review","volume":"332","author":"Vaughn","year":"2024","journal-title":"JAMA"},{"issue":"10","key":"10.1016\/j.jinf.2025.106589_bib5","doi-asserted-by":"crossref","first-page":"ITC145","DOI":"10.7326\/AITC202310170","article-title":"COVID-19","volume":"176","author":"Marks","year":"2023","journal-title":"Ann Intern Med"},{"key":"10.1016\/j.jinf.2025.106589_bib6","article-title":"Pandemics throughout history","volume":"11","author":"Piret","year":"2020","journal-title":"Front Microbiol"},{"issue":"1675","key":"10.1016\/j.jinf.2025.106589_bib7","doi-asserted-by":"crossref","first-page":"20140294","DOI":"10.1098\/rstb.2014.0294","article-title":"The role of the local microbial ecosystem in respiratory health and disease","volume":"370","author":"De Steenhuijsen Piters","year":"2015","journal-title":"Philos Trans R Soc B Biol Sci"},{"issue":"1","key":"10.1016\/j.jinf.2025.106589_bib8","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1128\/IAI.02627-14","article-title":"What is a host? Incorporating the microbiota into the damage-response framework","volume":"83","author":"Casadevall","year":"2015","journal-title":"Infect Immun"},{"issue":"6086","key":"10.1016\/j.jinf.2025.106589_bib9","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1126\/science.1223490","article-title":"Interactions between the microbiota and the immune system","volume":"336","author":"Hooper","year":"2012","journal-title":"Science"},{"issue":"12","key":"10.1016\/j.jinf.2025.106589_bib10","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1164\/rccm.201703-0554OC","article-title":"Maturation of the infant respiratory microbiota, environmental drivers, and health consequences. a prospective cohort study","volume":"196","author":"Bosch","year":"2017","journal-title":"Am J Respir Crit Care Med"},{"issue":"11","key":"10.1016\/j.jinf.2025.106589_bib11","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1164\/rccm.201407-1240OC","article-title":"Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children","volume":"190","author":"Biesbroek","year":"2014","journal-title":"Am J Respir Crit Care Med"},{"key":"10.1016\/j.jinf.2025.106589_bib12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fmed.2020.00554","article-title":"Role of lung microbiome in innate immune response associated with chronic lung diseases","volume":"7","author":"Paudel","year":"2020","journal-title":"Front Med"},{"issue":"7","key":"10.1016\/j.jinf.2025.106589_bib13","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0069559","article-title":"Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza","volume":"8","author":"Chaban","year":"2013","journal-title":"PLoS One"},{"issue":"9","key":"10.1016\/j.jinf.2025.106589_bib14","doi-asserted-by":"crossref","first-page":"2995","DOI":"10.1128\/JCM.00278-12","article-title":"Oral and airway microbiota in HIV-infected pneumonia patients","volume":"50","author":"Iwai","year":"2012","journal-title":"J Clin Microbiol"},{"issue":"1","key":"10.1016\/j.jinf.2025.106589_bib15","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1186\/s12866-024-03281-w","article-title":"The characteristics of microbiome in the upper respiratory tract of COVID-19 patients","volume":"24","author":"Zhang","year":"2024","journal-title":"BMC Microbiol"},{"issue":"10","key":"10.1016\/j.jinf.2025.106589_bib16","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2024.e31562","article-title":"Microbiome in the nasopharynx: Insights into the impact of COVID-19 severity","volume":"10","author":"Galeana-Cadena","year":"2024","journal-title":"Heliyon"},{"key":"10.1016\/j.jinf.2025.106589_bib17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fmicb.2022.871627","article-title":"Profile of the nasopharyngeal microbiota affecting the clinical course in COVID-19 patients","volume":"13","author":"Tchoupou Saha","year":"2022","journal-title":"Front Microbiol"},{"issue":"12","key":"10.1016\/j.jinf.2025.106589_bib18","doi-asserted-by":"crossref","first-page":"1495","DOI":"10.1016\/j.ijsu.2014.07.013","article-title":"The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement: guidelines for reporting observational studies","volume":"12","author":"von Elm","year":"2014","journal-title":"Int J Surg"},{"issue":"1","key":"10.1016\/j.jinf.2025.106589_bib19","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1007\/s00134-014-3486-2","article-title":"Pulse oximetry vs. PaO2 metrics in mechanically ventilated children: Berlin definition of ARDS and mortality risk","volume":"41","author":"Khemani","year":"2015","journal-title":"Intensive Care Med"},{"key":"10.1016\/j.jinf.2025.106589_bib20","doi-asserted-by":"crossref","DOI":"10.1016\/j.jbi.2019.103208","article-title":"The REDCap consortium: building an international community of software platform partners","volume":"95","author":"Harris","year":"2019","journal-title":"J Biomed Inf"},{"issue":"2","key":"10.1016\/j.jinf.2025.106589_bib21","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/j.jbi.2008.08.010","article-title":"Research electronic data capture (REDCap)\u2014a metadata-driven methodology and workflow process for providing translational research informatics support","volume":"42","author":"Harris","year":"2009","journal-title":"J Biomed Inf"},{"issue":"7","key":"10.1016\/j.jinf.2025.106589_bib22","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat Methods"},{"issue":"10","key":"10.1016\/j.jinf.2025.106589_bib23","article-title":"Differential nasopharyngeal microbiota composition in children according to respiratory health status","volume":"7","author":"Henares","year":"2021","journal-title":"Microb Genom"},{"issue":"1","key":"10.1016\/j.jinf.2025.106589_bib24","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/ismej.2015.99","article-title":"Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients","volume":"10","author":"de Steenhuijsen Piters","year":"2016","journal-title":"ISME J"},{"issue":"5","key":"10.1016\/j.jinf.2025.106589_bib25","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1093\/cid\/ciab568","article-title":"Bacterial and viral respiratory tract microbiota and host characteristics in adults with lower respiratory tract infections: a case-control study","volume":"74","author":"Haak","year":"2022","journal-title":"Clin Infect Dis"},{"key":"10.1016\/j.jinf.2025.106589_bib26","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2021.744727","article-title":"Rapid increase of oral bacteria in nasopharyngeal microbiota after antibiotic treatment in children with invasive pneumococcal disease","volume":"11","author":"Henares","year":"2021","journal-title":"Front Cell Infect Microbiol"},{"key":"10.1016\/j.jinf.2025.106589_bib27","doi-asserted-by":"crossref","first-page":"48","DOI":"10.12688\/gatesopenres.13561.1","article-title":"Nasopharyngeal dysbiosis precedes the development of lower respiratory tract infections in young infants, a longitudinal infant cohort study","volume":"6","author":"Lapidot","year":"2022","journal-title":"Gates Open Res"},{"key":"10.1016\/j.jinf.2025.106589_bib28","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.coi.2020.03.010","article-title":"Commensal bacteria in the upper respiratory tract regulate susceptibility to infection","volume":"66","author":"Clark","year":"2020","journal-title":"Curr Opin Immunol"},{"issue":"7","key":"10.1016\/j.jinf.2025.106589_bib29","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.3390\/v14071521","article-title":"Impact of COVID-19 lockdown on the nasopharyngeal microbiota of children and adults self-confined at home","volume":"14","author":"Rocafort","year":"2022","journal-title":"Viruses"},{"issue":"1","key":"10.1016\/j.jinf.2025.106589_bib30","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1038\/s41598-022-05618-9","article-title":"Associations and recovery dynamics of the nasopharyngeal microbiota during influenza-like illness in the aging population","volume":"12","author":"Shetty","year":"2022","journal-title":"Sci Rep"},{"issue":"3","key":"10.1016\/j.jinf.2025.106589_bib31","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/S2213-2600(14)70028-1","article-title":"Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis","volume":"2","author":"Dickson","year":"2014","journal-title":"Lancet Respir Med"},{"issue":"2","key":"10.1016\/j.jinf.2025.106589_bib32","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0017035","article-title":"Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis","volume":"6","author":"Bogaert","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.jinf.2025.106589_bib33","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.804935","article-title":"Corynebacterium species inhibit Streptococcus pneumoniae colonization and infection of the mouse airway","volume":"12","author":"Horn","year":"2022","journal-title":"Front Microbiol"},{"issue":"5","key":"10.1016\/j.jinf.2025.106589_bib34","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00852-20","article-title":"Dolosigranulum pigrum cooperation and competition in human nasal microbiota","volume":"5","author":"Brugger","year":"2020","journal-title":"mSphere"},{"issue":"1","key":"10.1016\/j.jinf.2025.106589_bib35","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01725-15","article-title":"Corynebacterium accolens releases antipneumococcal free fatty acids from human nostril and skin surface triacylglycerols","volume":"7","author":"Bomar","year":"2016","journal-title":"mBio"},{"key":"10.1016\/j.jinf.2025.106589_bib36","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fcimb.2024.1530178","article-title":"Corynebacteria from the respiratory microbiota modulate inflammatory responses and associate with a reduced pneumococcal burden in the lungs","volume":"14","author":"Bergenfelz","year":"2025","journal-title":"Front Cell Infect Microbiol"},{"issue":"2","key":"10.1016\/j.jinf.2025.106589_bib37","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/iai.00445-24","article-title":"Airway Corynebacterium interfere with Streptococcus pneumoniae and Staphylococcus aureus infection and express secreted factors selectively targeting each pathogen","volume":"93","author":"Tamkin","year":"2025","journal-title":"Infect Immun"},{"issue":"1","key":"10.1016\/j.jinf.2025.106589_bib38","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003057","article-title":"Viral and bacterial interactions in the upper respiratory tract","volume":"9","author":"Bosch","year":"2013","journal-title":"PLoS Pathog"},{"issue":"4","key":"10.1016\/j.jinf.2025.106589_bib39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/mBio.01777-21","article-title":"Signatures of COVID-19 severity and immune response in the respiratory tract microbiome","volume":"12","author":"Merenstein","year":"2021","journal-title":"mBio"},{"issue":"5","key":"10.1016\/j.jinf.2025.106589_bib40","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.04166-23","article-title":"Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities","volume":"12","author":"Aljabr","year":"2024","journal-title":"Microbiol Spectr"},{"issue":"6","key":"10.1016\/j.jinf.2025.106589_bib41","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/mBio.01969-20","article-title":"Metagenomic next-generation sequencing of nasopharyngeal specimens collected from confirmed and suspect COVID-19 patients","volume":"11","author":"Mostafa","year":"2020","journal-title":"mBio"},{"issue":"6","key":"10.1016\/j.jinf.2025.106589_bib42","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1002\/ppul.26393","article-title":"Impact of the bacterial nasopharyngeal microbiota on the severity of genus enterovirus lower respiratory tract infection in children: a case\u2013control study","volume":"58","author":"Penela\u2010S\u00e1nchez","year":"2023","journal-title":"Pediatr Pulmonol"},{"issue":"5","key":"10.1016\/j.jinf.2025.106589_bib43","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1038\/ismej.2014.250","article-title":"Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age","volume":"9","author":"Stearns","year":"2015","journal-title":"ISME J"},{"issue":"4","key":"10.1016\/j.jinf.2025.106589_bib44","doi-asserted-by":"crossref","first-page":"4127","DOI":"10.3390\/ijms24044127","article-title":"Analysis of 16S rRNA gene sequence of nasopharyngeal exudate reveals changes in key microbial communities associated with aging","volume":"24","author":"Candel","year":"2023","journal-title":"Int J Mol Sci"},{"issue":"1","key":"10.1016\/j.jinf.2025.106589_bib45","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-023-01640-9","article-title":"The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children","volume":"11","author":"Paulo","year":"2023","journal-title":"Microbiome"},{"issue":"9773","key":"10.1016\/j.jinf.2025.106589_bib46","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1016\/S0140-6736(10)61459-6","article-title":"Viral pneumonia","volume":"377","author":"Ruuskanen","year":"2011","journal-title":"Lancet"},{"issue":"9","key":"10.1016\/j.jinf.2025.106589_bib47","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1001\/jamainternmed.2017.1938","article-title":"Association of adverse events with antibiotic use in hospitalized patients","volume":"177","author":"Tamma","year":"2017","journal-title":"JAMA Intern Med"}],"container-title":["Journal of Infection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0163445325001896?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0163445325001896?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T15:29:53Z","timestamp":1772810993000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0163445325001896"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9]]},"references-count":47,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,9]]}},"alternative-id":["S0163445325001896"],"URL":"https:\/\/doi.org\/10.1016\/j.jinf.2025.106589","relation":{},"ISSN":["0163-4453"],"issn-type":[{"value":"0163-4453","type":"print"}],"subject":[],"published":{"date-parts":[[2025,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Differential nasopharyngeal microbiota patterns: A comparative study of pneumococcal pneumonia, COVID-19, and healthy adults","name":"articletitle","label":"Article Title"},{"value":"Journal of Infection","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jinf.2025.106589","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 The British Infection Association.","name":"copyright","label":"Copyright"}],"article-number":"106589"}}