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Chronic\n                      <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                      infections are associated with worsened lung function and poor outcomes. We sought to improve understanding of the effects of respiratory viral infections and immune response on the bacterial community of the airways.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We performed an observational longitudinal study of 38 adults with cystic fibrosis and collected sinus and sputum samples at 6-month intervals from 2017 to 2021. We performed 16S rRNA amplicon sequencing to characterise the airway microbiota, real-time reverse transcriptase PCR for viral infection detection, and cytokine quantification.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We observed viral positivity rates of 19% and 14% in sinus and sputum samples, respectively. Human rhinovirus was the most frequently observed viral pathogen in both sinus and sputum samples. We measured a significant perturbance of the bacterial community during viral infection that did not return to baseline following resolution of the viral infection. This perturbation was driven by a significant increase in\n                      <jats:italic>Pseudomonas<\/jats:italic>\n                      relative abundance during viral infection. Furthermore, we found significant associations with increased\n                      <jats:italic>Pseudomonas<\/jats:italic>\n                      relative abundance for several pro-inflammatory and antiviral cytokines, including interleukin (IL)-2, IL-8 and interferon-\u03bb1.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      These findings indicate an important role for respiratory viral infections and the host immune response in the development and maintenance of chronic\n                      <jats:italic>Pseudomonas<\/jats:italic>\n                      infections in the context of cystic fibrosis airway disease and broadly expand our understanding of viral\u2013bacterial co-infection of the airways.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1183\/23120541.01022-2025","type":"journal-article","created":{"date-parts":[[2025,11,27]],"date-time":"2025-11-27T16:55:15Z","timestamp":1764262515000},"page":"01022-2025","update-policy":"https:\/\/doi.org\/10.1183\/ers-crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Respiratory viral infection is associated with increased\n                    <i>Pseudomonas<\/i>\n                    abundance in the cystic fibrosis airway"],"prefix":"10.1183","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9322-7471","authenticated-orcid":false,"given":"Yasmin","family":"Hilliam","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine R.","family":"Armbruster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samar E.","family":"Atteih","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glenn J.","family":"Rapsinski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monika","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Moore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junu","family":"Koirala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leah","family":"Krainz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordan","family":"Gaston","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Williams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vaughn S.","family":"Cooper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stella E.","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer M.","family":"Bomberger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"81","published-online":{"date-parts":[[2025,11,27]]},"reference":[{"key":"2026060812350754000_12.2.01022-2025.1","unstructured":"Cystic Fibrosis Foundation . 2023 Patient Registry Annual Data Report 2023. 2024. www.cff.org\/medical-professionals\/patient-registry"},{"key":"2026060812350754000_12.2.01022-2025.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2023.10.014"},{"key":"2026060812350754000_12.2.01022-2025.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2023.09.011"},{"key":"2026060812350754000_12.2.01022-2025.4","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.molmed.2025.02.001","article-title":"Cystic fibrosis at a glance: from disease mechanism to therapy","volume":"31","author":"Gryspeert","year":"2025","journal-title":"Trends Mol Med"},{"key":"2026060812350754000_12.2.01022-2025.5","doi-asserted-by":"publisher","DOI":"10.1002\/ppul.10127"},{"key":"2026060812350754000_12.2.01022-2025.6","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(20)32542-3"},{"key":"2026060812350754000_12.2.01022-2025.7","unstructured":"Cystic Fibrosis Trust . 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