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Breath Res."],"published-print":{"date-parts":[[2026,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The diagnosis and monitoring of pneumonia remain a challenge due to its diverse etiology, overlapping clinical symptoms with other respiratory infections, and limitations in current diagnostic technologies for timely and accurate detection. We evaluated whether real-time secondary electrospray ionization\u2013high\u2010resolution mass spectrometry breathomics can capture pneumonia\u2010associated breath-profile changes in a paired longitudinal cohort. In this single-center longitudinal study at University Hospital Zurich, Switzerland, adults with clinically confirmed pneumonia (\n                    <jats:italic>n<\/jats:italic>\n                    = 47, median age: 63) were enrolled between 2020 and 2023 sampled during acute infection and again after recovery (median interval 85 d). After pre-processing, 3635 mass\u2010spectral features were retained across ion modes, and 1498 could be linked to at least one human metabolome database (HMDB) entry by accurate\u2010mass matching (\u00b11 ppm). Breath profiles were assessed using a subject\u2010grouped, nested cross\u2010validated partial least squares discriminate analysis (PLS\u2010DA) and paired differential analysis. PLS-DA showed framework moderate exploratory internal discrimination between pneumonia and post\u2010pneumonia measurements with moderate performance (median balanced accuracy 0.72; median AUROC 0.80;\n                    <jats:italic>Q<\/jats:italic>\n                    <jats:sup>2<\/jats:sup>\n                    0.24; two latent variables), with a permutation\n                    <jats:italic>p<\/jats:italic>\n                    -value of 0.112. Paired differential analysis identified 104 recovery\u2010associated features (58 higher and 46 lower during pneumonia) meeting |mean log\n                    <jats:sub>2<\/jats:sub>\n                    fold change| \u2a7e 1 and FDR\n                    <jats:italic>q<\/jats:italic>\n                    \u2a7d 0.05, with putative accurate-mass matches to 239 HMDB accessions. Real\u2010time breathomics captures reproducible changes in exhaled breath mass-spectral profiles from pneumonia to convalescence and reveals breath-profile heterogeneity not fully reflected by standard clinical indices. These results should be interpreted as exploratory and hypothesis-generating, motivating multicenter validation with tandem mass spectrometry\u2010supported compound identification, clinically relevant control groups, and longitudinal outcome linkage.\n                  <\/jats:p>","DOI":"10.1088\/1752-7163\/aead14","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T22:51:09Z","timestamp":1790635869000},"page":"046006","update-policy":"https:\/\/doi.org\/10.1088\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Metabolic alterations in pneumonia assessed by breath analysis: an exploratory paired longitudinal study comparing acute infection and post-recovery states"],"prefix":"10.1088","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-8630-9067","authenticated-orcid":true,"given":"Britta C","family":"Brugger","sequence":"first","affiliation":[{"name":"University Children\u2019s Hospital Basel (UKBB)"},{"name":"University of Basel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1758-4586","authenticated-orcid":true,"given":"Noriane A","family":"Sievi","sequence":"additional","affiliation":[{"name":"University Hospital Zurich Switzerland"},{"name":"University Zurich"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-5893-6037","authenticated-orcid":true,"given":"Sarah","family":"Basler","sequence":"additional","affiliation":[{"name":"University Hospital Zurich Switzerland"},{"name":"University Zurich"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4096-7438","authenticated-orcid":true,"given":"Patrick","family":"Baumgartner","sequence":"additional","affiliation":[{"name":"University Hospital Zurich Switzerland"},{"name":"University Zurich"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonas","family":"Herth","sequence":"additional","affiliation":[{"name":"University Hospital Zurich Switzerland"},{"name":"University Zurich"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felix","family":"Schmidt","sequence":"additional","affiliation":[{"name":"University Hospital Zurich Switzerland"},{"name":"University Zurich"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5682-0708","authenticated-orcid":true,"given":"Kapil Dev","family":"Singh","sequence":"additional","affiliation":[{"name":"University Children\u2019s Hospital Basel (UKBB)"},{"name":"University of Basel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5602-2880","authenticated-orcid":true,"given":"Pablo","family":"Sinues","sequence":"additional","affiliation":[{"name":"University Children\u2019s Hospital Basel (UKBB)"},{"name":"University of Basel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malcolm","family":"Kohler","sequence":"additional","affiliation":[{"name":"University Hospital Zurich Switzerland"},{"name":"University Zurich"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"266","published-online":{"date-parts":[[2026,10,9]]},"reference":[{"key":"jbraead14bib1","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/s41479-016-0012-z","type":"journal-article","article-title":"The definition and classification of pneumonia","volume":"8","author":"Mackenzie","year":"2016","journal-title":"Pneumonia"},{"key":"jbraead14bib2","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/s41572-021-00259-0","type":"journal-article","article-title":"Pneumonia","volume":"7","author":"Torres","year":"2021","journal-title":"Nat. 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