{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:28:14Z","timestamp":1785803294163,"version":"3.56.0"},"posted":{"date-parts":[[2026,1,2]]},"group-title":"Respiratory Medicine","reference-count":49,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T00:00:00Z","timestamp":1767312000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent \u201cClusters of Phylogeny and Functions\u201d (COPFs). Coupled with gradient-boosted random forests, COPFs predicted\n                  <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                  colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant\n                  <jats:italic>P. aeruginosa<\/jats:italic>\n                  signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent\n                  <jats:italic>Aspergillus fumigatus<\/jats:italic>\n                  signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting\n                  <jats:italic>P. aeruginosa<\/jats:italic>\n                  status across platforms and geographies, validating the model\u2019s universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.\n                <\/jats:p>","DOI":"10.64898\/2025.12.28.25342520","type":"posted-content","created":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T12:20:14Z","timestamp":1767356414000},"source":"Crossref","is-referenced-by-count":1,"title":["Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7062-843X","authenticated-orcid":false,"given":"Thomas R.","family":"Goddard","sequence":"first","affiliation":[{"name":"Department of Respiratory and Sleep Medicine, Women\u2019s and Children\u2019s Hospital, 72 King William Rd, Adelaide, SA, 5042, Australia"},{"name":"College of Medicine and Public Health, Flinders University, Sturt Road, Bedford Park, SA, 5042, Australia"},{"name":"Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide, SA, 5000, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2862-0338","authenticated-orcid":false,"given":"Jessica AP.","family":"Carlson-Jones","sequence":"additional","affiliation":[{"name":"Flinders Accelerator for Microbiome Exploration, Flinders University, Sturt Road, Bedford Park, SA, 5042, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1715-5573","authenticated-orcid":false,"given":"Judith","family":"Morton","sequence":"additional","affiliation":[{"name":"Department of Thoracic Medicine, The Royal Adelaide Hospital, 1 Port Road, Adelaide, SA, 5000, Australia"},{"name":"Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide, SA, 5000, 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Adelaide, North Terrace, Adelaide, SA, 5000, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4053-1610","authenticated-orcid":false,"given":"Morgyn S.","family":"Warner","sequence":"additional","affiliation":[{"name":"Microbiology & Infectious Diseases, SA Pathology, 1 Port Road, Adelaide, SA, 5000, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Wong","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Sleep Medicine, Women\u2019s and Children\u2019s Hospital, 72 King William Rd, Adelaide, SA, 5006, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9669-0805","authenticated-orcid":false,"given":"Ieuan ES.","family":"Evans","sequence":"additional","affiliation":[{"name":"Adult Cystic Fibrosis Centre, The Prince Charles Hospital, 627 Rode Road, Brisbane, QLD, 4032, Australia"},{"name":"Faculty of Medicine, 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