{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T23:23:06Z","timestamp":1768519386329,"version":"3.49.0"},"posted":{"date-parts":[[2025,1,15]]},"group-title":"Microbiology","reference-count":66,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,1,15]],"date-time":"2025-01-15T00:00:00Z","timestamp":1736899200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Pf bacteriophages, lysogenic viruses that infect\n                  <jats:italic>Pseudomonas aeruginosa (Pa),<\/jats:italic>\n                  are implicated in the pathogenesis of chronic\n                  <jats:italic>Pa<\/jats:italic>\n                  infections; phage-infected (Pf+) strains are known to predominate in people with cystic fibrosis (pwCF) who are older and have more severe disease. However, the transmission patterns of Pf underlying the progressive dominance of Pf+ strains are unclear. In particular, it is unknown whether phage transmission commonly occurs horizontally between bacteria within the airway via viral particles or if Pf+ bacteria are mostly acquired via new\n                  <jats:italic>Pseudomonas<\/jats:italic>\n                  infections. Here, we have studied\n                  <jats:italic>Pa<\/jats:italic>\n                  genomic sequences from 3 patient cohorts totaling 663 clinical isolates from 105 pwCF. We identify Pf+ isolates and analyze transmission patterns of Pf within patients between genetically similar groups of bacteria called \u201cclone types\u201d. We find that Pf is predominantly passed down vertically within\n                  <jats:italic>Pa<\/jats:italic>\n                  lineages and rarely via horizontal transfer between clone types within the airway. Conversely, we find extensive evidence of\n                  <jats:italic>Pa<\/jats:italic>\n                  superinfection by a new, genetically distinct\n                  <jats:italic>Pa<\/jats:italic>\n                  that is Pf+. Finally, we find that clinical isolates show reduced activity of the type IV pilus and reduced susceptibility to Pf\n                  <jats:italic>in vitro.<\/jats:italic>\n                  These results cast new light on the transmission of virulence-associated phages in the clinical setting.\n                <\/jats:p>","DOI":"10.1101\/2025.01.14.632786","type":"posted-content","created":{"date-parts":[[2025,1,15]],"date-time":"2025-01-15T04:35:14Z","timestamp":1736915714000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>Pseudomonas<\/i>\n                  superinfection drives Pf phage transmission within airway infections in patients with cystic fibrosis"],"prefix":"10.64898","author":[{"given":"Julie D.","family":"Pourtois","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naomi L.","family":"Haddock","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aditi","family":"Gupta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arya","family":"Khosravi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hunter","family":"Martinez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amelia K.","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Prema S.","family":"Prakash","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ronit","family":"Jain","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Piper","family":"Fleming","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tony H.","family":"Chang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos","family":"Milla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick R.","family":"Secor","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giulio A.","family":"De Leo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul L.","family":"Bollyky","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elizabeth B.","family":"Burgener","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2025011714151380000_2025.01.14.632786v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(01)20383-3"},{"key":"2025011714151380000_2025.01.14.632786v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.11.017"},{"key":"2025011714151380000_2025.01.14.632786v1.3","unstructured":"Ackermann HW , DuBow MS . 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