{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T10:07:25Z","timestamp":1780049245510,"version":"3.53.1"},"reference-count":73,"publisher":"American Society for Clinical Investigation","issue":"11","license":[{"start":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T00:00:00Z","timestamp":1749427200000},"content-version":"vor","delay-in-days":48,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["1K23HL169902-01"],"award-info":[{"award-number":["1K23HL169902-01"]}]},{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"crossref","award":["BURGEN23G0,BURGEN24A0-KB"],"award-info":[{"award-number":["BURGEN23G0,BURGEN24A0-KB"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIH","award":["R01 HL148184-01,R01 AI12492093,R01 DC019965"],"award-info":[{"award-number":["R01 HL148184-01,R01 AI12492093,R01 DC019965"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,9]]},"abstract":"<jats:p>\n                    Pf bacteriophages, lysogenic viruses that infect\n                    <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                    (\n                    <jats:italic>Pa<\/jats:italic>\n                    ), are implicated in the pathogenesis of chronic\n                    <jats:italic>Pa<\/jats:italic>\n                    infections; phage-infected (Pf\n                    <jats:sup>+<\/jats:sup>\n                    ) 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\n                    <jats:sup>+<\/jats:sup>\n                    strains are unclear. In particular, it is unknown whether phage transmission commonly occurs horizontally between bacteria via viral particles within the airway or whether Pf\n                    <jats:sup>+<\/jats:sup>\n                    bacteria are mostly acquired via de novo\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    infections. Here, we studied\n                    <jats:italic>Pa<\/jats:italic>\n                    genomic sequences from 3 patient cohorts totaling 662 clinical isolates from 105 pwCF. We identified Pf\n                    <jats:sup>+<\/jats:sup>\n                    isolates and analyzed transmission patterns of Pf within patients between genetically similar groups of bacteria called \u201cclone types.\u201d We found that Pf was predominantly passed down vertically within\n                    <jats:italic>Pa<\/jats:italic>\n                    clone types and rarely via horizontal transfer between clone types within the airway. Conversely, we found extensive evidence of\n                    <jats:italic>Pa<\/jats:italic>\n                    de novo infection by a new, genetically distinct Pf\n                    <jats:sup>+<\/jats:sup>\n                    <jats:italic>Pa<\/jats:italic>\n                    . Finally, we observed that clinical isolates showed reduced activity of type IV pili and reduced susceptibility to Pf in vitro. These results cast light on the transmission of virulence-associated phages in the clinical setting.\n                  <\/jats:p>","DOI":"10.1172\/jci.insight.188146","type":"journal-article","created":{"date-parts":[[2025,4,22]],"date-time":"2025-04-22T12:00:35Z","timestamp":1745323235000},"source":"Crossref","is-referenced-by-count":2,"title":["New Pseudomonas infections drive Pf phage transmission in CF airways"],"prefix":"10.1172","volume":"10","author":[{"given":"Julie D.","family":"Pourtois","sequence":"first","affiliation":[{"name":"Biology Department, Stanford University, Stanford, California, USA."},{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naomi L.","family":"Haddock","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aditi","family":"Gupta","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arya","family":"Khosravi","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hunter A.","family":"Martinez","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amelia K.","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Division of Biological Sciences, University of Montana, Missoula, Montana, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prema S.","family":"Prakash","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronit","family":"Jain","sequence":"additional","affiliation":[{"name":"Biology Department, Stanford University, Stanford, California, USA."},{"name":"Oceans Department, Stanford University, Pacific Grove, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Piper","family":"Fleming","sequence":"additional","affiliation":[{"name":"Oceans Department, Stanford University, Pacific Grove, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4227-6163","authenticated-orcid":true,"given":"Tony H.","family":"Chang","sequence":"additional","affiliation":[{"name":"Biology Department, Stanford University, Stanford, California, USA."},{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5515-3053","authenticated-orcid":true,"given":"Carlos","family":"Milla","sequence":"additional","affiliation":[{"name":"Center for Excellence in Pulmonary Biology, Division of Pulmonary Medicine, Department of Pediatrics, Stanford University, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick R.","family":"Secor","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulio A.","family":"De Leo","sequence":"additional","affiliation":[{"name":"Oceans Department, Stanford University, Pacific Grove, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul L.","family":"Bollyky","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8969-6232","authenticated-orcid":true,"given":"Elizabeth B.","family":"Burgener","sequence":"additional","affiliation":[{"name":"Center for Excellence in Pulmonary Biology, Division of Pulmonary Medicine, Department of Pediatrics, Stanford University, Stanford, California, USA."},{"name":"Division of Pediatric Pulmonology & Sleep Medicine, Department of Pediatrics, Children\u2019s Hospital Los Angeles, Keck School of Medicine at University of Southern California, Los Angeles, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"232","published-online":{"date-parts":[[2025,4,22]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(01)20383-3"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.11.017"},{"key":"B3"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.16"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.15252\/embr.201847427"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0510-x"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1098\/rsob.210188"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3527"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aau9748"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.00244"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2008.109"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2015.04.008"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaa146"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-24-1-1"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00932-12"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-017-0061-y"},{"issue":"2","key":"B17","first-page":"51","article-title":"Filamentous bacteriophage: biology, phage display and nanotechnology applications","volume":"13","author":"Rakonjac","year":"2011","journal-title":"Curr Issues Mol Biol"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(17)30753-3"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/171.4.930"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1016\/j.burns.2003.08.007"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.18683\/germs.2023.1406"},{"key":"B22","unstructured":"Cystic Fibrosis Foundation. Cystic Fibrosis Foundation Patient Registry 2023 Annual Data Report. https:\/\/www.cff.org\/medical-professionals\/patient-registry Accessed April 22, 2025"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(08)61162-9"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.15.2.194-222.2002"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1067\/mpd.2001.112897"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1002\/ppul.10127"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1093\/pnasnexus\/pgae390"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2022.100656"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00648-16"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1126\/science.aat9691"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-virology-091919-074551"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1250339"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2015.10.013"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.15698\/mic2016.01.475"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1917726117"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00193-21"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adl5576"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.02441-21"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010925"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1128\/jb.00402-23"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01548-22"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00472-23"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51617-x"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1164\/ajrccm.156.5.9701098"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2011.104"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01592-14"},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201404-166OC"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3148"},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-015-0563-9"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000167"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2023.105513"},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra2216474"},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.1165\/rcmb.2011-0253OC"},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.03242"},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.3390\/v13081614"},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0602138103"},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2016.01.008"},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.15.4585-4592.2003"},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2015.07.006"},{"key":"B60","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03109-23"},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2024.09.018"},{"key":"B62","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.200812-1943OC"},{"key":"B63","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2016.251"},{"key":"B64","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2016.79"},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.03010-24"},{"key":"B66","doi-asserted-by":"publisher","DOI":"10.1089\/phage.2020.0003"},{"key":"B67","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"B68","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.102"},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944"},{"key":"B70","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0524-x"},{"key":"B72","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbx108"},{"key":"B73","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490"}],"container-title":["JCI Insight"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/insight.jci.org\/articles\/view\/188146\/files\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T17:39:32Z","timestamp":1779125972000},"score":1,"resource":{"primary":{"URL":"https:\/\/insight.jci.org\/articles\/view\/188146"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,22]]},"references-count":73,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2025,6,9]]},"published-print":{"date-parts":[[2025,6,9]]}},"alternative-id":["10.1172\/jci.insight.188146"],"URL":"https:\/\/doi.org\/10.1172\/jci.insight.188146","relation":{},"ISSN":["2379-3708"],"issn-type":[{"value":"2379-3708","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,22]]},"article-number":"e188146"}}