{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T05:01:16Z","timestamp":1779339676700,"version":"3.51.4"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T00:00:00Z","timestamp":1707868800000},"content-version":"vor","delay-in-days":13,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Selective forces in the environment drive bacterial adaptation to novel niches, choosing the fitter variants in the population. However, in dynamic and changing environments, the evolutionary processes controlling bacterial adaptation are difficult to monitor. Here, we follow 9 people with cystic fibrosis chronically infected with Pseudomonas aeruginosa, as a proxy for bacterial adaptation. We identify and describe the bacterial changes and evolution occurring between 15 and 35 yr of within-host evolution. We combine whole-genome sequencing, RNA sequencing, and metabolomics and compare the evolutionary trajectories directed by the adaptation of 4 different P. aeruginosa lineages to the lung. Our data suggest divergent evolution at the genomic level for most of the genes, with signs of convergent evolution with respect to the acquisition of mutations in regulatory genes, which drive the transcriptional and metabolomic program at late time of evolution. Metabolomics further confirmed convergent adaptive phenotypic evolution as documented by the reduction of the quorum-sensing molecules acyl-homoserine lactone, phenazines, and rhamnolipids (except for quinolones). The modulation of the quorum-sensing repertoire suggests that similar selective forces characterize at late times of evolution independent of the patient. Collectively, our data suggest that similar environments and similar P. aeruginosa populations in the patients at prolonged time of infection are associated with an overall reduction of virulence-associated features and phenotypic convergence.<\/jats:p>","DOI":"10.1093\/molbev\/msae022","type":"journal-article","created":{"date-parts":[[2024,2,17]],"date-time":"2024-02-17T02:57:22Z","timestamp":1708138642000},"source":"Crossref","is-referenced-by-count":9,"title":["Adaptive Evolution of <i>Pseudomonas aeruginosa<\/i> in Human Airways Shows Phenotypic Convergence Despite Diverse Patterns of Genomic Changes"],"prefix":"10.1093","volume":"41","author":[{"given":"Akbar","family":"Espaillat","sequence":"first","affiliation":[{"name":"Department of Clinical Microbiology 9301, Rigshospitalet , Copenhagen \u00d8 2100 , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1782-3145","authenticated-orcid":false,"given":"Claudia Antonella","family":"Colque","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology 9301, Rigshospitalet , Copenhagen \u00d8 2100 , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniela","family":"Rago","sequence":"additional","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Lyngby 2800 , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6705-3989","authenticated-orcid":false,"given":"Ruggero","family":"La Rosa","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology 9301, Rigshospitalet , Copenhagen \u00d8 2100 , Denmark"},{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Lyngby 2800 , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7973-2639","authenticated-orcid":false,"given":"S\u00f8ren","family":"Molin","sequence":"additional","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Lyngby 2800 , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0268-3717","authenticated-orcid":false,"given":"Helle Krogh","family":"Johansen","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology 9301, Rigshospitalet , Copenhagen \u00d8 2100 , Denmark"},{"name":"Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen N 2200 , Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,2,14]]},"reference":[{"issue":"9","key":"2024022217175579800_msae022-B1","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1038\/nprot.2013.099","article-title":"Count-based differential expression analysis of RNA sequencing data using R and Bioconductor","volume":"8","author":"Anders","year":"2013","journal-title":"Nat Protoc"},{"issue":"5","key":"2024022217175579800_msae022-B2","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J Comput Biol"},{"issue":"1","key":"2024022217175579800_msae022-B3","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1186\/s12890-016-0339-5","article-title":"Cystic fibrosis lung environment and Pseudomonas aeruginosa 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