De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen
Abstract Bacteria evolving within human hosts encounter selective tradeoffs that render mutations adaptive in one context and deleterious in another. Here, we report that the cystic fibrosis-associated pathogen Burkholderia dolosa overcomes in-human selective tradeoffs by acquiring successive point...
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61168-4 |
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| author | Alexandra J. Poret Matthew Schaefers Christina Merakou Kathryn E. Mansour Connor D. Ahern Georgia K. Lagoudas Alyssa Haynes Ashley R. Cross Joanna B. Goldberg Roy Kishony Ahmet Z. Uluer Alexander J. McAdam Paul C. Blainey Sara O. Vargas Tami D. Lieberman Gregory P. Priebe |
| author_facet | Alexandra J. Poret Matthew Schaefers Christina Merakou Kathryn E. Mansour Connor D. Ahern Georgia K. Lagoudas Alyssa Haynes Ashley R. Cross Joanna B. Goldberg Roy Kishony Ahmet Z. Uluer Alexander J. McAdam Paul C. Blainey Sara O. Vargas Tami D. Lieberman Gregory P. Priebe |
| author_sort | Alexandra J. Poret |
| collection | DOAJ |
| description | Abstract Bacteria evolving within human hosts encounter selective tradeoffs that render mutations adaptive in one context and deleterious in another. Here, we report that the cystic fibrosis-associated pathogen Burkholderia dolosa overcomes in-human selective tradeoffs by acquiring successive point mutations that alternate phenotypes. We sequenced the whole genomes of 931 respiratory isolates from two recently infected cystic fibrosis patients and an epidemiologically-linked, chronically-infected patient. These isolates are contextualized using 112 historical genomes from the same outbreak strain. Within both newly infected patients, convergent mutations that disrupt O-antigen expression quickly arose, comprising 29% and 63% of their B. dolosa communities by 3 years. The selection for loss of O-antigen starkly contrasts with our previous observation of parallel O-antigen-restoring mutations after many years of chronic infection in the historical outbreak. Experimental characterization reveals that O-antigen loss increases uptake in immune cells while decreasing competitiveness in the mouse lung. We propose that the balance of these pressures, and thus whether O-antigen expression is advantageous, depends on tissue localization and infection duration. These results suggest that mutation-driven phenotypic alternation may be underestimated without dense temporal sampling, particularly for microbes with prolonged infection or colonization. |
| format | Article |
| id | doaj-art-e85b16a09fa940278c52c5c3433d57c4 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-e85b16a09fa940278c52c5c3433d57c42025-08-20T03:42:52ZengNature PortfolioNature Communications2041-17232025-07-0116111110.1038/s41467-025-61168-4De novo mutations mediate phenotypic switching in an opportunistic human lung pathogenAlexandra J. Poret0Matthew Schaefers1Christina Merakou2Kathryn E. Mansour3Connor D. Ahern4Georgia K. Lagoudas5Alyssa Haynes6Ashley R. Cross7Joanna B. Goldberg8Roy Kishony9Ahmet Z. Uluer10Alexander J. McAdam11Paul C. Blainey12Sara O. Vargas13Tami D. Lieberman14Gregory P. Priebe15Institute for Medical Engineering and Sciences, Massachusetts Institute of TechnologyDepartment of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children’s HospitalDepartment of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children’s HospitalDepartment of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children’s HospitalDepartment of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children’s HospitalDepartment of Biological Engineering, Massachusetts Institute of TechnologyInstitute for Medical Engineering and Sciences, Massachusetts Institute of TechnologyDepartment of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of MedicineDepartment of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of MedicineFaculty of Biology and Faculty of Computer Science, Technion–Israel Institute of TechnologyDepartment of Pediatrics, Division of Respiratory Diseases, Boston Children’s HospitalDepartment of Laboratory Medicine, Boston Children’s HospitalDepartment of Biological Engineering, Massachusetts Institute of TechnologyDepartment of Pathology, Harvard Medical SchoolInstitute for Medical Engineering and Sciences, Massachusetts Institute of TechnologyDepartment of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children’s HospitalAbstract Bacteria evolving within human hosts encounter selective tradeoffs that render mutations adaptive in one context and deleterious in another. Here, we report that the cystic fibrosis-associated pathogen Burkholderia dolosa overcomes in-human selective tradeoffs by acquiring successive point mutations that alternate phenotypes. We sequenced the whole genomes of 931 respiratory isolates from two recently infected cystic fibrosis patients and an epidemiologically-linked, chronically-infected patient. These isolates are contextualized using 112 historical genomes from the same outbreak strain. Within both newly infected patients, convergent mutations that disrupt O-antigen expression quickly arose, comprising 29% and 63% of their B. dolosa communities by 3 years. The selection for loss of O-antigen starkly contrasts with our previous observation of parallel O-antigen-restoring mutations after many years of chronic infection in the historical outbreak. Experimental characterization reveals that O-antigen loss increases uptake in immune cells while decreasing competitiveness in the mouse lung. We propose that the balance of these pressures, and thus whether O-antigen expression is advantageous, depends on tissue localization and infection duration. These results suggest that mutation-driven phenotypic alternation may be underestimated without dense temporal sampling, particularly for microbes with prolonged infection or colonization.https://doi.org/10.1038/s41467-025-61168-4 |
| spellingShingle | Alexandra J. Poret Matthew Schaefers Christina Merakou Kathryn E. Mansour Connor D. Ahern Georgia K. Lagoudas Alyssa Haynes Ashley R. Cross Joanna B. Goldberg Roy Kishony Ahmet Z. Uluer Alexander J. McAdam Paul C. Blainey Sara O. Vargas Tami D. Lieberman Gregory P. Priebe De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen Nature Communications |
| title | De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen |
| title_full | De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen |
| title_fullStr | De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen |
| title_full_unstemmed | De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen |
| title_short | De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen |
| title_sort | de novo mutations mediate phenotypic switching in an opportunistic human lung pathogen |
| url | https://doi.org/10.1038/s41467-025-61168-4 |
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