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Poret AJ, Schaefers M, Merakou C, Mansour KE, Lagoudas GK, Cross AR, Goldberg JB, Kishony R, Uluer AZ, McAdam AJ, Blainey PC, Vargas SO, Lieberman TD, Priebe GP. De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579193. [PMID: 38370793 PMCID: PMC10871308 DOI: 10.1101/2024.02.06.579193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
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 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, diverse parallel 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 revealed 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 alternation during infection may be more frequent than appreciated and is underestimated without dense temporal sampling.
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Affiliation(s)
- Alexandra J. Poret
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology
- Department of Biological Engineering, Massachusetts Institute of Technology
| | - Matthew Schaefers
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts
| | - Christina Merakou
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts
| | - Kathryn E. Mansour
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital
| | - Georgia K. Lagoudas
- Department of Biological Engineering, Massachusetts Institute of Technology
- Broad Institute of MIT and Harvard
| | - Ashley R. Cross
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine
| | - Joanna B. Goldberg
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine
| | - Roy Kishony
- Faculty of Biology and Faculty of Computer Science, Technion Israel
| | - Ahmet Z. Uluer
- Department of Pediatrics, Division of Respiratory Diseases, Boston Children’s Hospital
- Adult CF Program, Brigham and Women’s Hospital
- Department of Pediatrics, Harvard Medical School
| | - Alexander J. McAdam
- Department of Laboratory Medicine, Boston Children’s Hospital
- Department of Pathology, Harvard Medical School
| | - Paul C. Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology
- Broad Institute of MIT and Harvard
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | - Sara O. Vargas
- Department of Pathology, Harvard Medical School
- Department of Pathology, Boston Children’s Hospital
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital
| | - Gregory P. Priebe
- Department of Anesthesiology, Critical Care and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard
- Department of Pediatrics, Division of Infectious Diseases, Boston Children’s Hospital
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