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Bartell JA, Sommer LM, Marvig RL, Skov M, Pressler T, Molin S, Johansen HK. Omics-based tracking of Pseudomonas aeruginosa persistence in "eradicated" cystic fibrosis patients. Eur Respir J 2021; 57:13993003.00512-2020. [PMID: 33093121 PMCID: PMC8029213 DOI: 10.1183/13993003.00512-2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 10/09/2020] [Indexed: 01/18/2023]
Abstract
Whenever Pseudomonas aeruginosa is cultured from cystic fibrosis (CF) patient airways, the primary goal is eradication by antibiotic therapy. Success is defined by ≥6 months of negative bacterial airway cultures. However, we suspect that P. aeruginosa persists in airways without clinical detection for long periods. Out of 298 P. aeruginosa-infected Copenhagen CF patients, we identified 80 with complete P. aeruginosa monitoring records and measured their maximum P. aeruginosa-free eradication periods (MEP). Isolates from 72 patients were whole-genome sequenced (n=567) and clone typed. Select isolate relatedness was examined through phylogenetic analysis and phenotypic multivariate modelling. 69 (86%) patients exhibited eradication in the monitoring period (2002–2018). Sequenced isolates bridged the MEP of 42 patients, and the same clone type persisted over the MEP in 18 (43%) patients. Patients with failed eradication were on average treated more intensively with antibiotics, but this may be linked to their more severe pre-MEP infection trajectories. Of the 42 patients, 26 also had sinus surgery; the majority (n=15) showed MEPs adjacent to surgery, and only five had persisting clone types. Importantly, combined phylogenetic–phenomic evaluation suggests that persisting clone types are a result of re-emergence of the same strain rather than re-infection from the environment, and similar relatedness is exhibited by paired lower and upper airway samples and in transmission cases. In conclusion, nearly half of CF patients with supposed eradication may not truly be cleared of their original bacteria according to omics-based monitoring. This distinct cohort that is persistently infected would probably benefit from tailored antibiotic therapy. For 80 cystic fibrosis patients, this study used omics and positive culture history of P. aeruginosa infections to show that strains routinely persist over lengthy Pseudomonas-free periods. The authors recommend using genomic data in “eradication” metrics.https://bit.ly/2H318Ca
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Affiliation(s)
- Jennifer A Bartell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lea M Sommer
- Dept of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Marianne Skov
- Dept of Pediatrics, Rigshospitalet, Copenhagen, Denmark
| | | | - Søren Molin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Helle Krogh Johansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Dept of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Dept of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Bartell JA, Cameron DR, Mojsoska B, Haagensen JAJ, Pressler T, Sommer LM, Lewis K, Molin S, Johansen HK. Bacterial persisters in long-term infection: Emergence and fitness in a complex host environment. PLoS Pathog 2020; 16:e1009112. [PMID: 33315938 PMCID: PMC7769609 DOI: 10.1371/journal.ppat.1009112] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 12/28/2020] [Accepted: 10/31/2020] [Indexed: 12/20/2022] Open
Abstract
Despite intensive antibiotic treatment, Pseudomonas aeruginosa often persists in the airways of cystic fibrosis (CF) patients for decades, and can do so without antibiotic resistance development. Using high-throughput screening assays of bacterial survival after treatment with high concentrations of ciprofloxacin, we have determined the prevalence of persisters in a large patient cohort using 460 longitudinal isolates of P. aeruginosa from 39 CF patients. Isolates were classed as high persister variants (Hip) if they regrew following antibiotic treatment in at least 75% of the experimental replicates. Strain genomic data, isolate phenotyping, and patient treatment records were integrated in a lineage-based analysis of persister formation and clinical impact. In total, 19% of the isolates were classified as Hip and Hip emergence increased over lineage colonization time within 22 Hip+ patients. Most Hip+ lineages produced multiple Hip isolates, but few Hip+ lineages were dominated by Hip. While we observed no strong signal of adaptive genetic convergence within Hip isolates, they generally emerged in parallel or following the development of ciprofloxacin resistance and slowed growth. Transient lineages were majority Hip-, while strains that persisted over a clinically diagnosed 'eradication' period were majority Hip+. Patients received indistinguishable treatment regimens before Hip emergence, but Hip+ patients overall were treated significantly more than Hip- patients, signaling repeated treatment failure. When subjected to in vivo-similar antibiotic dosing, a Hip isolate survived better than a non-Hip in a structured biofilm environment. In sum, the Hip phenotype appears to substantially contribute to long-term establishment of a lineage in the CF lung environment. Our results argue against the existence of a single dominant molecular mechanism underlying bacterial antibiotic persistence. We instead show that many routes, both phenotypic and genetic, are available for persister formation and consequent increases in strain fitness and treatment failure in CF airways.
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Affiliation(s)
- Jennifer A. Bartell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - David R. Cameron
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Biljana Mojsoska
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Janus Anders Juul Haagensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Lea M. Sommer
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Søren Molin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Arndal E, Johansen HK, Haagensen JAJ, Bartell JA, Marvig RL, Alanin M, Aanæs K, Høiby N, Nielsen KG, Backer V, von Buchwald C. Primary ciliary dyskinesia patients have the same P. aeruginosa clone in sinuses and lungs. Eur Respir J 2020; 55:13993003.01472-2019. [PMID: 31558658 DOI: 10.1183/13993003.01472-2019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/04/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Elisabeth Arndal
- Dept of Otorhinolaryngology - Head and Neck Surgery and Audiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Helle K Johansen
- Dept of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Dept of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Janus A J Haagensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Jennifer A Bartell
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Rasmus L Marvig
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Mikkel Alanin
- Dept of Otorhinolaryngology - Head and Neck Surgery and Audiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kasper Aanæs
- Dept of Otorhinolaryngology - Head and Neck Surgery and Audiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Niels Høiby
- Dept of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Institute of Immunology and Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kim G Nielsen
- Danish PCD Center, Pediatric Pulmonary Service, Dept of Pediatric and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Vibeke Backer
- Centre for Physical Activity Research (CFAS), Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Christian von Buchwald
- Dept of Otorhinolaryngology - Head and Neck Surgery and Audiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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Bartell JA, Sommer LM, Haagensen JAJ, Loch A, Espinosa R, Molin S, Johansen HK. Evolutionary highways to persistent bacterial infection. Nat Commun 2019; 10:629. [PMID: 30733448 PMCID: PMC6367392 DOI: 10.1038/s41467-019-08504-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/10/2019] [Indexed: 01/18/2023] Open
Abstract
Persistent infections require bacteria to evolve from their naïve colonization state by optimizing fitness in the host via simultaneous adaptation of multiple traits, which can obscure evolutionary trends and complicate infection management. Accordingly, here we screen 8 infection-relevant phenotypes of 443 longitudinal Pseudomonas aeruginosa isolates from 39 young cystic fibrosis patients over 10 years. Using statistical modeling, we map evolutionary trajectories and identify trait correlations accounting for patient-specific influences. By integrating previous genetic analyses of 474 isolates, we provide a window into early adaptation to the host, finding: (1) a 2–3 year timeline of rapid adaptation after colonization, (2) variant “naïve” and “adapted” states reflecting discordance between phenotypic and genetic adaptation, (3) adaptive trajectories leading to persistent infection via three distinct evolutionary modes, and (4) new associations between phenotypes and pathoadaptive mutations. Ultimately, we effectively deconvolute complex trait adaptation, offering a framework for evolutionary studies and precision medicine in clinical microbiology. The pathogen Pseudomonas aeruginosa undergoes complex trait adaptation within cystic fibrosis patients. Here, Bartell, Sommer, and colleagues use statistical modeling of longitudinal isolates to characterize the joint genetic and phenotypic evolutionary trajectories of P. aeruginosa within hosts.
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Affiliation(s)
- Jennifer A Bartell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
| | - Lea M Sommer
- Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen Ø, Denmark.
| | - Janus A J Haagensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anne Loch
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Rocio Espinosa
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Søren Molin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen Ø, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen N, Denmark
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Varga JJ, Barbier M, Mulet X, Bielecki P, Bartell JA, Owings JP, Martinez-Ramos I, Hittle LE, Davis MR, Damron FH, Liechti GW, Puchałka J, dos Santos VAPM, Ernst RK, Papin JA, Albertí S, Oliver A, Goldberg JB. Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains. BMC Genomics 2015; 16:883. [PMID: 26519161 PMCID: PMC4628258 DOI: 10.1186/s12864-015-2069-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/03/2015] [Indexed: 01/24/2023] Open
Abstract
Background Pseudomonas aeruginosa is an environmentally ubiquitous Gram-negative bacterium and important opportunistic human pathogen, causing severe chronic respiratory infections in patients with underlying conditions such as cystic fibrosis (CF) or bronchiectasis. In order to identify mechanisms responsible for adaptation during bronchiectasis infections, a bronchiectasis isolate, PAHM4, was phenotypically and genotypically characterized. Results This strain displays phenotypes that have been associated with chronic respiratory infections in CF including alginate over-production, rough lipopolysaccharide, quorum-sensing deficiency, loss of motility, decreased protease secretion, and hypermutation. Hypermutation is a key adaptation of this bacterium during the course of chronic respiratory infections and analysis indicates that PAHM4 encodes a mutated mutS gene responsible for a ~1,000-fold increase in mutation rate compared to wild-type laboratory strain P. aeruginosa PAO1. Antibiotic resistance profiles and sequence data indicate that this strain acquired numerous mutations associated with increased resistance levels to β-lactams, aminoglycosides, and fluoroquinolones when compared to PAO1. Sequencing of PAHM4 revealed a 6.38 Mbp genome, 5.9 % of which were unrecognized in previously reported P. aeruginosa genome sequences. Transcriptome analysis suggests a general down-regulation of virulence factors, while metabolism of amino acids and lipids is up-regulated when compared to PAO1 and metabolic modeling identified further potential differences between PAO1 and PAHM4. Conclusions This work provides insights into the potential differential adaptation of this bacterium to the lung of patients with bronchiectasis compared to other clinical settings such as cystic fibrosis, findings that should aid the development of disease-appropriate treatment strategies for P. aeruginosa infections. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2069-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John J Varga
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. .,Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.
| | - Xavier Mulet
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain.
| | - Piotr Bielecki
- Synthetic and Systems Biology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany. .,Present address: Immunobiology Department, Yale University, School of Medicine, New Haven, CT, 06511, USA.
| | - Jennifer A Bartell
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| | - Joshua P Owings
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | | | - Lauren E Hittle
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - Michael R Davis
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. .,Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.
| | - George W Liechti
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - Jacek Puchałka
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain. .,Present address: Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany.
| | - Vitor A P Martins dos Santos
- Systems and Synthetic Biology, Wageningen University, Wageningen, Netherlands. .,Present address: Chair of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands. .,Present address: LifeGlimmer GmbH, Berlin, Germany.
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| | - Sebastian Albertí
- IUNICS, University of the Balearic Islands, Palma, de Mallorca, Spain.
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain.
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
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