title: Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains.
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.
authors.affiliation: Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. jvarga@emory.edu.|Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. jvarga@emory.edu.|Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. jvarga@emory.edu.
authors.forename: John J
authors.initials: JJ
authors.lastname: Varga
authors.affiliation: Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. mariette.barbier@gmail.com.|Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA. mariette.barbier@gmail.com.
authors.forename: Mariette
authors.initials: M
authors.lastname: Barbier
authors.affiliation: Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain. xavier.mulet@ssib.es.
authors.forename: Xavier
authors.initials: X
authors.lastname: Mulet
authors.affiliation: Synthetic and Systems Biology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany. piotr.bielecki@yale.edu.|Present address: Immunobiology Department, Yale University, School of Medicine, New Haven, CT, 06511, USA. piotr.bielecki@yale.edu.
authors.forename: Piotr
authors.initials: P
authors.lastname: Bielecki
authors.affiliation: Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA. jagbartell@gmail.com.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Bartell
authors.affiliation: Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. jpowings@gmail.com.|Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. jpowings@gmail.com.|Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. jpowings@gmail.com.
authors.forename: Joshua P
authors.initials: JP
authors.lastname: Owings
authors.affiliation: IUNICS, University of the Balearic Islands, Palma, de Mallorca, Spain. elbesodeldragon@hotmail.com.
authors.forename: Inmaculada
authors.initials: I
authors.lastname: Martinez-Ramos
authors.affiliation: Department of Microbial Pathogenesis, University of Maryland School of Dentistry, University of Maryland, Baltimore, MD, USA. lhitt001@gmail.com.
authors.forename: Lauren E
authors.initials: LE
authors.lastname: Hittle
authors.affiliation: Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. michaelrdavisjr@gmail.com.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Davis
authors.affiliation: Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. heathdamron@gmail.com.|Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA. heathdamron@gmail.com.
authors.forename: F Heath
authors.initials: FH
authors.lastname: Damron
authors.affiliation: Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. george.liechti.ctr@usuhs.edu.
authors.forename: George W
authors.initials: GW
authors.lastname: Liechti
authors.affiliation: Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain. Puchalka@med.uni-muenchen.de.|Present address: Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany. Puchalka@med.uni-muenchen.de.
authors.forename: Jacek
authors.initials: J
authors.lastname: Puchałka
authors.affiliation: Systems and Synthetic Biology, Wageningen University, Wageningen, Netherlands. vitor.martinsdossantos@wur.nl.|Present address: Chair of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands. vitor.martinsdossantos@wur.nl.|Present address: LifeGlimmer GmbH, Berlin, Germany. vitor.martinsdossantos@wur.nl.
authors.forename: Vitor A P Martins
authors.initials: VA
authors.lastname: dos Santos
authors.affiliation: Department of Microbial Pathogenesis, University of Maryland School of Dentistry, University of Maryland, Baltimore, MD, USA. Rkernst@umaryland.edu.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Ernst
authors.affiliation: Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA. papin@virginia.edu.
authors.forename: Jason A
authors.initials: JA
authors.lastname: Papin
authors.affiliation: IUNICS, University of the Balearic Islands, Palma, de Mallorca, Spain. sebastian.alberti@uib.es.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Albertí
authors.affiliation: Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain. antonio.oliver@ssib.es.
authors.forename: Antonio
authors.initials: A
authors.lastname: Oliver
authors.affiliation: Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. joanna.goldberg@emory.edu.|Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. joanna.goldberg@emory.edu.|Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. joanna.goldberg@emory.edu.
authors.forename: Joanna B
authors.initials: JB
authors.lastname: Goldberg
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D000483:Alleles; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D018441:Biofilms; D001987:Bronchiectasis / Q000382:microbiology*; D002908:Chronic Disease; D019295:Computational Biology; D003550:Cystic Fibrosis / Q000150:complications*; D024881:Drug Resistance, Bacterial; D020869:Gene Expression Profiling; D023061:Gene Order; D016680:Genome, Bacterial; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008826:Microbial Sensitivity Tests; D008969:Molecular Sequence Data; D009154:Mutation; D059645:Mutation Rate; D010641:Phenotype; D011552:Pseudomonas Infections / Q000209:etiology* / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000187:drug effects / Q000302:isolation & purification / Q000472:pathogenicity / Q000502:physiology*; D053038:Quorum Sensing / Q000235:genetics; D064210:Secondary Metabolism; D059467:Transcriptome; D014774:Virulence / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins