title: Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs.
abstract: BACKGROUND
  While the taxonomy and genomics of environmental strains from the P. fluorescens species-complex has been reported, little is known about P. fluorescens strains from clinical samples. In this report, we provide the first genomic analysis of P. fluorescens strains in which human vs. environmental isolates are compared.
  
  
  RESULTS
  Seven P. fluorescens strains were isolated from respiratory samples from cystic fibrosis (CF) patients. The clinical strains could grow at a higher temperature (>34 °C) than has been reported for environmental strains. Draft genomes were generated for all of the clinical strains, and multi-locus sequence analysis placed them within subclade III of the P. fluorescens species-complex. All strains encoded type- II, -III, -IV, and -VI secretion systems, as well as the widespread colonization island (WCI). This is the first description of a WCI in P. fluorescens strains. All strains also encoded a complete I2/PfiT locus and showed evidence of horizontal gene transfer. The clinical strains were found to differ from the environmental strains in the number of genes involved in metal resistance, which may be a possible adaptation to chronic antibiotic exposure in the CF lung.
  
  
  CONCLUSIONS
  This is the largest comparative genomics analysis of P. fluorescens subclade III strains to date and includes the first clinical isolates. At a global level, the clinical P. fluorescens subclade III strains were largely indistinguishable from environmental P. fluorescens subclade III strains, supporting the idea that identifying strains as 'environmental' vs 'clinical' is not a phenotypic trait. Rather, strains within P. fluorescens subclade III will colonize and persist in any niche that provides the requirements necessary for growth.
authors.affiliation: Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA. britstar@umich.edu.|Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA. britstar@umich.edu.
authors.forename: Brittan S
authors.initials: BS
authors.lastname: Scales
authors.affiliation: Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA. jre@umich.edu.
authors.forename: John R
authors.initials: JR
authors.lastname: Erb-Downward
authors.affiliation: Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA. imhuffnagle@gmail.com.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Huffnagle
authors.affiliation: Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI, USA. jlipuma@umich.edu.
authors.forename: John J
authors.initials: JJ
authors.lastname: LiPuma
authors.affiliation: Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA. ghuff@umich.edu.|Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA. ghuff@umich.edu.
authors.forename: Gary B
authors.initials: GB
authors.lastname: Huffnagle
mesh_terms: D058947:Bacterial Secretion Systems / Q000235:genetics; D001482:Base Composition; D003550:Cystic Fibrosis / Q000150:complications; D056426:Genetic Loci; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D005838:Genotype; D006801:Humans; D008670:Metals / Q000378:metabolism; D005810:Multigene Family; D010641:Phenotype; D010802:Phylogeny; D018410:Pneumonia, Bacterial / Q000382:microbiology*; D011552:Pseudomonas Infections / Q000382:microbiology*; D011551:Pseudomonas fluorescens / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D064210:Secondary Metabolism / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D058947:Bacterial Secretion Systems; D008670:Metals