title: Genome mosaicism is conserved but not unique in Pseudomonas aeruginosa isolates from the airways of young children with cystic fibrosis.
abstract: Pseudomonas aeruginosa strains from the chronic lung infections of cystic fibrosis (CF) patients are phenotypically and genotypically diverse. Using strain PAO1 whole genome DNA microarrays, we assessed the genomic variation in P. aeruginosa strains isolated from young children with CF (6 months to 8 years of age) as well as from the environment. Eighty-nine to 97% of the PAO1 open reading frames were detected in 20 strains by microarray analysis, while subsets of 38 gene islands were absent or divergent. No specific pattern of genome mosaicism defined strains associated with CF. Many mosaic regions were distinguished by their low G + C content; their inclusion of phage related or pyocin genes; or by their linkage to a vgr gene or a tRNA gene. Microarray and phenotypic analysis of sequential isolates from individual patients revealed two deletions of greater than 100 kbp formed during evolution in the lung. The gene loss in these sequential isolates raises the possibility that acquisition of pyomelanin production and loss of pyoverdin uptake each may be of adaptive significance. Further characterization of P. aeruginosa diversity within the airways of individual CF patients may reveal common adaptations, perhaps mediated by gene loss, that suggest new opportunities for therapy.
authors.affiliation: Department of Microbiology, University of Washington, Health Sciences Building, K-140, Box 357710, Seattle, WA 98195, USA.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Ernst
authors.forename: David A
authors.initials: DA
authors.lastname: D'Argenio
authors.forename: Jeffrey K
authors.initials: JK
authors.lastname: Ichikawa
authors.forename: M Gita
authors.initials: MG
authors.lastname: Bangera
authors.forename: Sara
authors.initials: S
authors.lastname: Selgrade
authors.forename: Jane L
authors.initials: JL
authors.lastname: Burns
authors.forename: Peter
authors.initials: P
authors.lastname: Hiatt
authors.forename: Karen
authors.initials: K
authors.lastname: McCoy
authors.forename: Mitchell
authors.initials: M
authors.lastname: Brittnacher
authors.forename: Arnold
authors.initials: A
authors.lastname: Kas
authors.forename: David H
authors.initials: DH
authors.lastname: Spencer
authors.forename: Maynard V
authors.initials: MV
authors.lastname: Olson
authors.forename: Bonnie W
authors.initials: BW
authors.lastname: Ramsey
authors.forename: Stephen
authors.initials: S
authors.lastname: Lory
authors.forename: Samuel I
authors.initials: SI
authors.lastname: Miller
mesh_terms: D000222:Adaptation, Physiological; D001482:Base Composition; D002648:Child; D002675:Child, Preschool; D003550:Cystic Fibrosis / Q000382:microbiology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D007223:Infant; D008543:Melanins / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D009842:Oligopeptides; D010860:Pigments, Biological / Q000235:genetics / Q000378:metabolism; D011552:Pseudomonas Infections / Q000235:genetics / Q000382:microbiology*; D017105:Pseudomonas Phages; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000302:isolation & purification* / Q000472:pathogenicity; D011709:Pyocins / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics; D017384:Sequence Deletion
chemical_list: D004269:DNA, Bacterial; D008543:Melanins; D009842:Oligopeptides; D010860:Pigments, Biological; D011709:Pyocins; C023793:pyomelanin; C042453:pyoverdin; D012343:RNA, Transfer