title: Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates.
abstract: The distributed genome hypothesis (DGH) states that each strain within a bacterial species receives a unique distribution of genes from a population-based supragenome that is many times larger than the genome of any given strain. The observations that natural infecting populations are often polyclonal and that most chronic bacterial pathogens have highly developed mechanisms for horizontal gene transfer suggested the DGH and provided the means and the mechanisms to explain how chronic infections persist in the face of a mammalian host's adaptive defense mechanisms. Having previously established the validity of the DGH for obligate pathogens, we wished to evaluate its applicability to an opportunistic bacterial pathogen. This was accomplished by construction and analysis of a highly redundant pooled genomic library containing approximately 216,000 functional clones that was constructed from 12 low-passage clinical isolates of Pseudomonas aeruginosa, 6 otorrheic isolates and 6 from other body sites. Sequence analysis of 3,214 randomly picked clones (mean insert size, approximately 1.4 kb) from this library demonstrated that 348 (10.8%) of the clones were unique with respect to all genomic sequences of the P. aeruginosa prototype strain, PAO1. Hypothetical translations of the open reading frames within these unique sequences demonstrated protein homologies to a number of bacterial virulence factors and other proteins not previously identified in P. aeruginosa. PCR and reverse transcription-PCR-based assays were performed to analyze the distribution and expression patterns of a 70-open reading frame subset of these sequences among 11 of the clinical strains. These sequences were unevenly distributed among the clinical isolates, with nearly half (34/70) of the novel sequences being present in only one or two of the individual strains. Expression profiling revealed that a vast majority of these sequences are expressed, strongly suggesting they encode functional proteins.
authors.affiliation: Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, 320 East North Ave., 11th Floor South Tower, Pittsburgh, PA 15212, USA.
authors.forename: Kai
authors.initials: K
authors.lastname: Shen
authors.forename: Sameera
authors.initials: S
authors.lastname: Sayeed
authors.forename: Patricia
authors.initials: P
authors.lastname: Antalis
authors.forename: John
authors.initials: J
authors.lastname: Gladitz
authors.forename: Azad
authors.initials: A
authors.lastname: Ahmed
authors.forename: Bethany
authors.initials: B
authors.lastname: Dice
authors.forename: Benjamin
authors.initials: B
authors.lastname: Janto
authors.forename: Richard
authors.initials: R
authors.lastname: Dopico
authors.forename: Randy
authors.initials: R
authors.lastname: Keefe
authors.forename: Jay
authors.initials: J
authors.lastname: Hayes
authors.forename: Sandra
authors.initials: S
authors.lastname: Johnson
authors.forename: Sujun
authors.initials: S
authors.lastname: Yu
authors.forename: Nathan
authors.initials: N
authors.lastname: Ehrlich
authors.forename: Jennifer
authors.initials: J
authors.lastname: Jocz
authors.forename: Laura
authors.initials: L
authors.lastname: Kropp
authors.forename: Ray
authors.initials: R
authors.lastname: Wong
authors.forename: Robert M
authors.initials: RM
authors.lastname: Wadowsky
authors.forename: Malcolm
authors.initials: M
authors.lastname: Slifkin
authors.forename: Robert A
authors.initials: RA
authors.lastname: Preston
authors.forename: Geza
authors.initials: G
authors.lastname: Erdos
authors.forename: J Christopher
authors.initials: JC
authors.lastname: Post
authors.forename: Garth D
authors.initials: GD
authors.lastname: Ehrlich
authors.forename: Fen Z
authors.initials: FZ
authors.lastname: Hu
mesh_terms: D001435:Bacteriophages / Q000302:isolation & purification; D001483:Base Sequence; D020869:Gene Expression Profiling; D005798:Genes, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D015698:Genomic Library; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics; D011552:Pseudomonas Infections / Q000382:microbiology*; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA