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PMID: 16926421 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates.

Infection and immunity ·Vol. 74 ·No. 9 ·2006-09-00 ·Pages 5272-83

Shen K, Sayeed S, Antalis P, Gladitz J, Ahmed A, Dice B, Janto B, Dopico R, Keefe R, Hayes J, Johnson S, Yu S, Ehrlich N, Jocz J, Kropp L, Wong R, Wadowsky RM, Slifkin M, Preston RA, Erdos G, Post JC, Ehrlich GD, Hu FZ

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.

MeSH Terms
Bacteriophages/isolation & purification Base Sequence Gene Expression Profiling Genes, Bacterial Genome, Bacterial/genetics Genomic Library Humans Molecular Sequence Data Open Reading Frames/genetics Protein Biosynthesis/genetics Pseudomonas Infections/microbiology Pseudomonas aeruginosa/genetics,isolation & purification Sequence Analysis, DNA
Authors & Affiliations
23 authors, click to expand affiliations / ORCID
Shen Kai
Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, 320 East North Ave., 11th Floor South Tower, Pittsburgh, PA 15212, USA.
Sayeed Sameera
Antalis Patricia
Gladitz John
Ahmed Azad
Dice Bethany
Janto Benjamin
Dopico Richard
Keefe Randy
Hayes Jay
Johnson Sandra
Yu Sujun
Ehrlich Nathan
Jocz Jennifer
Kropp Laura
Wong Ray
Wadowsky Robert M
Slifkin Malcolm
Preston Robert A
Erdos Geza
Post J Christopher
Ehrlich Garth D
Hu Fen Z
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Article Info
Journal
Infection and immunity
Abbr.
Infect Immun
ISSN
0019-9567
DOI
10.1128/IAI.00546-06
Published
2006-09-00
Pages
5272-83
Language
English
Region
United States
NLM ID
0246127
PMCID
PMC1594838
Subset
IM
Grants
NIDCD NIH HHS · R01 DC002148 · United States
NIDCD NIH HHS · R01 DC004173 · United States
NIDCD NIH HHS · DC 02148 · United States
NIDCD NIH HHS · DC 04173 · United States
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External Links
PubMed source DOI: 10.1128/IAI.00546-06 PMC Full Text View journal details
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