Identification of a Genomic Island Present in the Majority of Pathogenic Isolates of Pseudomonas aeruginosa

Abstract

Pseudomonas aeruginosa, a ubiquitous gram-negative bacterium, is capable of colonizing a wide range of environmental niches and can also cause serious infections in humans. In order to understand the genetic makeup of pathogenic P. aeruginosa strains, a method of differential hybridization of arrayed libraries of cloned DNA fragments was developed. An M13 library of DNA from strain X24509, isolated from a patient with a urinary tract infection, was screened using a DNA probe from P. aeruginosa strain PAO1. The genome of PAO1 has been recently sequenced and can be used as a reference for comparisons of genetic organization in different strains. M13 clones that did not react with a DNA probe from PAO1 carried X24509-specific inserts. When a similar array hybridization analysis with DNA probes from different strains was used, a set of M13 clones which carried sequences present in the majority of human P. aeruginosa isolates from a wide range of clinical sources was identified. The inserts of these clones were used to identify cosmids encompassing a contiguous 48.9-kb region of the X24509 chromosome called PAGI-1 (for "P. aeruginosa genomic island 1"). PAGI-1 is incorporated in the X24509 chromosome at a locus that shows a deletion of a 6,729-bp region present in strain PAO1. Survey of the incidence of PAGI-1 revealed that this island is present in 85% of the strains from clinical sources. Approximately half of the PAGI-1-carrying strains show the same deletion as X24509, while the remaining strains contain both the PAGI-1 sequences and the 6,729-bp PAO1 segment. Sequence analysis of PAGI-1 revealed that it contains 51 predicted open reading frames. Several of these genes encoded products with predictable function based on their sequence similarities to known genes, including insertion sequences, determinants of regulatory proteins, a number of dehydrogenase gene homologs, and two for proteins of implicated in detoxification of reactive oxygen species. It is very likely that PAGI-1 was acquired by a large number of P. aeruginosa isolates through horizontal gene transfer. The selection for its maintenance may be the consequence of expression of any one of the genes of unknown function or the genes which allow P. aeruginosa to survive under the conditions that generate reactive oxygen species. Alternatively, one or both of the transcriptional regulators encoded in PAGI-1 may control the expression of genes in the P. aeruginosa chromosome, which provides a selective advantage for strains that have acquired this genomic island.

The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes

“…All P. aeruginosa strains are human isolates (6,15,16). The TnphoA mutant 33A9 has been described (21).…”

“…aeruginosa possesses a large and diverse genome that is both highly conserved and plastic (14)(15)(16)(17). Although clinical and environmental isolates have a remarkably conserved genome (14)(15)(16)(17)(18)(19), distinct P. aeruginosa strains carry additional specific sequences, interspersed as genomic blocks in the conserved core genome, that account for 10% or more of their DNA (14,18). To date, no distinct P. aeruginosa genomic island that carries virulence genes has been identified, with the exception of a recently identified genomic island that harbors the exoU virulence gene (14-17, 19, 20).…”

The Accessory Genome of Pseudomonas aeruginosa

“…In addition to the relatively small rhs elements and the exoS gene, many larger accessory genetic elements also display no clear genetic mechanism of acquisition. PAGI-1, for example, is a 49-kb island that was the first genomic island identified in P. aeruginosa (128). Portions of this island are present in 85% of clinical isolates.…”

Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa

“…Islands encoding virulence determinants (pathogenicity islands, PAIs) have been described in a wide variety of pathogens and, in many instances, have been implicated as the genetic determinants responsible for endowing a nonpathogenic species with virulence traits (3). Several GIs, termed PAGI-1, -2, and -3, were identified in different strains of the opportunistic pathogen Pseudomonas aeruginosa (4,5). The majority of the proteins encoded within these islands have unknown function, which makes it difficult to assess the selection forces that facilitated their acquisition in the recipient strains.…”