Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients

Pseudomonas aeruginosa 96 (PA96) was isolated during a multicenter surveillance study in Guangzhou, China, in 2000. Wholegenome sequencing of this outbreak strain facilitated analysis of its IncP-2 carbapenem-resistant plasmid, pOZ176. The plasmid had a length of 500,839 bp and an average percent G؉C content of 57%. Of the 618 predicted open reading frames, 65% encode hypothetical proteins. The pOZ176 backbone is not closely related to any plasmids thus far sequenced, but some similarity to pQBR103 of Pseudomonas fluorescens SBW25 was observed. Two multiresistant class 1 integrons and several insertion sequences were identified. The bla IMP-9 -carrying integron contained aacA4¡bla IMP-9 ¡aacA4, flanked upstream by Tn21 tnpMRA and downstream by a complete tni operon of Tn402 and a mer module, named Tn6016. The second integron carried aacA4¡catB8a¡bla OXA-10 and was flanked by Tn1403-like tnpRA and a sul1-type 3= conserved sequence (3=-CS), named Tn6217. Other features include three resistance genes similar to those of Tn5, a tellurite resistance operon, and two pil operons. The replication and maintenance systems exhibit similarity to a genomic island of Ralstonia solanacearum GM1000. Codon usage analysis suggests the recent acquisition of bla IMP-9 . The origins of the integrons on pOZ176 indicated separate horizontal gene transfer events driven by antibiotic selection. The novel mosaic structure of pOZ176 suggests that it is derived from environmental bacteria.

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“…3. Other close homologs include RepAs of genomic islands of P. aeruginosa PACS171b, 39016, PA2192, and PA7 (38,40,43,44).…”

Section: Resultsmentioning

confidence: 99%

Complete Sequence of pOZ176, a 500-Kilobase IncP-2 Plasmid Encoding IMP-9-Mediated Carbapenem Resistance, from Outbreak Isolate Pseudomonas aeruginosa 96

Xiong

Alexander

Jennifer

et al. 2013

Antimicrob Agents Chemother

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“…The plt gene cluster is found in plant-associated pseudomonads (e.g., P. fluorescens Pf-5 and CHAO) and contributes to the ecological fitness of these pseudomonads in the rhizosphere (27). The plt operon has been identified in a few P. aeruginosa isolates, namely, PACS171b, PACS88, and LESB58 (18,28). LESB58, the earliest archived P. aeruginosa isolate from the Liverpool CF epidemic, carries the plt gene cluster on a genomic island, suggesting that it was acquired through horizontal transfer (18).…”

Section: Discussionmentioning

confidence: 99%

Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon

Chugani

Kim

Phattarasukol

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

101

115

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Quorum sensing allows bacteria to sense and respond to changes in population density. Acyl-homoserine lactones serve as quorumsensing signals for many Proteobacteria, and acyl-homoserine lactone signaling is known to control cooperative activities. Quorum-controlled activities vary from one species to another. Quorum-sensing controls a constellation of genes in the opportunistic pathogen Pseudomonas aeruginosa, which thrives in a number of habitats ranging from soil and water to animal hosts. We hypothesized that there would be significant variation in quorumsensing regulons among strains of P. aeruginosa isolated from different habitats and that differences in the quorum-sensing regulons might reveal insights about the ecology of P. aeruginosa. As a test of our hypothesis we used RNA-seq to identify quorumcontrolled genes in seven P. aeruginosa isolates of diverse origins. Although our approach certainly overlooks some quorum-sensingregulated genes we found a shared set of genes, i.e., a core quorum-controlled gene set, and we identified distinct, strain-variable sets of quorum-controlled genes, i.e., accessory genes. Some quorumcontrolled genes in some strains were not present in the genomes of other strains. We detected a correlation between traits encoded by some genes in the strain-variable subsets of the quorum regulons and the ecology of the isolates. These findings indicate a role for quorum sensing in extension of the range of habitats in which a species can thrive. This study also provides a framework for understanding the molecular mechanisms by which quorum-sensing systems operate, the evolutionary pressures by which they are maintained, and their importance in disparate ecological contexts.bacterial communication | systems biology | transcription control B acteria use quorum-sensing signals to communicate with each other and control gene expression in a cell density-dependent manner. Many species of Proteobacteria use diffusible acyl-homoserine lactones (AHLs) as quorum-sensing signals. AHLs are produced by signal synthase enzymes and are detected by signalspecific transcriptional regulators. AHL quorum-sensing circuits regulate a wide spectrum of phenotypes in a diverse array of α-, β-, and γ-Proteobacteria (1). Interspecies differences in quorum regulons often are a reflection of the diverse habitats that bacteria occupy, and quorum-controlled phenotypes often play a crucial role in niche persistence. The classic example is quorum control of luminescence in Vibrio fischeri, which allows this bacterium to discriminate between its free-living, low-populationdensity seawater habitat and its high-density symbiotic habitats, the light organs of certain fish and squid (2, 3). It is well established that there are species-specific differences in quorum regulons, but there is little information regarding the possibility of intraspecies strain-specific differences. We hypothesized that, particularly for versatile species that occupy diverse niches, there might be a shared core of quorum-controlled genes an...

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“…PAGI-9 and PAGI-10 are rhs-like ORFs that are 6.7 kb and 2.5 kb in size, respectively, and were identified in the hypervirulent P. aeruginosa strain PSE9 by subtractive hybridization with a less virulent strain (15). rhs elements have also been reported in P. aeruginosa isolates from patients with cystic fibrosis and in strain PAO1 (47,86).…”

Section: Other Genetic Elementsmentioning

confidence: 98%

“…In addition to the clcRABDE genes, which encode enzymes for 3-and 4-chlorocatechol degradation, the clc element cargo includes a functional operon for 2-aminophenol degradation, a putative aromatic compound transporter gene, and a gene predicted to encode an aromatic ring dioxygenase (71). In terms of mobility, the clc element appears to be transferred readily between not only gammaproteobacteria (including P. aeruginosa) but also betaproteobacteria (70,86,183). Its chlorocatechol degradation cargo genes are highly similar to those of Ralstonia sp.…”

Section: Icesmentioning

confidence: 99%

The Accessory Genome of Pseudomonas aeruginosa

Kung¹,

Ozer

Hauser

2010

Microbiol Mol Biol Rev

263

303

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SUMMARY Pseudomonas aeruginosa strains exhibit significant variability in pathogenicity and ecological flexibility. Such interstrain differences reflect the dynamic nature of the P. aeruginosa genome, which is composed of a relatively invariable “core genome” and a highly variable “accessory genome.” Here we review the major classes of genetic elements comprising the P. aeruginosa accessory genome and highlight emerging themes in the acquisition and functional importance of these elements. Although the precise phenotypes endowed by the majority of the P. aeruginosa accessory genome have yet to be determined, rapid progress is being made, and a clearer understanding of the role of the P. aeruginosa accessory genome in ecology and infection is emerging.

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Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients

Cited by 25 publications

References 37 publications

Complete Sequence of pOZ176, a 500-Kilobase IncP-2 Plasmid Encoding IMP-9-Mediated Carbapenem Resistance, from Outbreak Isolate Pseudomonas aeruginosa 96

Complete Sequence of pOZ176, a 500-Kilobase IncP-2 Plasmid Encoding IMP-9-Mediated Carbapenem Resistance, from Outbreak Isolate Pseudomonas aeruginosa 96

Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon

The Accessory Genome of Pseudomonas aeruginosa

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