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Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection.

Bianconi I, Jeukens J, Freschi L, Alcalá-Franco B, Facchini M, Boyle B, Molinaro A, Kukavica-Ibrulj I, Tümmler B, Levesque RC, Bragonzi A - BMC Genomics (2015)

Bottom Line: Pathological analysis of murine lungs confirmed advanced chronic pulmonary disease, inflammation and mucus secretory cells hyperplasia.Further, comparative genomic analyses with sequential RP isolates showed signatures of pathoadaptive mutations in virulence factors potentially linked to the development of chronic infections in CF.The genome plasticity of P. aeruginosa particularly in the RP73 strain strongly indicated that these alterations may form the genetic basis defining host-bacteria interactions leading to a persistent lifestyle in human lungs.

View Article: PubMed Central - PubMed

Affiliation: Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy. bianconi.irene@hsr.it.

ABSTRACT

Background: Pseudomonas aeruginosa establishes life-long chronic airway infections in cystic fibrosis (CF) patients. As the disease progresses, P. aeruginosa pathoadaptive variants are distinguished from the initially acquired strain. However, the genetic basis and the biology of host-bacteria interactions leading to a persistent lifestyle of P. aeruginosa are not understood. As a model system to study long term and persistent CF infections, the P. aeruginosa RP73, isolated 16.9 years after the onset of airways colonization from a CF patient, was investigated. Comparisons with strains RP1, isolated at the onset of the colonization, and clonal RP45, isolated 7 years before RP73 were carried out to better characterize genomic evolution of P. aeruginosa in the context of CF pathogenicity.

Results: Virulence assessments in disease animal model, genome sequencing and comparative genomics analysis were performed for clinical RP73, RP45, RP1 and prototype strains. In murine model, RP73 showed lower lethality and a remarkable capability of long-term persistence in chronic airways infection when compared to other strains. Pathological analysis of murine lungs confirmed advanced chronic pulmonary disease, inflammation and mucus secretory cells hyperplasia. Genomic analysis predicted twelve genomic islands in the RP73 genome, some of which distinguished RP73 from other prototype strains and corresponded to regions of genome plasticity. Further, comparative genomic analyses with sequential RP isolates showed signatures of pathoadaptive mutations in virulence factors potentially linked to the development of chronic infections in CF.

Conclusions: The genome plasticity of P. aeruginosa particularly in the RP73 strain strongly indicated that these alterations may form the genetic basis defining host-bacteria interactions leading to a persistent lifestyle in human lungs.

No MeSH data available.


Related in: MedlinePlus

Circular map of P. aeruginosa RP isolates and prototype strain PA14. Circular map constructed with the CGView Comparison Tool [56]. Starting from the outside: genomic islands predicted with IslandViewer (see Table 1 for details) [52], RP73, RP45, RP1, PA14 and GC content. Colored regions are shared with RP73 according to blast search. Dotted lines: known genomic islands (GIs) that distinguish RP73 because they are incomplete or absent in the 12 complete P. aeruginosa genomes available at pseudomonas.com. RP isolates also carry LESGI-4, identified in the Liverpool epidemic strain
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Fig4: Circular map of P. aeruginosa RP isolates and prototype strain PA14. Circular map constructed with the CGView Comparison Tool [56]. Starting from the outside: genomic islands predicted with IslandViewer (see Table 1 for details) [52], RP73, RP45, RP1, PA14 and GC content. Colored regions are shared with RP73 according to blast search. Dotted lines: known genomic islands (GIs) that distinguish RP73 because they are incomplete or absent in the 12 complete P. aeruginosa genomes available at pseudomonas.com. RP isolates also carry LESGI-4, identified in the Liverpool epidemic strain

Mentions: To link the persistent lifestyle with a genetic basis, we sequenced the genome of RP73 [19], in addition to those of preceding RP1 and clonal RP45 isolates, and performed comparative genomic analysis. The fully assembled RP73 genome consists of a single circular chromosome of 6,342,034 base pairs (Additional file 3 for genome description). Twelve genomic islands were predicted in this genome (Table 1); three of them distinguished RP73 from other prototype strains and corresponded to regions of genome plasticity (Fig. 4) [5]. They include known genomic islands PAGI-9, which is similar to rearrangement hot spots (Rhs) [20], and plasmid pKLC102, which carries the pil gene cluster and chvB glucan synthetase [21]. Nucleotide blast search on NCBI limited to P. aeruginosa showed that the former can be found in multiple clinical isolates, while the latter is identical to RP73 only in strain 8380, isolated from the human gut. However, plasmid pKLC102 is often partially present [22]. A SMC4389 CRISPR repeat sequence also differentiates RP73 from most prototype strains [6]. In fact, blast search for this sequence resulted in a single hit from soil strain Azotobacter chroococcum NCIMB 8003. The RP73 genome also contains full length LESGI-4, which was identified in the Liverpool epidemic strain (LES) [23]. Genomic islands predicted in RP73 were investigated in the draft genomes of RP1 and RP45. While RP45 carries all 12, RP1 lacks full-length plasmid pKLC102 and an ABC transporter protein. A circular map comparing the 3 sequenced RP genomes clearly shows the genomic similarity between RP45 and RP73 on one hand, and between RP1 and strain PA14, which showed similar results in the murine infection model, on the other (Fig. 4).Table 1


Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection.

Bianconi I, Jeukens J, Freschi L, Alcalá-Franco B, Facchini M, Boyle B, Molinaro A, Kukavica-Ibrulj I, Tümmler B, Levesque RC, Bragonzi A - BMC Genomics (2015)

Circular map of P. aeruginosa RP isolates and prototype strain PA14. Circular map constructed with the CGView Comparison Tool [56]. Starting from the outside: genomic islands predicted with IslandViewer (see Table 1 for details) [52], RP73, RP45, RP1, PA14 and GC content. Colored regions are shared with RP73 according to blast search. Dotted lines: known genomic islands (GIs) that distinguish RP73 because they are incomplete or absent in the 12 complete P. aeruginosa genomes available at pseudomonas.com. RP isolates also carry LESGI-4, identified in the Liverpool epidemic strain
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4696338&req=5

Fig4: Circular map of P. aeruginosa RP isolates and prototype strain PA14. Circular map constructed with the CGView Comparison Tool [56]. Starting from the outside: genomic islands predicted with IslandViewer (see Table 1 for details) [52], RP73, RP45, RP1, PA14 and GC content. Colored regions are shared with RP73 according to blast search. Dotted lines: known genomic islands (GIs) that distinguish RP73 because they are incomplete or absent in the 12 complete P. aeruginosa genomes available at pseudomonas.com. RP isolates also carry LESGI-4, identified in the Liverpool epidemic strain
Mentions: To link the persistent lifestyle with a genetic basis, we sequenced the genome of RP73 [19], in addition to those of preceding RP1 and clonal RP45 isolates, and performed comparative genomic analysis. The fully assembled RP73 genome consists of a single circular chromosome of 6,342,034 base pairs (Additional file 3 for genome description). Twelve genomic islands were predicted in this genome (Table 1); three of them distinguished RP73 from other prototype strains and corresponded to regions of genome plasticity (Fig. 4) [5]. They include known genomic islands PAGI-9, which is similar to rearrangement hot spots (Rhs) [20], and plasmid pKLC102, which carries the pil gene cluster and chvB glucan synthetase [21]. Nucleotide blast search on NCBI limited to P. aeruginosa showed that the former can be found in multiple clinical isolates, while the latter is identical to RP73 only in strain 8380, isolated from the human gut. However, plasmid pKLC102 is often partially present [22]. A SMC4389 CRISPR repeat sequence also differentiates RP73 from most prototype strains [6]. In fact, blast search for this sequence resulted in a single hit from soil strain Azotobacter chroococcum NCIMB 8003. The RP73 genome also contains full length LESGI-4, which was identified in the Liverpool epidemic strain (LES) [23]. Genomic islands predicted in RP73 were investigated in the draft genomes of RP1 and RP45. While RP45 carries all 12, RP1 lacks full-length plasmid pKLC102 and an ABC transporter protein. A circular map comparing the 3 sequenced RP genomes clearly shows the genomic similarity between RP45 and RP73 on one hand, and between RP1 and strain PA14, which showed similar results in the murine infection model, on the other (Fig. 4).Table 1

Bottom Line: Pathological analysis of murine lungs confirmed advanced chronic pulmonary disease, inflammation and mucus secretory cells hyperplasia.Further, comparative genomic analyses with sequential RP isolates showed signatures of pathoadaptive mutations in virulence factors potentially linked to the development of chronic infections in CF.The genome plasticity of P. aeruginosa particularly in the RP73 strain strongly indicated that these alterations may form the genetic basis defining host-bacteria interactions leading to a persistent lifestyle in human lungs.

View Article: PubMed Central - PubMed

Affiliation: Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy. bianconi.irene@hsr.it.

ABSTRACT

Background: Pseudomonas aeruginosa establishes life-long chronic airway infections in cystic fibrosis (CF) patients. As the disease progresses, P. aeruginosa pathoadaptive variants are distinguished from the initially acquired strain. However, the genetic basis and the biology of host-bacteria interactions leading to a persistent lifestyle of P. aeruginosa are not understood. As a model system to study long term and persistent CF infections, the P. aeruginosa RP73, isolated 16.9 years after the onset of airways colonization from a CF patient, was investigated. Comparisons with strains RP1, isolated at the onset of the colonization, and clonal RP45, isolated 7 years before RP73 were carried out to better characterize genomic evolution of P. aeruginosa in the context of CF pathogenicity.

Results: Virulence assessments in disease animal model, genome sequencing and comparative genomics analysis were performed for clinical RP73, RP45, RP1 and prototype strains. In murine model, RP73 showed lower lethality and a remarkable capability of long-term persistence in chronic airways infection when compared to other strains. Pathological analysis of murine lungs confirmed advanced chronic pulmonary disease, inflammation and mucus secretory cells hyperplasia. Genomic analysis predicted twelve genomic islands in the RP73 genome, some of which distinguished RP73 from other prototype strains and corresponded to regions of genome plasticity. Further, comparative genomic analyses with sequential RP isolates showed signatures of pathoadaptive mutations in virulence factors potentially linked to the development of chronic infections in CF.

Conclusions: The genome plasticity of P. aeruginosa particularly in the RP73 strain strongly indicated that these alterations may form the genetic basis defining host-bacteria interactions leading to a persistent lifestyle in human lungs.

No MeSH data available.


Related in: MedlinePlus