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Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

Turner KH, Everett J, Trivedi U, Rumbaugh KP, Whiteley M - PLoS Genet. (2014)

Bottom Line: Generally we discovered that expression of a gene in vivo is not correlated with its importance for fitness, with the exception of metabolic genes.Specifically, we found that long-chain fatty acids represent a major carbon source in both chronic and acute wounds, and P. aeruginosa must biosynthesize purines, several amino acids, and most cofactors during infection.Our results provide novel insight into the genetic requirements for acute and chronic P. aeruginosa wound infections and demonstrate the power of using both gene expression and fitness profiling for probing bacterial virulence.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America.

ABSTRACT
Opportunistic infections caused by Pseudomonas aeruginosa can be acute or chronic. While acute infections often spread rapidly and can cause tissue damage and sepsis with high mortality rates, chronic infections can persist for weeks, months, or years in the face of intensive clinical intervention. Remarkably, this diverse infectious capability is not accompanied by extensive variation in genomic content, suggesting that the genetic capacity to be an acute or a chronic pathogen is present in most P. aeruginosa strains. To investigate the genetic requirements for acute and chronic pathogenesis in P. aeruginosa infections, we combined high-throughput sequencing-mediated transcriptome profiling (RNA-seq) and genome-wide insertion mutant fitness profiling (Tn-seq) to characterize gene expression and fitness determinants in murine models of burn and non-diabetic chronic wound infection. Generally we discovered that expression of a gene in vivo is not correlated with its importance for fitness, with the exception of metabolic genes. By combining metabolic models generated from in vivo gene expression data with mutant fitness profiles, we determined the nutritional requirements for colonization and persistence in these infections. Specifically, we found that long-chain fatty acids represent a major carbon source in both chronic and acute wounds, and P. aeruginosa must biosynthesize purines, several amino acids, and most cofactors during infection. In addition, we determined that P. aeruginosa requires chemotactic flagellar motility for fitness and virulence in acute burn wound infections, but not in non-diabetic chronic wound infections. Our results provide novel insight into the genetic requirements for acute and chronic P. aeruginosa wound infections and demonstrate the power of using both gene expression and fitness profiling for probing bacterial virulence.

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P. aeruginosa differentially regulates genes involved in metabolism, motility, and outer surface remodeling in wound infections.(A) Log2-transformed differential gene expression of P. aeruginosa in murine burn (y axis) and chronic (x axis) wound infections as compared to growth in MOPS-succinate (Succ.). Significant changes (fold change ≥4, P<0.01, negative binomial test) are colored as shown (Diff. Exp., differentially expressed in). (B) Significantly enriched or scarce COG categories in differentially expressed gene sets (P<0.01, Fisher's exact test; †, significantly less present than expected; *, significantly more present than expected).
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pgen-1004518-g001: P. aeruginosa differentially regulates genes involved in metabolism, motility, and outer surface remodeling in wound infections.(A) Log2-transformed differential gene expression of P. aeruginosa in murine burn (y axis) and chronic (x axis) wound infections as compared to growth in MOPS-succinate (Succ.). Significant changes (fold change ≥4, P<0.01, negative binomial test) are colored as shown (Diff. Exp., differentially expressed in). (B) Significantly enriched or scarce COG categories in differentially expressed gene sets (P<0.01, Fisher's exact test; †, significantly less present than expected; *, significantly more present than expected).

Mentions: We found that P. aeruginosa differentially regulates 14% and 19% of its genome during growth in murine burn and chronic wounds, respectively, as compared to MOPS-succinate (P<0.01, negative binomial test, fold change ≥4) (Table S2). The transcriptional responses of P. aeruginosa during growth in these two wound types as compared to MOPS-succinate are highly correlated (Spearman rank correlation coefficient = 0.840), suggesting that the cues sensed by P. aeruginosa in acute and chronic wound infections are largely similar (Figure 1A). Notably, 7.3% of the genome is commonly up- or down-regulated in both wound infections, which is a significant overlap (P<4.72×10−110, Fisher's exact test). The P. aeruginosa genome encodes numerous virulence factors, and our data provides a genome-wide perspective on the expression of these virulence genes (Table S3). We saw that many genes in the PA3160-PA3141 cluster, which encodes genes required for lipopolysaccharide O antigen biosynthesis [24], were down-regulated in vivo, and to a greater extent in chronic wounds. This suggests either that P. aeruginosa may alter its outer surface during infection, or that O antigen biosynthesis is regulated as a consequence of more static growth in vivo. We also saw that genes responsible for the biosynthesis of the siderophores pyochelin and pyoverdine were greatly up-regulated in vivo. Iron is known to be a limited resource in numerous infections, and our results suggest that iron acquisition is important in P. aeruginosa soft tissue infections as well [25]. Many type II and type III secretion system genes were up-regulated in both acute and chronic wounds as well, indicating that P. aeruginosa may be modulating host cellular physiology and extracellular environment through these well-characterized secretion systems [26], [27]. Finally, we saw down-regulation of many genes in the psl cluster, which is responsible for synthesis of the Psl exopolysaccharide. In strain PAO1, Psl is the primary exopolysaccharide involved in biofilm formation on abiotic surfaces [28]. Thus, P. aeruginosa differentially regulates much of its virulence repertoire upon wound infection, further underscoring the multifaceted nature of its virulence.


Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

Turner KH, Everett J, Trivedi U, Rumbaugh KP, Whiteley M - PLoS Genet. (2014)

P. aeruginosa differentially regulates genes involved in metabolism, motility, and outer surface remodeling in wound infections.(A) Log2-transformed differential gene expression of P. aeruginosa in murine burn (y axis) and chronic (x axis) wound infections as compared to growth in MOPS-succinate (Succ.). Significant changes (fold change ≥4, P<0.01, negative binomial test) are colored as shown (Diff. Exp., differentially expressed in). (B) Significantly enriched or scarce COG categories in differentially expressed gene sets (P<0.01, Fisher's exact test; †, significantly less present than expected; *, significantly more present than expected).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4109851&req=5

pgen-1004518-g001: P. aeruginosa differentially regulates genes involved in metabolism, motility, and outer surface remodeling in wound infections.(A) Log2-transformed differential gene expression of P. aeruginosa in murine burn (y axis) and chronic (x axis) wound infections as compared to growth in MOPS-succinate (Succ.). Significant changes (fold change ≥4, P<0.01, negative binomial test) are colored as shown (Diff. Exp., differentially expressed in). (B) Significantly enriched or scarce COG categories in differentially expressed gene sets (P<0.01, Fisher's exact test; †, significantly less present than expected; *, significantly more present than expected).
Mentions: We found that P. aeruginosa differentially regulates 14% and 19% of its genome during growth in murine burn and chronic wounds, respectively, as compared to MOPS-succinate (P<0.01, negative binomial test, fold change ≥4) (Table S2). The transcriptional responses of P. aeruginosa during growth in these two wound types as compared to MOPS-succinate are highly correlated (Spearman rank correlation coefficient = 0.840), suggesting that the cues sensed by P. aeruginosa in acute and chronic wound infections are largely similar (Figure 1A). Notably, 7.3% of the genome is commonly up- or down-regulated in both wound infections, which is a significant overlap (P<4.72×10−110, Fisher's exact test). The P. aeruginosa genome encodes numerous virulence factors, and our data provides a genome-wide perspective on the expression of these virulence genes (Table S3). We saw that many genes in the PA3160-PA3141 cluster, which encodes genes required for lipopolysaccharide O antigen biosynthesis [24], were down-regulated in vivo, and to a greater extent in chronic wounds. This suggests either that P. aeruginosa may alter its outer surface during infection, or that O antigen biosynthesis is regulated as a consequence of more static growth in vivo. We also saw that genes responsible for the biosynthesis of the siderophores pyochelin and pyoverdine were greatly up-regulated in vivo. Iron is known to be a limited resource in numerous infections, and our results suggest that iron acquisition is important in P. aeruginosa soft tissue infections as well [25]. Many type II and type III secretion system genes were up-regulated in both acute and chronic wounds as well, indicating that P. aeruginosa may be modulating host cellular physiology and extracellular environment through these well-characterized secretion systems [26], [27]. Finally, we saw down-regulation of many genes in the psl cluster, which is responsible for synthesis of the Psl exopolysaccharide. In strain PAO1, Psl is the primary exopolysaccharide involved in biofilm formation on abiotic surfaces [28]. Thus, P. aeruginosa differentially regulates much of its virulence repertoire upon wound infection, further underscoring the multifaceted nature of its virulence.

Bottom Line: Generally we discovered that expression of a gene in vivo is not correlated with its importance for fitness, with the exception of metabolic genes.Specifically, we found that long-chain fatty acids represent a major carbon source in both chronic and acute wounds, and P. aeruginosa must biosynthesize purines, several amino acids, and most cofactors during infection.Our results provide novel insight into the genetic requirements for acute and chronic P. aeruginosa wound infections and demonstrate the power of using both gene expression and fitness profiling for probing bacterial virulence.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America.

ABSTRACT
Opportunistic infections caused by Pseudomonas aeruginosa can be acute or chronic. While acute infections often spread rapidly and can cause tissue damage and sepsis with high mortality rates, chronic infections can persist for weeks, months, or years in the face of intensive clinical intervention. Remarkably, this diverse infectious capability is not accompanied by extensive variation in genomic content, suggesting that the genetic capacity to be an acute or a chronic pathogen is present in most P. aeruginosa strains. To investigate the genetic requirements for acute and chronic pathogenesis in P. aeruginosa infections, we combined high-throughput sequencing-mediated transcriptome profiling (RNA-seq) and genome-wide insertion mutant fitness profiling (Tn-seq) to characterize gene expression and fitness determinants in murine models of burn and non-diabetic chronic wound infection. Generally we discovered that expression of a gene in vivo is not correlated with its importance for fitness, with the exception of metabolic genes. By combining metabolic models generated from in vivo gene expression data with mutant fitness profiles, we determined the nutritional requirements for colonization and persistence in these infections. Specifically, we found that long-chain fatty acids represent a major carbon source in both chronic and acute wounds, and P. aeruginosa must biosynthesize purines, several amino acids, and most cofactors during infection. In addition, we determined that P. aeruginosa requires chemotactic flagellar motility for fitness and virulence in acute burn wound infections, but not in non-diabetic chronic wound infections. Our results provide novel insight into the genetic requirements for acute and chronic P. aeruginosa wound infections and demonstrate the power of using both gene expression and fitness profiling for probing bacterial virulence.

Show MeSH
Related in: MedlinePlus