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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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Genome-wide P. aeruginosa gene expression and knockout fitness in wound infection are not correlated.(A) Log2-transformed fold change gene expression (y axis) and knockout abundance (x axis) of P. aeruginosa in murine burn wound infections as compared to growth in MOPS-succinate (Succ.). Significant (Sig.) changes in gene expression (fold change ≥4, P<0.01, negative binomial test) and mutant abundance (fold change ≥4, P<0.05, negative binomial test) are colored as shown (N.C., no change). (B) Spearman rank correlation coefficient between fold change expression and fold change mutant abundance in the burn wound-MOPS-succinate and the chronic wound-MOPS-succinate comparisons (x axis) for COG categories with more than 10 differentially regulated members and an associated correlation greater than 0.1 or less than −0.1 (y axis). Only genes with transposon-derived Tn-seq reads were considered.
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pgen-1004518-g002: Genome-wide P. aeruginosa gene expression and knockout fitness in wound infection are not correlated.(A) Log2-transformed fold change gene expression (y axis) and knockout abundance (x axis) of P. aeruginosa in murine burn wound infections as compared to growth in MOPS-succinate (Succ.). Significant (Sig.) changes in gene expression (fold change ≥4, P<0.01, negative binomial test) and mutant abundance (fold change ≥4, P<0.05, negative binomial test) are colored as shown (N.C., no change). (B) Spearman rank correlation coefficient between fold change expression and fold change mutant abundance in the burn wound-MOPS-succinate and the chronic wound-MOPS-succinate comparisons (x axis) for COG categories with more than 10 differentially regulated members and an associated correlation greater than 0.1 or less than −0.1 (y axis). Only genes with transposon-derived Tn-seq reads were considered.

Mentions: Since transcriptomics has been used in the past to identify bacterial genes potentially important for in vivo fitness [14], [15], [31], we hypothesized that genes identified as important for fitness using Tn-seq would display increased expression in vivo. If this hypothesis is true, one would expect that a correlation coefficient (which expresses correlation between two variables on a scale from −1, or perfectly anticorrelated, to 1, or perfectly correlated) would be closer to −1. However, we found that mutant fitness and differential expression are uncorrelated, suggesting that in this case RNA-seq is not a good predictor of genes important for fitness in wounds (Figures 2A and S1, Table 1). One should keep in mind that Tn-seq is a competitive infection since most strains are wild-type for a given genetic locus, and RNA-seq may be more predictive if individual mutants are examined.


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

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

Genome-wide P. aeruginosa gene expression and knockout fitness in wound infection are not correlated.(A) Log2-transformed fold change gene expression (y axis) and knockout abundance (x axis) of P. aeruginosa in murine burn wound infections as compared to growth in MOPS-succinate (Succ.). Significant (Sig.) changes in gene expression (fold change ≥4, P<0.01, negative binomial test) and mutant abundance (fold change ≥4, P<0.05, negative binomial test) are colored as shown (N.C., no change). (B) Spearman rank correlation coefficient between fold change expression and fold change mutant abundance in the burn wound-MOPS-succinate and the chronic wound-MOPS-succinate comparisons (x axis) for COG categories with more than 10 differentially regulated members and an associated correlation greater than 0.1 or less than −0.1 (y axis). Only genes with transposon-derived Tn-seq reads were considered.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004518-g002: Genome-wide P. aeruginosa gene expression and knockout fitness in wound infection are not correlated.(A) Log2-transformed fold change gene expression (y axis) and knockout abundance (x axis) of P. aeruginosa in murine burn wound infections as compared to growth in MOPS-succinate (Succ.). Significant (Sig.) changes in gene expression (fold change ≥4, P<0.01, negative binomial test) and mutant abundance (fold change ≥4, P<0.05, negative binomial test) are colored as shown (N.C., no change). (B) Spearman rank correlation coefficient between fold change expression and fold change mutant abundance in the burn wound-MOPS-succinate and the chronic wound-MOPS-succinate comparisons (x axis) for COG categories with more than 10 differentially regulated members and an associated correlation greater than 0.1 or less than −0.1 (y axis). Only genes with transposon-derived Tn-seq reads were considered.
Mentions: Since transcriptomics has been used in the past to identify bacterial genes potentially important for in vivo fitness [14], [15], [31], we hypothesized that genes identified as important for fitness using Tn-seq would display increased expression in vivo. If this hypothesis is true, one would expect that a correlation coefficient (which expresses correlation between two variables on a scale from −1, or perfectly anticorrelated, to 1, or perfectly correlated) would be closer to −1. However, we found that mutant fitness and differential expression are uncorrelated, suggesting that in this case RNA-seq is not a good predictor of genes important for fitness in wounds (Figures 2A and S1, Table 1). One should keep in mind that Tn-seq is a competitive infection since most strains are wild-type for a given genetic locus, and RNA-seq may be more predictive if individual mutants are examined.

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