Transcriptomics

Dataset Information

25

Identification of differentially expressed genes between clinical and bovine-biased Escherichia coli O157:H7 genotypes


ABSTRACT: Escherichia coli O157:H7 strains have been classified into different genotypes based on the presence of specific shiga toxin-encoding bacteriophage insertion sites. Genotypes that are predominant in clinical isolates are named clinical genotypes and those that are isolated mostly from bovine sources are bovine-biased genotypes. To determine whether inherent differences in gene expression could possibly explain the variation in infectivity of these genotypes, we compared the expression patterns of O157:H7 strains isolated from cattle, which belonged to either clinical genotype 1 or bovine-biased genotype 5. Important virulence factors of O157, including locus of enterocyte effacement, enterohemolysin, and pO157 plasmid encoded genes, showed increased expression in clinical genotype. Genes essential for acid resistance such as gadA, gadB, and gadC and other stress fitness-associated genes were up-regulated in the bovine-biased genotype 5. Overall, these results suggest that clinical genotype 1 strains more commonly cause human illness because of an enhanced ability to express O157 virulence factors known to be important for disease pathogenesis. By contrast, strains of the bovine-biased genotype 5 appear to be more resistant to adverse environmental conditions, which enable them to survive well in bovines without causing disease. Overall design: The results are based on O157:H7 clinical and bovine-biased genotype cultures grown in DMEM medium to exponential phase. Four strains were selected from each genotype and strains were considered as biological replicates. A double loop microarray design was used for comparing the samples. Differences in transcript levels were determined using a mixed model ANOVA in R/MAANOVA which tested for significant differences due to strain (clinical or bovine-biased) using the following linear model: array+dye+sample (biological replicate)+strain+error. We incorporated the dye-swaps among the biological replicates.

INSTRUMENT(S): MSU E. coli 6.1.K Ver. 1.0.2

ORGANISM(S): Escherichia coli  

SUBMITTER: Thomas S Whittam  

PROVIDER: GSE15783 | GEO | 2009-04-24

SECONDARY ACCESSION(S): PRJNA116857

REPOSITORIES: GEO

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