K-114. Identification of Differentially Expressed Genes in Clinical and Bovine-Specific Genotypes of Escherichia coli O157:H7

S. Kailasan Vanaja1, J. T. Riordan1, T. E. Besser2, T. S. Whittam1;
1Michigan State Univ., East Lansing, MI, 2Washington State Univ., Pullman, WA.

E. coli O157:H7 is a human pathogen of zoonotic origin that inhabits the bovine gastrointestinal tract without causing clinical disease. A recent typing method classified E. coli O157:H7 into clinical and bovine-specific genotypes based on the Shiga toxin (stx)-encoding bacteriophage insertion sites in the genome. Clinical genotypes are strains recovered from both cattle and clinical cases, whereas bovine-specific genotypes are found in cattle only. Here we identified the genes that are differentially expressed between clinical (genotype 3) and bovine-specific (genotype 7) genotypes. To compare the 2 genotypes, RNA from 4 strains, representing 4 biological replicates, from each genotype were used for a double loop microarray hybridization design. cDNA populations from late exponential phase transcriptomes of strains grown in minimal media were compared using microarrays with probes representing 5978 ORFs from three strains, E. coli O157:H7 Sakai, EDL933 and K12 MG1655. The data were analyzed by nonparametric significance analysis of microarrays (SAM) with a false discovery rate (FDR) of 0.05 to correct for multiple comparisons and a fold change cut off of > 1.5 for biological significance. Gene set enrichment analysis (GSEA) was also used to identify enrichment of gene sets with common biological function in the tested genotypes. SAM identified 25 genes significantly differentially expressed between the two genotypes including 9 locus of enterocyte effacement (LEE) genes, which were up-regulated in clinical genotype (1.9 - 3.8 fold). GSEA identified significant enrichment of 5 gene sets in the clinical genotype and 13 gene sets in the bovine-specific genotype (FDR < 0.05). The LEE gene set was significantly enriched in the clinical genotype, whereas the acid fitness island gene set, associated with the acid resistance of E. coli, was more expressed in the bovine-specific genotype. These results show that clinical and bovine-specific genotypes of E. coli O157:H7 differentially express certain virulence genes, which might account for differences in human disease.