Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli

We have used RNA sequencing to compare transcriptomes of 30 stx2a and eae positive STEC strains of non-O157 serogroups isolated from children < 5 years of age. The strains were from children with HUS (HUS group, n=15), and children with asymptomatic or mild disease (non-HUS group, n=15), either induced with mitomycin C or non-induced, to reveal potential differences in gene expression levels between groups. When the HUS and non-HUS group were compared for differential expression of protein-encoding gene families, 399 of 6119 gene families were differentially expressed (log2 fold change ≥ 1, FDR < 0.05) in the non-induced condition, whereas only one gene family was differentially expressed in the induced condition. Gene ontology and cluster analysis showed that several fimbrial operons, as well as a putative type VI secretion system (T6SS) were more highly expressed in the HUS group than in the non-HUS group, indicating a role of these in the virulence of STEC strains causing severe disease. Comparison of 30 non-O157 STEC strains, one group of strains having caused HUS (n=15) and one causing no or mild disease (n=15), induced with mitomycin c or non-induced, at exponential growth in SILAC medium. Please note that locations of genomic features are provided in associated .gtf file for each sample pair (i.e. non-induced and induced samples; e.g. *nIND.HUS and *IND.HUS), linked to the corresponding uninduced sample records.