Genomic comparison of shiga toxin-producing E. coli O157:H7 from ruminants and humans

Shiga toxin-producing E. coli (STEC) are zoonotic pathogens that frequently colonise ruminants without them showing any symptoms. In humans, STEC cause diarrhoeal disease and occasionally leads to the life-threatening disease haemolytic-uraemic syndrome (HUS). In this study, the aim is to identify any genomic differences between Swedish STEC O157:H7 isolates that have caused HUS and isolates that did not, as well as between isolates taken from animals and isolates taken from humans. I constructed a pan-genome analysis pipeline and performed statistical analyses to find genes that differed between these groups. I also constructed a phylogenetic analysis pipeline to visualise any clustering of isolates based on different categories. The results from the phylogenetic analysis showed that the isolates tended to not form clear clusters based on their category. When comparing isolates from animals to isolates from humans, an elastic net regression analyses yielded a list of 23 genes that differed between them, while a statistical analysis using Scoary found 1854 genes. The genes found by the regression analysis consists largely of genes associated with metabolism, with other notable genes being transposases as well as two genes from the prp operon. Gene ontology analysis of the genes from Scoary showed that no particular molecular functions or biological processes stand out when compared to the background frequency of gene ontology terms. When comparing isolates that caused HUS against isolates that did not, no genes were found to be statistically significant. In order to find more conclusive results about the genomic differences between STEC in animals and humans, as well as between STEC that leads to HUS and STEC that does not, further studies are needed.