Diarrheal-associated microbiome is linked to higher STEC colonization and virulence in an in vitro model of the infant colon: a multi-omics approach

Shiga-toxin producing Escherichia coli (STEC) is a major food-borne pathogen causing human disease ranging from diarrhea to life-threatening complications, mainly in young children. Colonization, virulence and interactions of STEC strains with human gut microbiota are pivotal during infection, but remain poorly described particularly in children, the most affected population. Using a multi-omics approach, we evaluated in an infant artificial colon infected with EHEC O157:H7 strain EDL 933, the impact of microbiota from stool samples collected in children with STEC-positive diarrhea, compared to stool from the same child after recovery of the diarrheal episode (n=5) on STEC colonization and virulence. Comparing diarrheal versus recovery conditions, we observed higher STEC colonization and prolonged expression of STEC virulence genes (especially in the youngest donor), lower bacterial diversity, increased abundance of potential pathobionts such as Clostridia, as well as higher acetate, succinate and N-acetylneuraminic acid levels under diarrheal conditions. Results suggest that diarrheal-associated microbiome could favor STEC pathogenesis in the simulated infant colon, paving the way to better understand their physiopathology in this at-risk population, taking into account inter-individual variabilities in gut microbiota.