Metagenomic characterization of the human intestinal microbiota in faecal samples from STEC-infected patients

The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatics approaches, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with STEC infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Regardless of the bioinformatic procedure used, a good resolution of the taxonomic profiles of the samples was achieved. The faeces collected from the STEC infected patients showed a lower intestinal abundance of the beneficial microorganisms Bifidobacterium and Clostridiales spp. in comparison to controls where those microorganisms predominated. These differences were observed with both bioinformatic approaches used and seemed to be related with the STEC infection although the variation in the relative abundance of the members of the Bifidobacterium genus could have also been associated with the dysbiotic status following the diarrhoea.Finally, the metagenomic sequencing allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.