Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients.

Federica Gigliucci,Stefano Morabito,Arnold Knijn,Hamideh M Ahmad,Bas E Dutilh,Alex W Friedrich,F A Bastiaan Von Meijenfeldt,Fabio Minelli,Gerwin C Raangs,Valeria Michelacci,Gaia Scavia,John W A Rossen

doi:10.3389/fcimb.2018.00025

Abstract

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 bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. 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.

Highlights

Shiga toxin-producing Escherichia coli (STEC) are a heterogeneous E. coli pathogroup causing food-borne outbreaks and sporadic cases of disease worldwide (Armstrong et al, 1996)
One possibility is that the human intestinal microbiota play a role by interfering with the ability of STEC to efficiently colonize the gastro-intestinal tract, as it has been proposed for other bacterial infections (Fujiwara et al, 2001; Gueimonde et al, 2007)
Four stool samples from four patients suffering from Crohn’s Disease (CD) and hospitalized at the University Medical Center Groningen, The Netherlands, were included in the analysis (Samples 1, 2, 5, and 6). These samples were previously analyzed by real-time PCR for the presence of virulence genes associated with STEC and Enteropathogenic E. coli (EPEC) (Gauthier et al, 2003) pathogroups, revealing the presence of stx2 gene in Sample 2, the presence of the escV gene in Sample 1 and 5, and none of the mentioned virulence genes in Sample 6

Summary

Introduction

Shiga toxin-producing Escherichia coli (STEC) are a heterogeneous E. coli pathogroup causing food-borne outbreaks and sporadic cases of disease worldwide (Armstrong et al, 1996). STEC may cause severe afflictions in humans due to their ability to produce potent cytotoxins, the Shiga toxins (Stx), acquired upon infection with bacteriophages carrying stx genes, which can remain stably integrated into the bacterial chromosome (O’Brien et al, 1984). Stx exert their action by blocking the protein synthesis in the target cells by inactivating ribosomes (Okuda et al, 2006). Gamage and colleagues proposed that different bacterial species in the host microbiota can act as amplifiers of the Stx-converting phage resulting in an augmented ability to produce the toxin (Gamage et al, 2003)

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Conclusion