The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children

Derick N M Osakunor,Mark E J Woolhouse,Christian Brinch,Theresa Chimponda,Francisca Mutapi,Thomas N Petersen,Frank M Aarestrup,Takafira Mduluza,Alasdair Ivens,Janice Murray,Patrick Munk,Seth A Amanfo

doi:10.1038/s42003-020-0859-7

Abstract

Helminth parasites have been shown to have systemic effects in the host. Using shotgun metagenomic sequencing, we characterise the gut microbiome and resistome of 113 Zimbabwean preschool-aged children (1–5 years). We test the hypothesis that infection with the human helminth parasite, Schistosoma haematobium, is associated with changes in gut microbial and antimicrobial resistance gene abundance/diversity. Here, we show that bacteria phyla Bacteroidetes, Firmicutes, Proteobacteria, and fungi phyla Ascomycota, Microsporidia, Zoopagomycota dominate the microbiome. The abundance of Proteobacteria, Ascomycota, and Basidiomycota differ between schistosome-infected versus uninfected children. Specifically, infection is associated with increases in Pseudomonas, Stenotrophomonas, Derxia, Thalassospira, Aspergillus, Tricholoma, and Periglandula, with a decrease in Azospirillum. We find 262 AMR genes, from 12 functional drug classes, but no association with individual-specific data. To our knowledge, we describe a novel metagenomic dataset of Zimbabwean preschool-aged children, indicating an association between urogenital schistosome infection and changes in the gut microbiome.

Highlights

Helminth parasites have been shown to have systemic effects in the host
The composition of the gut microbiome is influenced by age[8,12], diet and geography[5,13,14], host genotype[15], exposure to maternal microbiota[16], as well as environmental factors[17] including the role of protozoal and helminth parasites[18]
We found differences in the gut microbiome between S. haematobium infected versus uninfected children, aged up to 13 years old[35]

Summary

Introduction

Helminth parasites have been shown to have systemic effects in the host. Using shotgun metagenomic sequencing, we characterise the gut microbiome and resistome of 113 Zimbabwean preschool-aged children (1–5 years). We test the hypothesis that infection with the human helminth parasite, Schistosoma haematobium, is associated with changes in gut microbial and antimicrobial resistance gene abundance/diversity. We describe a novel metagenomic dataset of Zimbabwean preschool-aged children, indicating an association between urogenital schistosome infection and changes in the gut microbiome. The composition of the gut microbiome is influenced by age[8,12], diet and geography[5,13,14], host genotype[15], exposure to maternal microbiota[16], as well as environmental factors[17] including the role of protozoal and helminth parasites[18]. The gut microbial population continues to evolve until about age 3–5 years[8,12], it is important to establish how external factors, especially infections, that young children are exposed to, influence the microbiome

Methods

Results

Conclusion