Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

Amber C A Hendriks,Bas E Dutilh,Frans A G Reubsaet,A M D Mirjam Kooistra-Smid,Maaike J C Van Den Beld,Aldert L Zomer,John W A Rossen

doi:10.1186/s12864-020-6555-7

Abstract

BackgroundWe investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that predict disease outcome per individual patient could be used to prioritize control measures. For this purpose, genome wide association studies (GWAS) were performed using presence or absence of single genes, combinations of genes, and k-mers. All genetic variants were derived from draft genome sequences of isolates from a multicenter cross-sectional study conducted in the Netherlands during 2016 and 2017. Clinical data of patients consisting of binary/dichotomous representation of symptoms and their calculated severity scores were also available from this study. To verify the suitability of the methods used, the genetic differences between the genera Shigella and Escherichia were used as control.ResultsThe isolates obtained were representative of the population structure encountered in other Western European countries. No association was found between single genes or combinations of genes and separate symptoms or disease severity scores. Our benchmark characteristic, genus, resulted in eight associated genes and > 3,000,000 k-mers, indicating adequate performance of the algorithms used.ConclusionsTo conclude, using several microbial GWAS methods, genetic variants in Shigella spp. and EIEC that can predict specific symptoms or a more severe course of disease were not identified, suggesting that disease severity of shigellosis is dependent on other factors than the genetic variation of the infecting bacteria. Specific genes or gene fragments of isolates from patients are unsuitable to predict outcomes and cannot be used for development, prioritization and optimization of guidelines for control measures of shigellosis or infections with EIEC.

Highlights

We investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that predict disease outcome per individual patient could be used to prioritize control measures
The purpose of our study is to investigate whether there is an association between symptoms and disease severity of the patients and genetic determinants of infecting Shigella and EIEC isolates in the Netherlands
The lower fraction of patients with coinfection that experienced blood in stool was reflected in the de Wit severity score, in which blood in stool is a criterion with double weighing, as it was significantly lower for patients with coinfection (T-test, p = 0.017)

Summary

Introduction

We investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that predict disease outcome per individual patient could be used to prioritize control measures. For this purpose, genome wide association studies (GWAS) were performed using presence or absence of single genes, combinations of genes, and k-mers. All Shigella spp. are genetically closely related to Escherichia coli to the extent that they should be classified as one species [2, 3] It is a taxonomical decision based on historical and clinical arguments that has maintained the current classification [4]. Because of the similarity in pathogenetic features of EIEC and Shigella spp, differentiation using diagnostic laboratory tests is difficult [7]

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