University of Groningen Shigella spp. and entero-invasive Escherichia coli van den Beld, Maaike

University of Groningen

Shigella spp. and entero-invasive Escherichia coli

van den Beld, Maaike

DOI:

10.33612/diss.101452646

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Publication date: 2019

Link to publication in University of Groningen/UMCG research database

Citation for published version (APA):

van den Beld, M. (2019). Shigella spp. and entero-invasive Escherichia coli: diagnostics, clinical

implications and impact on public health. University of Groningen. https://doi.org/10.33612/diss.101452646

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Shigella spp.

and entero-invasive

Escherichia coli

Diagnostics, clinical implications

and impact on public health

ISBN: 978-94-034-2097-4 (printed version) ISBN: 978-94-034-2096-7 (electronic version)

Cover design and layout: Wendy Schoneveld || wenzid.nl Printed by ProefschriftMaken || Proefschriftmaken.nl

©Maaike J. C. van den Beld, 2019

No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, without prior written permission of the holder of the copyright.

Shigella spp. and entero-invasive

Escherichia coli

Diagnostics, clinical implications and impact on public health

PhD thesis

to obtain the degree of PhD at the University of Groningen

on the authority of the Rector Magnificus Prof. C. Wijmenga

and in accordance with the decision by the College of Deans. This thesis will be defended in public on Wednesday 11 December 2019 at 12.45 hours

by

Maaike Johanna Cornelia van den Beld

Supervisor

Prof. dr. J.W.A. Rossen

Co-supervisors

Assessment Committee

The work presented in this thesis was performed at and funded by the Centre for Infectious Disease research, diagnostics and laboratory Surveillance (IDS) of the National Institute for Public Health and the Environment (RIVM), the Department of Medical Microbiology and Infection Prevention of the University of Groningen and the University Medical Center Groningen, and the Department of Medical Microbiology of Certe in Groningen. Additional funding was received from the Programmabudget Regionale Ondersteuning of the Centre for Infectious Disease Control of the RIVM. Financial support for printing this thesis was kindly provided by the RIVM, the Groningen University Institute for Drug Exploration (GUIDE), and by CO consult & onderwijs in Maarssen.

Table of Contents

Chapter 1 General introduction 9

Part I Taxonomy and diagnostics of Shigella spp. and EIEC

Chapter 2 Genomic taxonomy of Shigella spp. and Entero-invasive

Escherichia coli (EIEC); current classification needs to be reconsidered

31

Chapter 3 Multicenter evaluation of molecular and culture-dependent

diagnostics for Shigella spp. and entero-invasive Escherichia coli in the Netherlands

61

Part II Optimizing diagnostics of Shigella spp. and EIEC

Chapter 4 Evaluation of a culture dependent algorithm and a molecular

algorithm for identification of Shigella spp., Escherichia coli, and entero-invasive E. coli (EIEC)

81

Chapter 5 Matrix-Assisted Laser Desorption-Ionization Time-of-Flight mass

spectrometry using a custom-made database, biomarker assignment or mathematical classifiers does not differentiate Shigella spp. and Escherichia coli

103

Part III Incidence, epidemiology, clinical implications and impact on public health

Chapter 6 Incidence, clinical implications and impact on public health of

infections with Shigella spp. and entero-invasive Escherichia coli (EIEC): results of a multicenter cross-sectional study in the Netherlands during 2016-2017

125

Chapter 7 Genome-wide association studies of Shigella spp. and

Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

147

Chapter 8 The importance of a multifactorial approach for (inter)national

surveillance of Shigella spp. and entero-invasive Escherichia coli

185

Part IV General discussion

Chapter 9 Summarizing discussion, future perspectives and conclusions 229

Part V Appendices Appendix I Appendix II Appendix III Appendix IV Bibliography Nederlandse samenvatting Dankwoord

About the author

247 273 281 289