The human gut microbiota as a reservoir for antimicrobial resistance genes

171 Pages·2015·4.79 MB·English

The human gut microbiota as a reservoir
for antimicrobial resistance genes
Elena Buelow
The human microbiota as a reservoir for antimicrobial resistance genes
PhD Thesis, University of Utrecht, The Netherlands
ISBN/EAN: 978-94-6295-117-4
Cover art: Elena Buelow, Ivo Jelinek.
Layout and design: Elena Buelow, Ivo Jelinek
Printed by: Uitgeverij BOXPress | Proefschriftmaken.nl
© Elena Buelow, Utrecht, The Netherlands. All rights reserved. No part of this thesis may be reproduced, stored in
a retrieval system or transmitted by any means without permission of the author. The copyright of the articles that
have been published or accepted for publication has been transferred to the respective journals.
This work was supported by The Netherlands Organisation for Health Research and Development ZonMw (Priority
Medicine Antimicrobial Resistance; grant 205100015) and by the European Union Seventh Framework Programme
(FP7-HEALTH-2011-single-stage) ‘Evolution and Transfer of Antibiotic Resistance’ (EvoTAR) under grant agreement
number 282004
The printing of this thesis was kindly supported by: University Medical Center Utrecht; Infection and Immunity
Center Utrecht; and the Netherlands Society of Medical Microbiology (NVMM) and the Royal Netherlands Society
for Microbiology (KNVM).
The human gut microbiota as a reservoir
for antimicrobial resistance genes
De darm microbiota van de mens als een reservoir van
antimicrobiële resistentiegenen
(met een samenvatting in het Nederlands)
Proefschrift
ter verkrijging van de graad van doctor aan de Universiteit Utrecht op gezag
van de rector magnificus, prof. dr. G.J. van der Zwaan, ingevolge het besluit
van het college voor promoties in het openbaar te verdedigen op dinsdag
24 maart 2015 des middags te 12.45 uur
door
Elena Bülow
geboren op 7 augustus 1982 te Kevelaer, Duitsland
Promotor: Prof. dr. M.J.M. Bonten
Copromotoren: Dr. ir. W. van Schaik
Dr. R.J.L. Willems
Es kann die Ehre dieser Welt
Dir keine Ehre geben,
Was dich in Wahrheit hebt und hält,
Muß in dir selber leben.
Wenn’s deinem Innersten gebricht
An echten Stolzes Stütze,
Ob dann die Welt dir Beifall spricht,
Ist dir all wenig nütze.
Das flücht’ge Lob des Tages Ruhm
Magst du dem Eitlen gönnen;
Das aber sei dein Heiligtum:
Vor dir bestehen können.
Theodor Fontane
Commisse: Prof. dr. P.I.W. de Bakker
Prof. dr. M. Kleerebezem
Prof. dr. M.O.A. Sommer
Prof. dr. J.A.J.W. Kluytmans
Dr. B.E. Dutilh
Paranimfen: Nuno Rodrigues Faria
Fernanda Paganelli
Content
Chapter 1 General introduction 9
Chapter 2 Effects of selective decontamination (SDD) 28
on the gut resistome
J Antimicrob Chemother, 2014, 69 (8): 2215-2223. doi:10.1093/jac/dku092
Chapter 3 Dynamics of the gut microbiota and resistome 51
during ICU hospitalization
Manuscript in preparation
Chapter 4 Limited dispersal of antibiotic resistance 84
genes through the sewerage system
Manuscript in preparation
Chapter 5 Genes conferring resistance to the disinfectant 112
benzalkonium chloride in the gut microbiota of
hospitalized patients
Manuscript in preparation
Chapter 6 General discussion 132
English summary 148
Dutch summary 152
Acknowledgements 158
Curriculum Vitae 164

Chapter 1
General introduction
Chapter 1
The human microbiota
The human body is densely populated with trillions of microbes which are referred to as the
human microbiota. The human microbiota mostly consists of bacterial cells, and is estimated
to outnumber the cells of the human body by a factor of ten. The number of bacterial genes
in the human microbiota outnumbers the number of genes in the human genome by several
orders of magnitude [1, 2]. The collection of genes contained by the human microbiota
is referred to as the human microbiome. Historically, the human microbiota was studied
by laboratory culture, but culture techniques are limited in their ability to capture the full
diversity of the bacteria that inhabit the human body [3]. The introduction of microbial
DNA-based culture-independent approaches to study microbial communities (termed
‘metagenomics’) has revolutionized our understanding of microbiology and substantially
contributed to the advances in human microbiome research in the last decade [4, 5].
Metagenomic approaches are commonly used in studies of the human microbiota, either
by means of 16S rRNA sequencing for taxonomic profiling, or by means of metagenomic
shotgun-sequencing, which allows both taxonomic profiling and the identification of
functionally associated features of sequences [1, 5] (Figure 1). A complementary approach
to assign biological functions to the genes that are identified by high-throughput sequencing
approaches is termed functional metagenomics. In functional metagenomics, DNA isolated
from a microbial ecosystem is randomly cloned into a vector and transformed to a microbial
host (most commonly E. coli), resulting in large clone libraries. These clone libraries can then
be used to screen for novel enzymatic activities, resistance to antimicrobial compounds or
other relevant phenotypes [6-8].
10