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Research Topic: Complex systems & Metagenomics

Complex interactions between different environments, between animals and humans, microbes or genes and their products affect infectious disease dynamics and the epidemiology of pathogens. The projects in the NCOH PhD tract topic “Complex systems & Metagenomics” tackle different aspects of these interactions, such as transmission of microbial strains or mobile genetic elements, susceptibility to infection and selection for resistant microorganisms. Current methods describing the epidemiology of pathogens generally focus on analysis of single isolates. In this topic we will investigate the use of metagenomics analysis of the microbiome including fungi and viruses at the animal-human-environmental interface. We aim to develop novel methods to describe the complex dynamics of dissemination of (antibiotic resistance) genes and pathogens. We will examine effects on the development of (infectious) disease or syndromes, host processes, and on the environment as emissions.


Project #1

Host-microbe interactions as elicitors of cryptic antibiotics in actinomycetes and spread of antimicrobial resistance under low antibiotic stress

PhD student: Doris van Bergeijk

Organisation: Leiden University

Project #2

Molecular mechanisms of microbiota-mediated colonization resistance against intestinal outgrowth of multidrug-resistant Enterobacteriaceae (E. coli, K. pneumoniae) and enterococci

PhD student: Paul Stege

Organisation: University Medical Center Utrecht

Project #3

Mechanisms of microbiota-mediated defence against various infectious diseases

PhD student: Quinten Ducarmon

Organisation: Leiden University Medical Center

Project #4

Microbiome fortification for healthier pigs through metagenomics-driven culturomics and microbial bioactive metabolite discovery

PhD student: Simen Fredrikesen

Organisation: Wageningen University & Research

Project #5

Metagenomic analysis of animal, environmental and human microbiomes in the context of excess pneumonia risk around livestock production farms in the Netherlands: effects in humans

PhD student: Warner van Kersen

Organisation: Utrecht University / Institute for Risk Assessment Sciences

Project #6

Metagenomic analysis of animal, environmental and human microbiomes in the context of excess pneumonia risk around livestock production farms in the Netherlands: flow of microorganisms

PhD student: Kirsty Kwok

Organisation: Erasmus MC

Project #7

CoCoNod (Coma, Convulsions and Nodding Syndrome): aetiology, risk factors and outcome of paediatric neuroemergencies in resource poor settings

PhD student: Arthur Edridge

Organisation: Academic Medical Center

Project #8

Immunological, microbiological and pharmacological aspects of invasive fungal infections

PhD student: Nico Janssen

Organisation: Radboudumc

Project #9

Development of Bayesian inference methods for estimating transmission trees for antibiotic-resistant pathogens in hospitals and farms

PhD student: Bastiaan Van der Roest

Organisation: UMC Utrecht

Associated: Utrecht University, RIVM, Wageningen University & Research

Project #10a – NCOH-LSH Project

DiSSeMINATE - Drivers of Selection and Spread of Mobile Genetic Elements INvolved in Antimicrobial Resistance

Tracking and tackling goat farm-associated pneumonia using a metagenomics approach

PhD student: Wouter Lokhorst

Organisations: UMC Utrecht (coordinator), Wageningen University & Research

Associated: Utrecht University, RIVM

Project #11

Antimicrobial resistance in relation to the persistence of antimicrobial residues after treatment of farm animal: input for risk management (RESRISK)

PhD student: Aram Swinkels

Organisation: Utrecht University

Associated: Wageningen University & Research

Project #12

Prepared for anything: detection and interpretation of novel viruses by metagenomics

PhD student: to be appointed

Organisations: Metagenomics Group, IBB, UU, UBC, ErasmusMC


Project #13 – OH EJP Project

Tracking the public health hazard of foodborne Hepatitis E

PhD student: Renate Hakze van der Honing

Organisations: Rijksinstituut voor Volksgezondheid en Milieu (coordinator), Wageningen Bioveterinary Research

Project #15

CANVAS - Broadly protective glycoconjugate vaccines targeting major animal and zoonotic Gram-positive pathogens

PhD student: Kitty Exel

Organisation: Utrecht University

Project #14 – OH EJP Project

Developing evidence-based surveillance for emerging rat-borne zoonoses in changing environments

PhD student: Marieke de Cock

Organisations: National Institute for Public Health and the Environment (RIVM), Wageningen Bioveterinary Research (WBVR), and Friedrich-Loeffler-Institut (FLI)