ESR 3.1
Characterization of waterborne bacteria, antibiotic resistance genes and heavy metal associated resistance genes through analysis of hospital-related water and human gastrointestinal tract microbiome using high-throughput sequencing technologies


Hospitals are major ecological niches of antibiotic resistant bacteria (ARB). The antibiotic pressure, a susceptible population (severely ill patients) and the constant “traffic” of potentially pathogenic microorganisms help the dissemination and the emergence of antimicrobial resistance. Some water-containing compartments may act as reservoirs of ARB and may contribute to the arise of healthcare-associated infections. The goal of this project is to investigate the presence of ARB in hospital humid compartments and to track the spread of multi-drug resistance bacteria and antibiotic resistance genes in the clinical environment using high-throughput sequencing technologies (e.g. shot gun metagenomics). In addition, the PhD student will study the presence of disinfectants, heavy metals and antibiotic resistance genes in the human gastrointestinal tract microbiome.
Furthermore, the development of rapid molecular tests will be examined in collaboration with project partners. The results will be used to support prevention and improve diagnostics and detection of ARB in the clinical environment.

The PhD student will be trained in the Molecular Bacteriology and Genomics for Infection Prevention groups at the Department of Medical Microbiology of the University Medical Center Groningen in Groningen, which are highly experienced in cross-border network studies addressing the molecular epidemiology of ARB and infection control; the Centre of Excellence for Water Technology in Leeuwarden for a secondment of four months, and the Nanobiophotonics Department of the Institute of Photonic Technology in Jena, Germany for a six-month internship.


  • Prof. Dr. Alexander Friedrich
  • Dr. Hermie Harmsen
  • Dr. John Rossen
  • Dr. Silvia Garcia Cobos
  • Dr. Ruud Deurenberg



Dr. Lucia Hernández Leal, Wetsus » Link
Dr. Sophie Jarraud, Institute for Infectious Agents, National Reference Centre for Legionella, Groupement Hospitalier Nord, Hospices Civils de Lyon.
Assistant Prof. Christian Brinch, National Food Institute, DTU

Relevant publications

  1. Harmsen HJM, de Goffau MC. The Human Gut Microbiota. Adv Exp Med Biol. United States; 2016;902:95–108.
  2. Zhou K, Lokate M, Deurenberg RH, Tepper M, Arends JP, Raangs EGC, et al. Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum beta-lactamase producing ST15 Klebsiella pneumoniae. Sci Rep. 2016 Feb 11;6.
  3. Schröder U-C, Beleites C, Assmann C, Glaser U, Hübner U, Pfister W, et al. Detection of vancomycin resistances in enterococci within 3 ½ hours. Sci Rep [Internet]. 2015;5:8217.


antibiotics, gut, microbiome, water