Department Surface Waters - Research and Management

Antibiotic resistance as an emerging environmental contaminant

Antibiotic resistance is on the rise, and this represents one of the greatest biological risks of our time. Environmental bacteria are a natural source of resistance genes. However, the environment is also increasingly contaminated by resistant bacteria released with wastewater or from agricultural sources.

We study how resistant bacteria and their resistance genes spread in the aquatic environment. We investigate the dynamics of resistance during wastewater treatment and study strategies for an improved elimination of resistant bacteria.


Dr. Helmut Bürgmann Microbial Ecology Tel. +41 58 765 2165 Send Mail
Karin Beck Tel. +41 58 765 2150 Send Mail
Dr. Giulia Gionchetta Postdoctoral Scientist Tel. +41 58 765 2169 Send Mail


Dr. Helmut Bürgmann Microbial Ecology Tel. +41 58 765 2165 Send Mail

Current Projects

We study the reserviors, fate and exposure of antibiotic resistance in Swiss rivers and streams that receives wastewater-borne resistance bacteria.
In situ expression patterns and gene exchange of Swiss wastewater resistome revealed by quantitative metatranscriptomics and metagenomics.
We survey the effect of sand filters and other biological post-treatment of ozonated wastewater on the release of antibiotic resistances from wastewater treatment plants in Switzerland.
Healthy, diverse ecosystems are more resilient against invasive species. Is this also true for antibiotic resistant bacteria?

Concluded Projects

Dynamics of antibiotic resistance during oxidative treatment of wastewater

Wastewater treatments plants (WWTP) discharge antibiotic resistant bacteria with the treated wastewater. In this project we quantified the extent to which different WWTP in Switzerland eliminate and discharge resistant bacteria and how this affects the receiving waters.
Oxidative wastewater treatment is an important strategy for the removal of micropollutants from wastewater, and is one of the main technologies that will be used for this purpose in Switzerland. In this project we studied how this treatment affects resistant bacteria. Laboratory studies were performed to obtain detailed information on how ozonation damages resistant cells and resistance genes to provide Information about dose dependence and kinetics of the process. Investigations at the first full scale ozonation plant in Switzerland, ARA Neugut, provided data from a real world implementation of this treatment process.

Key results

The project showed that ozonation of wastewater ultimately provides a less complete disinfections and a less effective deactivation of DNA (and thus resistance genes) in wastewater ozonation then simple laboratory experiments may suggest. The interactions with the complex chemistry in the wastewater matrix, microbiological populations that are less sensitive than laboratory strains such as E. coli, and the formation of larger biomass structures (flocs) all interfere. Under process conditions that are optimized for micropollutant reduction most bacterial cells are killed, but a residual population survives, and the genetic material (theoretically capable of being taken up and incorporated into the genome of other bacteria) survives. The full scale plant in Neugut revealed another potential problem – the biological post-treatment of ozonated water, which is necessary to reduce toxic oxidation products, allows resistant bacteria to grow, reducing the overall effectiveness of the process for reducing the load of resistant bacteria with the wastewater stream into rivers and lakes. Further research will be necessary to identify potential improvements to maximize the potential of wastewater ozonation as a barrier to the dissemination of antibiotic resistance into the environment.


Microbial resistance, exotoxicological impact and risk assessment of micropollutants in a mid-sized lake

Antibiotics resistance is increasingly seen as an emerging environmental contaminant.  In this project we studied antibiotic resistance in the wastewater stream of Lausanne, and the effect of the discharge of treated wastewater on the water and sediment of Lake Geneva, Switzerland. 


Leman 21 Project


SNF Prodoc module


  • Bürgmann H. (2014) Eintrag von Antibiotika und Antibiotikaresistenzen in Wassersysteme der Schweiz. Prävention und Gesundheitsförderung 2014, 9:185–190, doi:10.1007/s11553-014-0444-3

  • Czekalski N., Gascón Díez E., Bürgmann H. (2014) Wastewater as a point source of antibiotic-resistance genes in the sediment of a freshwater lake. The The ISME Journal (2014) 8, 1381–1390, doi:10.1038/ismej.2014.8

  • Cantas L., Shah Syed Q.A., Cavaco L.M., Manaia C.M., Walsh F., Popowska M., Garelick H., Bürgmann H., Sørum H. (2013) A brief multi-disciplinary review on antimicrobial resistance in medicine and its linkage to the global environmental microbiota. Frontiers in Microbiology, May 2013, Vol. 4, Art. 96, 1-14, doi:10.3389/fmicb.2013.00096

  • Czekalski N. (2013) Dissertation: Sources, Spreading and Fate of Antibiotic Resistance Genes and Resistant Bacteria in Vidy Bay, Lake Geneva, Switzerland, doi:10.5075/epfl-thesis-5637

  • Czekalski N., Berthold T., Caucci S., Egli A., Bürgmann B. (2012) Increased levels of multiresistant bacteria and resistance genes after waste water treatment and their dissemination into Lake Geneva, Switzerland. Frontiers in Microbiology, March 2012, Vol. 3, Art. 106, doi:10.3389/fmicb.2012.00106

Antibiotic resistant microorganisms in the drinking water system of Lausanne

The occurrence of antibiotic resistant bacteria and resistance genes was studied in the drinking water production facilities and distribution network of Lausanne. Raw water, different treatment stages and the distribution network were analyzed over the course of one year.


Eauservice Lausanne

Elimination of antibiotic resistant microorganisms from wastewater by membrane filtration

A pilot scale activated carbon powder – Ultrafiltration system was tested by the wastewater treatment plant of Lausanne. We investigated the prevalence of resistance at different stages of the WWTP and it’s temporal variability. The effectiveness of eliminating resistant bacteria by membrane  filtration was determined.


Frederik Hammes, Environmental Microbiology, Eawag


Service d’Assainissement  Lausanne