KKL Lucerne
Europaplatz 1
6005 Lucerne


Symposium 2020

One Health meets Sequencing 2.0

The symposium will not take place in June 2020, but will be held in autumn 2020. The new date has not yet been fixed.

After the great success of the first symposium in May 2019, it is clearly time for a second follow-up symposium on “One Health meets Sequencing”. The key points of the first meeting have recently been published (Egli A, Koch D, et al. Microbes Infect 2019). It became clear that whole genome sequencing (WGS) is the new gold standard for typing of pathogens. WGS enables to understand transmission chains of bacteria, mobile genetic elements, and viruses with the highest resolution across various sources. A national database is currently constructed, which will allow tracking pathogen transmissions based on WGS data in humans, animals, food, water and other environmental sources. Integration of clinical, epidemiological and molecular data to form a new context will be key. In addition, rapid progress in sequencing technology and digitalization will offer new opportunities to identify outbreak and track transmission chains.

This follow-up symposium aims to presenting current and ongoing projects in One Health and WGS taking place in Switzerland – fostering the ongoing discussion on the identified challenges and paving the way for solutions in public health, diagnostics, and research. The symposium is again supported by various institutions and the NRP72 program.

Goals of the meeting:
Learning new perspectives based on presentations and discussions between scientists, clinicians, public health experts, and regulatory institutions. Learning about newest technologies and concepts, and networking within the community. Starting new incentives.

Target audience:
Clinical microbiologists, biologists, epidemiologists, public health experts and infectious disease specialists interested in molecular epidemiology and usage of whole genome sequencing for one Health-related aspects such as antibiotic resistance, transmission of pathogens and clinical impact.

Headerimage: © Micronaut 2007

CME credits:
FAMH credits and FMH credits will be organized

Further information: Email

Organization committee:
Adrian Egli,
University Hospital Basel

Jacques Schrenzel,
University Hospital Geneva

Roger Stephan,
University of Zurich 


Regular talks will be 15 min in length including 5 minutes for discussion. Keynote talks will be 30 min in length followed by 10 min discussion. Sessions will be moderated by experts in the field. 

08:30 – 09:15
Registration and Coffee
09:15 – 09:30
Welcome (Adrian Egli, Jacques Schrenzel, Roger Stephan)

Chairs: Vincent Perreten and Roger Stephan

09:30 – 09:50
Valeria Gaia (Legionella reference center, Bellinzona)
Legionella in Switzerland
09:50 – 10:10
Helmut Bürgermann (EAWAG)
Antibiotic resistance from waste water treatment facilities in Swiss streams and rivers (NRP72 project)
10:10 – 10:30
Pascale Vonäsch (Swiss Tropical Institute)
Microbiome in nutrition
10:30 – 10:50
Markus Hilty (University of Bern)
Antibiotic resistance on Swiss pig farms (NRP72 project)
10:50 – 11:20
Coffee break

Chairs: Adrian Egli and Jacques Schrenzel

11:20 – 12:00
Jesse Shapiro, University of Montreal, Canada
Keynote: bacterial genome wide association study – tools to detect virulence and resistance
12:00 – 12:40
Thomas van Boeckel, ETH Zurich
Keynote: Modelling of “One Health” data
12:40 – 13:40

Chairs: Aitana Lebrand and Gilbert Greub

13:40 – 14:00
Helena Seth-Smith (University Hospital Basel)
Communication of WGS data to public health and clinical experts – challenges and solutions.
14:00 – 14:40
Eelco Franz, Department Epidemiology and Surveillance Enteric Infections & Zoonoses, at the National Institute for Public Health and the Environment of the Netherlands
Keynote: HEVNet: an example for oneHealth and viruses.
14:40 – 15:00
Coffee break

Chairs: Markus Hilty and Helmut Bürgmann

15:00 – 15:40
Alison Mather (Quadram Institute, UK)
Metagenomics in “OneHealth”
15:40 – 16:00
Maria Stergiou (Agroscope)
Resistance on lettuce plants (NRP72 project)
16:00 – 16:20
Coffee break

Chairs: Adrian Egli and Jacques Schrenzel

16:20 – 16:40
Adrian Egli (University Hospital Basel)

Overview Swiss Pathogen Surveillance Platform (NRP72 project)

16:40 – 17:00
Diana Coman Schmid (ETH Zurich)

Data exchange in Switzerland for public health, research and beyond

17:00 – 17:40
Jean-Yves Madec (Research Director at the French Agency for Food, Environmental and Health Safety)

Keynote: Data integration of multidrug resistance into public health platforms (NRP72 associated)

17:40 – 18:00
Closing remarks

Adrian Egli (University Hospital Basel), Roger Stephan (University of Zurich), Jacques Schrenzel (University Hospital Geneva)

Organizational institutions:
Sponsored by:


Coman SChmid
Diana Elena Coman Schmid

ETH Zürich

The talk will give a perspective on handling sensitive biomedical data in secure computing environments. The special context is setup by the patient data, which has high legal and ethical requirements but also high and challenging computing demands. To offer top class services for Personalized Health Research, secure and powerful IT infrastructures for data storage, computing and sharing are a must. This is instrumental but not sufficient. What we also need in this diverse and dynamic ecosystem are innovative teams with hybrid expertise (for example, medicine, bioinformatics, IT). With the user experience as a central focus, the challenges are on finding the right balance between security and usability.


Adrian Egli

University Basel and University of Basel Hospital

My research focus is the host-pathogen interaction and how this influences the transmission of pathogens within communities. In the talk I will introduce a NRP72 funded project to build a Swiss-wide surveillance platform using whole genome sequencing data of pathogens.


Eelco Franz 

National Institute for Public Health and the Environment of the Netherlands

Dr. Eelco Franz is heading the department epidemiology and surveillance of enteric infections and zoonoses. He led the process of using whole-genome-sequencing as routine typing within the national surveillance of STEC, Listeria and Salmonella. Currently his main personal interest is the integration of genomics (incl. microbiome) into epidemiology.

GREUB Gilbert, chef de projet Microbiologie Enseignement/Recherc
Gilbert Greub 

University Hospital Lausanne

Chlamydia-related bacteria represents a large diversity of so far understudied and under-recognized strict intracellular bacteria, which might represent novel emerging zoonotic pathogens. Thus, Waddlia might be  associated to abortion in animals and miscarriage in humans and infection might occur following exposure to ruminants whereas Rhabdochlamydia have been shown to be present at high level in Ixodes ticks, suggesting their possible transmission to humans by tick bites.


Markus Hilty

University of Bern

Markus‘ main research focus is bacterial genomics: Microbiome and resistome. More specifically, his current interest is the investigation of the transmission pathways of resistant bacteria on Swiss pig farms using the ‚One Health‘ approach. The relevance of the composition of the microbiome for transmission is also taken into account.

Vincent Perreten

University of Berne

Prof. Vincent Perreten is Head of the Bacterial Molecular Epidemiology and Infectiology Division at the Institute of Veterinary Bacteriology, Vetsuisse Faculty of the University of Bern. He is a leading expert in the field of antibiotic resistance studying transmission of zoonotic bacteria and their genetic elements between animals and humans. Part of his research is dedicated to the molecular characterization of antibiotic resistance mechanisms and their genetic elements and in the application of novel molecular techniques in bacteriology and infection control in animal hospitals, such as microarrays and whole genome sequencing.


Jacques Schrenzel

University Hospital Geneva 

NGS and shotgun metagenomics can help elucidating challenging clinical cases. 
Three such situations will be described, and the contribution of WGS will be discussed from a clinical and a technical viewpoint.


Helena MB Seth-Smith

University Hospital Basel and University of Basel

Helena has worked for many years in bacterial genomics: human, animal and zoonotic pathogens. Much of her current work has a clinical focus, and she has combined many interests in her current project exploring the sources of Campylobacter using whole genome sequencing.


Roger Stephan

University of Zurich 

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Pascale Vonaesch

Swiss Tropical and Public Health Institute

Bridging experimental and clinical approaches, my research interests are in tropical diseases with a focus on infection and nutrition. I am especially fascinated about the human intestinal ecosystem and the contribution of the microbiota to health and disease. My current research is centered on the role of the microbiome in nutrition and nutrition-related disorders with the aim of developing microbiota-targeted interventions allowing all children a healthy growth.
In the talk I will present recent work on a specific bacterial signature associated with stunted child growth in Africa and discuss the pathophysiological changes induced by these bacteria leading to malabsorption.


KKL Luzern
Europaplatz 1,
6005 Luzern,
Tel. +41 41 226 70 70

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Universitätsspital Basel
Petersgraben 4
4031 Basel

Represented by:
Prof. Dr. Dr. Adrian Egli
Head of Clinical Bacteriology/Mycology


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