Online Event

Online-Symposium 2021

One Health meets Sequencing 2.0

The 2nd „One Health meets Sequencing“ Symposium presents current and ongoing projects in One Health and Whole Genome Sequencing taking place in Switzerland, complemented by international experts discussing the latest scientific advances in the field. This year’s focus is on antimicrobial resistance, with several talks as well as a high-level panel discussion also relating scientific insights to practice, not least to questions of surveillance and outbreak management.

Expect an exciting day with the opportunity to exchange ideas with the attending scientists as well as national and international representatives from government bodies in the field of One Health and AMR surveillance. Accordingly, this event is aimed at scientists and clinicians as well as public health professionals who are interested in molecular epidemiology and usage of whole genome sequencing for One Health-related aspects.

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. 

08:00 – 08:10
Adrian Egli (University Hospital Basel)


You can watch the agenda item here as a video.

08:10 – 08:40
Joachim Frey (President Steering Committee National Research Programme „Antimicrobial Resistance“ (NRP 72))

Opening talk: Learning from the past for the future: Metadata is the key to relevance

08:40 – 09:10
Jean-Yves Madec (French Agency for Food, Environmental and Health Safety (Anses), Lyon, France, Member of the NRP 72 Steering Committee)

Opening talk: Current next-generation sequencing platforms and their potential to serving science and policy making in One Health questions

09:10 – 09:20
09:20 – 09:40
Valeria Gaia (Legionella reference center, Bellinzona)

Legionella in Switzerland

You can watch the agenda item here as a video.

09:40 – 10:00
Helmut Bürgmann (EAWAG)

Antibiotic resistance from waste water treatment facilities in Swiss streams and rivers (NRP72 project)

You can watch the agenda item here as a video.

10:00 – 10:20
Pascale Vonäsch (Swiss Tropical Institute)

Microbiome in nutrition

You can watch the agenda item here as a video.

10:20 – 10:40
Markus Hilty (University of Bern)

Antibiotic resistance on Swiss pig farms (NRP72 project)

You can watch the agenda item here as a video.

10:40 – 11:00
Break-Out / Discussion
11:00 – 11:40
Jesse Shapiro, University of Montreal, Canada

Keynote: WGS analysis for multidrug resistance pathogens

You can watch the agenda item here as a video.

11:40 – 12:20
Thomas van Boeckel, ETH Zurich

Keynote: Modelling of “One Health” data

12:20 – 13:50
Break-out / Discussion / Lunch
13:50 – 14:10
Helena Seth-Smith (University Hospital Basel)

Communication of WGS data to public health and clinical experts – challenges and solutions

You can watch the agenda item here as a video.

14:10 – 14:30
Maria-Theresia Stergiou-Gekenidis (Agroscope)

Metagenomics: Resistance on lettuce plants (NRP72 project)

You can watch the agenda item here as a video.

14:30 – 14:50
Michael Biggel (Institut für Lebensmittelsicherheit und -hygiene der Universität Zürich)

Whole-genome sequencing to uncover bacterial determinants of severe E.coli urinary tract infections

You can watch the agenda item here as a video.

14:50 – 15:10
Break-out / Discussion
15:10 – 15:50
Nicholas Bokulich (Institute of Food, Nutrition, and Health ETH Zürich)

Keynote: Microbiomics in 2021: learn to play FAIR

You can watch the agenda item here as a video.

15:50 – 16:10
Break-out / Discussion
16:10 – 16:30
Aitana Lebrand (SIB)

Overview Swiss Pathogen Surveillance Platform (NRP72 project)

You can watch the agenda item here as a video.

16:30 – 16:50
Diana Coman Schmid (ETH Zurich)

Data exchange in Switzerland for public health, research and beyond

You can watch the agenda item here as a video.

16:50 – 17:40
Panel Discussion including

– Andreas Kronenberg: Head of project ANRESIS and
– Sophia Johler: President of the Swiss Society for Food Hygiene (SGLH)
– Saheer Gharbia, Chief Scientific Lead for Genomics Research and Head of Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England
– Jean-Yves Madec, Scientific Director of Antimicrobial Resistance Research at French Agency for Food, Environmental and Health Safety (Anses) / Head of Research Unit Antimicrobial Resistance and Virulence at Anses Lyon
– Gudrun Overesch, Head of Subdivision Reference and Antimicrobial Resistance Monitoring of ZOBA at the Institute of Veterinary Bacteriology, University of Bern
– Fabian Wahl, Head of Food Microbial Systems Strategic Research Division, Agroscope
– Adrian Egli, Head of Division, Clinical Bacteriology, University Hospital Basel
– Richard Ellis, Head of Genome Analysis, Laboratory Service Operations Manager (Molecular Lead), Animal and Plant Health Agency (APHA), Weybridge

17:40 – 17:50
Closing of session

Adrian Egli, Jacques Schrenzel and Roger Stephan


The link for participation will be sent out shortly before the event.

Sponsored by:


Michael Biggel
Michael Biggel

University of Zurich

Whole-genome sequencing has become a powerful tool to explore genetic determinants that affect disease outcome. In this talk, Michael presents recent findings from a large-scale genomic analysis of extraintestinal pathogenic Escherichia coli, the major cause of urinary tract and bloodstream infections. He explains how specific evolutionary events led to the emergence of E. coli lineages that frequently cause kidney infections and urosepsis and discusses how these results could improve clinical management.

Nicholas Bokulich

Institute of Food, Nutrition, and Health
ETH Zürich

DNA sequencing technologies for microbiome profiling and metagenomics are now widely used in research, commercial, and clinical/public health applications. Standardized, traceable bioinformatics platforms are critically needed to support the reproducibility and interoperability of microbiomics analyses. I will discuss the QIIME 2 platform for microbiome analysis, demonstrate its use for spatiotemporal tracking of microbiomes in food systems and humans, and describe how it can be used to make microbiome analyses more FAIR (Findable, Accessible, Interoperable, Reusable).

Helmut Bürgmann


Helmut Bürgmann is an environmental microbiologist at the aquatic science research Institute Eawag. Since 2009, he has been investigating the behavior of antibiotic resistance in wastewater and in surface water environments. In his talk Helmut will highlight how metagenomic sequencing provides detailed information on how the resistome changes during wastewater treatment an what reaches the environment, and how the release of wastewater changes the resistome in the receiving ecosystems.

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
Organization committee

My research focus is the host-pathogen interaction and how this influences the transmission of pathogens within communities. 


Richard Ellis

Animal and Plant Health Agency (APHA), Weybridge

Richard Ellis is Head of Genome Analysis at the Animal and Plant Health Agency, which is responsible for safeguarding animal health and plant health for the benefit of people, the environment and the economy in Great Britain. His work focuses on the application of high-throughput sequencing technologies for understanding the evolution and spread of pathogens (both bacterial and viral, including zoonotics), for investigating diseases of unknown aetiology, and the development of new diagnostic procedures and disease surveillance programmes.

Joachim Frey
Joachim Frey

President Steering Committee National Research Programme „Antimicrobial Resistance“ (NRP 72)

In this talk, Joachim will draw a bridge from the former NRP 49 «Antibiotic Resistance» (2001-2006) to the current NRP 72 «Antimicrobial Resistance» (since 2016), and will, in doing so, review on the technological progress on bacterial genome analysis from PCR test to microchips and finally whole genome sequencing and its potential to improve diagnostics, therapy and prevention of infectious diseases. Based on his experience as head of the National Reference Centre for Anthrax NANT during the global anthrax scare, he demonstrates the value of whole genome sequencing to get detailed knowledge of spread of epidemics to pandemics. He shows that besides new technology, metadata on samples are essential in order to avoid misconception. This evocates the problematic on data management and legal measures to ultimately protect the individuals rather than data themselves.

Valeria Gaia

Legionella reference center, Bellinzona

The presentation will include an overview of the epidemiological situation of legionellosis in Switzerland: the main bacterial clones circulating in Switzerland and in Europe will be presented and traditional and alternative routes of disease transmission will be discussed.

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.

Aitana Lebrand

SIB Swiss Institute of Bioinformatics

Multidrug-resistant (MDR) bacterial pathogens are one of the most important challenges for our society. The spread of highly virulent and resistant pathogens can be described using molecular typing technologies; in particular, whole genome sequencing (WGS) data can be used for molecular typing purposes with high resolution. WGS data analysis can explain the spatiotemporal patterns of pathogen transmission. However, the transmission between compartments (human, animal, food, environment) is very complex. Interoperable and standardized metadata are a key requirement for fully understanding this complexity, and high quality sequencing data is a key element for diagnostic and epidemiological applications. We implemented the Swiss Pathogen Surveillance Platform (SPSP), a molecular surveillance platform allowing integration of high resolution WGS typing and epidemiological data across multiple centers. In the context of the Covid-19 pandemic, this platform is also serving as a hub for Swiss SARS-CoV-2 sequencing data.

Jean-Yves Madec

French Agency for Food, Environmental and Health Safety (Anses), Lyon, France, Member of the NRP 72 Steering Committee

In his talk, Jean-Yves will give an overview on the landscape of next-generation sequencing platforms and how they contribute to better integration of data between sectors (human, animal, environmental) – and therefore science and policy making. He will discuss overlaps of platforms, missing features, and the potential for integration in a One Health approach. Finally, he goes into greater detail about the new French ABRomics project and explains how it intends to achieve the ambitious goal of making accessible bacterial infectious disease (meta)genomics data and their associated clinical and epidemiological metadata to a broad research community.

Jacques Schrenzel

University Hospital Geneva
Organization committee

NGS and shotgun metagenomics can help elucidating challenging clinical cases.


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 
Organization committee


shapiro crop
B. Jesse Shapiro

McGill University

Direct and indirect selection for AMR in patients and the environment

A key question of the One Health research program is to what extent does AMR evolve due to antibiotic selection within patients, compared to transmission of already-resistant organisms. A second question is how do non-antibiotic compounds indirectly select for AMR genes, and how do we identify AMR genes in the first place?

In this talk, I will address these questions drawing on recent work in aquatic mesocosms at the Large Experimental Array of Ponds and in cholera patients from Bangladesh. I will describe how glyphosate (the most commonly used pesticide in the world, marketed as RoundUp) indirectly selects for known AMR genes in aquatic metagenomes. I will also show how genome-wide association studies conducted under anaerobic conditions (more representative of the gut environment than experiments typically conducted under aerobic conditions) allow us to identify a larger number of potential AMR genes in Vibrio cholerae. Finally, I will discuss key challenges in connecting AMR in the environment and humans.

Maria-Theresia Stergiou-Gekenidis


We are what we eat. Antibiotic resistant bacteria and their resistance determinants can be transferred through foods to the consumer. Fresh produce, often consumed raw or minimally processed, is an ideal vector for such contaminants from the environment to humans. We therefore analyzed the microbiome and resistome of field-grown lettuce and its production environment during a whole growth season. In her talk, Maria-Theresia will shed light on which environment contributes most to shaping the lettuce plant’s bacterial communities and resistome.

Thomas Van Boeckel

ETH Zurich 

Thomas Van Boeckel is a spatial epidemiologist working at ETH Zurich as an SNF assistant professor. He is also a visiting fellow at the Center for Disease Dynamics Economics and Policy. He has previously held positions at Princeton, Oxford, and originally obtained his PhD in from the Free University of Brussels. His work focuses on assembling large databases to document global trends in antimicrobial resistance in animals raised for food.

Pascale Vonaesch

University of Lausanne/ Swiss Tropical and Public Health Institute

Bridging experimental and clinical approaches, Pascale Vonaesch’s research interests are in tropical diseases with a focus on infection and nutrition. She is especially fascinated about the human intestinal ecosystem and the contribution of the microbiota to health and disease. Her 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 she 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. She will further also discuss the role of lifestyle and diet on the gut microbiota in African children.

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Universitätsspital Basel
Petersgraben 4
4031 Basel

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


Phone: +41 (0) 61 556 57 49

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