8th ICCMg Conference


Geneva, Switzerland

16-17 November 2023

8th ICCMg Conference

This year, the 8th ICCMg Conference will take place in Geneva on 16 & 17 November 2023. Register to this unique conference!

What is

clinicalmetagenomics ?

Metagenomics, based on next-generation sequencing (NGS), has been available for a decade and is now widely used for research purposes.

In parallel, clinicians are currently paying a growing interest in how NGS could help in the diagnosis and management of several diseases. In the field of infectious diseases, metagenomics has demonstrated its potential in the identification of pathogens and the
inference of the antibiotic susceptibility profiles of bacteria. On a broader perspective, metagenomics of the intestinal microbiota has open several opportunities in various clinical fields such as obesity, autism and cancer.

Satellite Meeting Program, 15 November

Geneva University Hospitals (HUG) -Fred Bamatter auditorium – Rue Willy-Donze 6 – Geneva


8th ICCMg Program, 16-17 November

Campus Biotech – Chemin des Mines 9 – Geneva


Note that The Satellite Meeting and the ICCMg Conference are held at different venues

Cell Press LabLinks meeting ‘Antimicrobial resistance: from mechanisms to global implications’ will take place at the Geneva University Hospital on November 15th, 2023 and will be a satellite event of the 8th International Conference on Clinical Metagenomics. The aim of the meeting is to highlight the growing concern in global health posed by antimicrobial resistance, from the investigation of the mechanisms of resistance to the current clinical approaches against this challenge and its global perspective. Participation at this meeting is free of charge, but registration is compulsory.


8:30-9:20 Registration
9:20-9:30 Welcome Remarks (Salvatore Fabbiano, Sheba Agarwal-Jans, Jacques Schrenzel)
Emerging antimicrobial resistance(Chair : Salvatore Fabbiano)
9:30-10:00 Patrice Nordmann University of Fribourg
10:00-10:30 Trish Simner Johns Hopkins University
10:30-11:00 Gaud Catho Geneva University Hospital
11:00-11:15 Coffee break
Metagenomics in AMR(Chair : Sheba-Agarwal-Jans)
11:15-11:45 Chloé Loiseau Swiss Tropical and Public Health Institute
11:45-12:15 Aitana Neves Swiss Institute of Bioinformatics
12:15-12:45 Etienne Ruppé University of Paris
12:45-14:00 Lunch break
Clinical AMR(Chair : Salvatore Fabbiano)
14:00-14:30 Lisandra Aguilar Bultet University Hospital Basel
14:30-15 :00 Tristan Ferry Hospices Civils de Lyon
15:00-15 :30 TBC
15 :30-16 :00 TBC
16:00-16:15 Coffee break
Epidemiology and surveillance(Chair : Sheba-Agarawal-Jans)
16:15-16:45 Stephan Harbarth Geneva University Hospital
16:45-17:15 Cristoph Dehio NCCR AntiResist
17:15-17:45 Keynote talk: Haileyesus Getahun WHO
17:45-18:00 Closing remarks Sheba Agarwal-Jans and Salvatore Fabbiano
Introduction: welcome to ICCMg8!
9:55 – 10:00 Introduction: welcome to ICCMg8!
What’s hot in clinical metagenomics tools?
10 – 10:35 Benchmarking metagenomics: the CAMI2 project Alice McHardy , Brunswick , Germany
10:35 – 11:05 Introducing the Human contaminome Lisa Karstens , Portland , US
11:15 – 11:45 Coffee break
Urinary tract infections
11:45 – 12:15 Impact of clinical metagenomics on the diagnosis of urinary tract infections Constance Schultsz , Amsterdam , Netherlands
12:15 – 12:45 Estrogen and Recurrent UTI Shape Urinary Microbiome Structure and Function Nicole de Nisco , Houston , US
12:45 -13:45 Lunch
13:45 – 14:05 Finding genomes in metagenomes: StrainExpress Alexander Schönhuth , Bielefeld , Germany
14:05 – 14:35 Transmission of pathogens in healthcare structures Ami Bhatt , Stanford , US
14:35 – 14:45 Moderation/session closure Mohammad Abbas , Geneva , Switzerland
Abstract Session:Clinical metagenomics in practice
14:45 – 15:00 Performance of clinical metagenomics: an observational prospective study in France Jacques Fourgeaud ,Paris, France
15:00 – 15:15 Assessing the Diagnostic Performance of NGS-based mcfDNA Sequencing in Routine Blood Stream Infection Diagnostics: A Retrospective Single Center Study of the First 300 Cases Marijo Parčina, Bonn, Germany
15:15 – 15:45 Coffee break
Abstract presentation:viral metagenomics
15:45 – 16:00 Pathogen discovery in severe encephalitides Philippe Pérot, Paris, France
16:00 – 16:15 Clinical metagenomics for viral diagnostics using short-read, long-read and targeted approaches Sarah Buddle, London, UK
ICCMg prizes and abstract presentation of the winner
16:15 – 16:35 ICCMg prizes : Predicting risk of in-hospital death in patients with sepsis by leveraging simultaneous host-microbe metagenomics Natasha Spottiswoode, San Francisco, US
Prestige lecture
16:35 – 17:15 Ancient DNA sequencing Maria Spyrou , Tübingen, Germany
Posters and drinks
17:15 – 18:30 Welcome Cocktail offered by the State of Geneva
19:00 – 22:00 Dinner at Perle du Lac
Modulation of the microbiota
9:00 – 9:30 How Akkermansia counteracts the effects of dietary emulsifiers Benoît Chassaing , Paris, France
09:30 – 10:00 Modulation of the microbiota by sweeteners Rafael Valdes , Tel Aviv, Israel
Sponsor session
10:00 – 10:30 Stabilisation of Microbial Gut Microbiome Composition in Preanalytics: A Problem Solved! Axel Strittmatter , Switzerland
10:30 – 11:00 Coffee break
11:00 – 11:30 Regulation pro/con talk #1: point of view of the industry Steve Miller , San Francisco, US
11:30 – 12:00 Regulation pro/con talk #2: point of view of the academics Patricia Simner , Baltimore, US
Meet the editor
12:00 – 12:30 Everything you wanted to know about scientific publishing but were too afraid to ask Salvatore Fabbiano and Shankar Iyer , On site
12:30 – 13:30 Lunch
Abstract session: making the best out of the microbiota
13:30 – 13:45 Novel bioinformatic tools for overcoming obstacles in the clinical translation of microbiome science Gustav Lindvev, Copenhagen, Denmark
13:45 – 14:00 Optimisation of extraction and bioinformatic analyses of the mycobiome using shotgun metagenomics Neelu Begum , London, UK
Clinical metagenomics, parasites and fungi
14:00 – 14:30 Eukaryotic protists in complex samples Kenneth Dumack , Cologne, Germany
14:30 – 15:00 Host-mycobiome interactions Saeed Shoaie , Stockholm, Sweden
15:00 – 15:30 Metagenomics in malaria and non-malarial febrile illnesses Christian Nsanzabana, Allschwil, Switzerland
Conclusion: see you at ICCMg9!
15:30 – 15:35 Conclusion: see you at ICCMg9!

Download the final program here!

Abstract program

The 8th ICCMg Conference welcomes abstracts reporting work that focuses on the diverse aspects of clinical metagenomics such as (and not limited) silico tools, diagnostic solutions, clinical studies, pathogen discovery, microbiota and molecular epidemiology.

Accepted abstracts will be made available during the two days of the conference as electronic posters and selected abstracts will be presented live as oral presentations.


FEMS will cover the registration fee/conference dinner for 15 early career scientists (under 35 years of age; a CV should be provided). To apply, please send a copy of your CV and ID to:

2 days Regular admission

CHF 300.-

2 days Student admission

CHF 150.-

1 day (Regular/Student) admission

CHF 150.-


Excellent conference, insights into the future of clinical microbiology!

Insights into the future of clinical microbiology!

Helena Seth-Smith‏ PhD

Clinical Microbiology at the University Hospital, Basel

Great meeting and really nice talking to various very interesting and lovely people! Thanks for having me at ICCMg3 ! See you next year!  

Nice meetings with ICCMg3 participants

Liana Kafetzopoulou‏ PhD student,

Public Health,England

J’ai beaucoup apprécié les présentations et appris beaucoup. C’est une communauté très sympa qui partage et est très ouverte.

Une communauté ouverte avec qui échanger

Jacques Ravel PhD

The Institute of Genome Science, University of Maryland, USA

Past ICCMg Conference (2022)

Local Committee

Discover the members of our Local Committee.


Have a look at the preliminary list of speakers!



Institutional sponsorship


We are grateful to the corporate and institutional sponsors that support the ICCMg.



Chemin des Mines 9, 1202 Genève, Suisse

Campus Biotech is a new initiative that aims to drive forward the biotechnology sector in the Lake Geneva region, creating new opportunities for scientists and entrepreneurs.

Campus Biotech was formed following the announcement by Merck Serono in 2012 that it would be closing its Geneva site. Formerly the global headquarters of Serono, the biotechnology company built over three generations by the Bertarelli family, this site had been the hub for life sciences in the region.

Campus Biotech’s mission was to acquire the site from Merck Serono and to ensure that it could be utilized as a focal point for scientists and entrepreneurs in the life sciences sector, rather than be purchased for property development. That mission is now being realized, with, among others, the Human Brain Project and the Bertarelli Professorships in Translational Neuroscience located – or soon to be located – at the emerging hub.

Campus Biotech is nicely located close to the lake and the botanical garden, and is easily accessible by public transportation from the Cointrin airport and the Cornavin train station.

Useful informations


Among European cities, Geneva is one of the best connected by low-cost airlines. Altogether, there are more than a hundred direct daily flights landing in Geneva connecting it to European capitals and important cities such as Berlin, Frankfurt, London, Madrid and Lisbon.

Geneva’s international airport is located in the NW of town, 4 km from Geneva city center and very well connected to the city center.

Flight information: 0900 57 15 00

Transfer time by public transport to the city center is approximately 15-20 minutes. Upon arrival at Geneva International Airport, you can benefit from a 80 minutes free ticket for a ride to the place of your accommodation. The ticket machine is in the luggage retrieval hall. To reach the city center from airport:

  • Bus line No 5, direction Thônex-Vallard: travel time approximately 20 minutes; get off at stop Gare Cornavin. Frequency: approx. every 10 minutes.
  • Train SBB: every train departing from Geneva airport stops at Cornavin station. Travel time approximately: 6 minutes; get off at stop Gare Cornavin. Frequency: approx. every 10 minutes.
  • Taxi to the city center will take about 20 minutes, and cost approx. CHF 35.00

For further information about airport network, please visit the website of GVA Airport.

If you arrive at Zürich Airport, you can reach Geneva either by train (approx. 3 hours) or book a domestic flight (approx. 45 min).


Switzerland’s rail network meets the highest European standards. Thanks to its central location, Geneva is easily accessible by train, e.g. Paris (3h30min) or Milan (3h50min). Cornavin station is the central station in the heart of the city with a non-stop connection to Geneva airport (6 min).

Switzerland’s national rail network keeps Geneva connected to the rest of Switzerland as well as Europe. For further information, please consult the SBB website.

From Cornavin station, the best way to reach the congress venue is by public transport. You will find the platforms just in front of the station building, trams are leaving approximately every 5 minutes.


Thanks to the highly efficient road network throughout Switzerland and Europe, Geneva is easily accessible by car. Arriving from the direction of Zürich you can reach Geneva via the A1 motorway.

Please note that a motorway sticker, “vignette”, is compulsory to drive on motorways and semi-highways. Valid for 1 year, the vignette costs CHF 40.00 and is on sale at post offices, petrol stations and customs offices. Read more.

Zürich: 279 km
Paris: 541 km
Munich: 588 km

Public transport

Unireso stands for a group of 7 transportation companies in Geneva and its region. The circuits represent more than 450 kilometers in Geneva and into the near vicinities of the canton Vaud and France. With one ticket, you have the possibility to benefit from the whole network (buses, trams, boats, etc.).

Unireso tickets and day passes must be purchased before boarding the vehicle from one of the automatic vending machines located at the stops.

A valid ticket must always be carried during the journey and presented in the event of a control. Fares are CHF 3.50 for one hour public transport in Geneva, or CHF 2.00 for a “saut de puce” (max. 3 stops or 1 transfer by boat, “Mouettes Genevoises”).


Unireso stands for a group As of January 1st 2007, all visitors staying at a hotel, youth hostel or camping site in Geneva can benefit from the Geneva Transport Card, available free of charge.

This personal and non-transferable pass is established upon the visitor’s check-in at the hotel of his choice, enabling its holder to use the entire Geneva public transport network without restriction network (UNIRESO: bus and tram (TPG), train (SBB) and boats (“Mouettes Genevoises”). It is valid for the entire duration of the stay including the departure day. Furthermore, on the arrival floor at the airport, visitors can retrieve their free 80-minute ticket from a ticket machine in the luggage retrieval hall.

For more information please visit tpg website.


You can also borrow bicycles for FREE! Enjoy getting around on two wheels and pedal throughout the city during your stay.

Find a borrowing site HERE

This year the headquarter hotel is “Mon Repos“.

Mon Repos

Hotel Mon Repos is located right in front of an outstanding park on the right bank side of Lake Geneva, close to all international organizations.

Meet the city of Geneva, The bar, the restaurant “Le Prométhée” and the private living rooms welcome you all year around, for your lunches, dinners, receptions and seminars. During summertime, don’t hesitate to discover our flowered terrace, a privileged moment for you to relax and forget your daily worries All travelers coming back to the city of Calvin, Hotel Mon Repos and its Residence have become their definite dwelling.

European Low-Cost Hub

Among European cities, Geneva is one of the best connected by low-cost airlines. Altogether, there are more than a hundred direct daily flights landing in Geneva. It’s so easy to take a city break!

A ‘City Pass’ for a budget price

The Geneva Pass is a true Open up! With more than 47 tourist attractions and activities, free or at preferential rates, including a few gifts. Get all of Geneva for a budget price!

More about the Geneva Pass


In Geneva city and around Geneva you will be able to find several hostels for low prices. Please discover here the Geneva tourism list.

Free public transport

Unireso stands for a group As of January 1st 2007, all visitors staying at a hotel, youth hostel or camping site in Geneva can benefit from the Geneva Transport Card, available free of charge.

This personal and non-transferable pass is established upon the visitor’s check-in at the hotel of his choice, enabling its holder to use the entire Geneva public transport network without restriction network (UNIRESO: bus and tram (TPG), train (SBB) and boats (“Mouettes Genevoises”). It is valid for the entire duration of the stay including the departure day. Furthermore, on the arrival floor at the airport, visitors can retrieve their free 80-minute ticket from a ticket machine in the luggage retrieval hall.

For more information please visit the TPG website.

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374m (1,227ft) above sea level


Geneva has a temperate climate, temperatures range from -2 to +5°C (28 to 41°F) in winter and 12 to 28°C (54 to 82°F) in summer . The annual rainfall is aproximately 1 000 mm/year (including 32cm of snow) The average temperature in June is 18°C.


Swiss Franc (CHF or SFr) Average rate: 1 Euro = CHF 1.10. The exchange rate for the Euro and the Swiss Franc is not officially fixed and is subject to daily market fluctuations. Conversion rates are available at foreign exchange offices, banks and in newspapers.


In town speed is limited to 50 km/h or 30 km/h in some areas, on national roads beyond city limits 80 km/h, and on motorways 120 km/h. A motorway sticker, « vignette », is compulsory on highways and semi-highways. It is valid for 1 year and available at the price of CHF 40.00 – at post offices and customs offices. Wearing seat belts, both in the front and in the back of a vehicle is compulsory.


220 volts. Plug type J, socket converters are available in local shops and CICG (CHF 15.00).

Public Transport

The public transport network in Geneva covers perfectly the entire city. It is reliable and used by the majority of the population. All visitors staying at a hotel in Geneva can benefit from this personal and non-transferable pass with free of charge.

Visit Geneva

Geneva is an amazing city to visit, with its gardens, manufacturers and lake views you will enjoy your stay.
A city pass will offer you preferential fares, free entries, and gifts. Valid for 24, 48 or 72 hours it is your “open Sesame” to museums, cruises, visits, tours and many other surprises. For more information about the city tours and Geneva pass, please click here.


There are four official languages in Switzerland: French, German, Italian and Romansh.
The official language in the western part of Switzerland and therefore also in Geneva is French. Due to its international character English and also German are often spoken in Geneva.


City and Canton: 476 006 inhabitants.

City of Geneva: 194 458 inhabitants.


Prices in hotels, restaurants, taxi fares etc. include taxes and service. A tip, therefore, is not indispensable, but justified for good service.

Airport access

The Geneva Airport is largely accessible to persons with disabilities. The airport is well connected by public transport. There are regular trains connecting the airport to Gare Cornavin (the train station). Bus routes 5 and 10 connect with the airport. For more information other bus routes, you can consult the Geneva Airport website.

If using public transport on arrival, you should remember to get a free public transport ticket that is valid for 80 minutes. The free ticket machine is located in the baggage claim area, just before the exit to the main arrival hall.

For persons using wheelchairs, the bus is a better option to and from the airport as the trains are usually not accessible. To use the train you are required to book special assistance at least an hour in advance for assist in boarding and getting off the train. However, no special notice is needed to use the bus. The bus stop is located at level E (Enregistrement, in French, departure level). From the arrival lounge take the lift to level E, exit out of the terminal and go toward the left for about 15 meters. Cross the road over the pedestrian crossing and you will reach the bus stop.

At the time of departure you may take bus route 5 to the airport from the Gare Cornavin bus stop.

Accessibility in public transport

Most hotels in Geneva will give you a free transport card. This card will allow you to travel for free on bus, tram, and boat in Geneva. If you do not have a free transport card, then you should buy your ticket from the machine before you get on the bus/tram/boat. Please be aware that not all ticket machines provide change.

Most trams and buses are accessible and the Geneva transport authority is constantly replacing inaccessible vessels with accessible ones. However, on any route, if there is an inaccessible bus or tram that you encounter, then ask the driver when the next accessible bus or tram will be arriving, and she or he may call the dispatcher to find out.

While there is a button to press to indicate to the driver that a person with disabilities wishes to board, you need to indicate to the bus driver directly that you wish to board the bus. The driver will come and open the ramp so that you can enter. Let the driver know the stop where you want to get off. For the tram, while it is completely accessible, it is better to get into the carriage right behind the driver as those are indicated as accessible. Moreover, the driver can provide assistance if required.

Mobilité pour tous (Mobility for All) is a program in partnership with Geneva Public Transport service network that provides free service to enable persons with vision impairments or walking difficulties (not wheelchair users) to travel on public transport network with a guide. The guides mostly speak only French.

The service is available from Monday to Friday from 8 a.m. to 6 p.m. You need to book the assistance 48 hours in advance. Tel.: +41 22 328 1111. More details of the program are available in French on the website.

Taxi Services

Regular taxis must be reserved in advance, as they cannot be hailed in the street. Tel.: +41 22 331 4133.

UBER service is also readily available throughout the city.


Get in touch