Emerging challenges of clinical metagenomics


A virtual Conference

21-22 October 2021

6th ICCMg Conference

Because of the uncertainty related to Covid-19 pandemic, the 6th ICCMg Conference is going virtual again! Save the date: 21-22 October 2021. Register to this unique virtual conference!

What is

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.

6th ICCMg Program

  • Thursday21-10-2021
  • Friday22-10-2021

Welcome speech


Technology and tools: Live Evaluation of Computational Methods for Metagenome Investigation: the LEMMI way

Evgeny Zdobnov

Technology and tools: Searching for evidence of microbial nucleic acids in cancer sequencing data


Technology and tools: Challenges in bacterial DNA enrichment and quantification in clinical samples

Vladimir Lazarevic

Morning coffee break


Respiratory infections: Rapid respiratory metagenomics using nanopore Flongle sequencing


Respiratory infections: Talk 2

Jean-Damien Ricard

Selected abstract: Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

Jutte De Vries

Selected posters presentations 1

Catarina Inês Mendes: LMAS: Evaluating metagenomic de novo assembly methods through defined communities Maria Kim Doan Nguyen: Can the new super-accurate nanopore basecaller improve detection of microbes in metagenomic sequencing? Nannur Rahman: Modulation of gut microbiota in subjects on antibiotic, Augmentin with probiotics: a pilot study. Philippe Pérot: Necker-Pasteur Clinical Metagenomics: 2. Contribution to Pathogen Discovery Norma Fabregas: From WGS to long-read RNA-seq of the skin commensal Staphylococcus pseudintermedius ...


Lunch break


Covid: Expanding SARS-CoV-2 genomic surveillance in France : challenges and perspectives

Laurence Josset

Covid: Talk 2

Darren Smith
United Kingdom

Selected abstract: ResFinderFG 2.0: a database of antibiotic resistance genes obtained by functional metagenomics.

Rémi Gschwind

Selected abstract: Necker-Pasteur Clinical Metagenomics: Part 1. Contribution to patient care


Selected posters presentations 2

Advait Balaji: KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities Maud Salmona: Metagenomic Next Generation Sequencing restores the diagnosis of a rare infectious complica-tion of B cell depletion Mélanie Fromentin: Lung microbiome in critical care: evolution and risk factors of VAP Marine Ibranosyan: Characterisation of the lung virome in patients with Legionnaires’ disease


Afternoon coffee break




Prestige conference: Clinical Metagenomic Sequencing for Diagnosis of Infections


Ethics: : « We have something to hide »: the importance of confidentiality in a transparent age


Truly Privacy-Preserving Federated Analytics for Precision Medicine with Multiparty Homomorphic Encryption

Using real-world evidence in biomedical research, an indispensable complement to clinical trials, requires access to large quantities of patient data that are typically held separately by multiple healthcare institutions. Centralizing those data for a study is often infeasible due to privacy and security concerns. Federated analytics is rapidly emerging as a solution for enabling joint analyses of distributed medical data ...

Jean Pierre Hubaux

Morning coffee break


Tools and antibioresistance: Resfinder – past, present and future

Frank Møller Aarestrup

Tools and antibioresistance: Transcriptional profiling to accelerate infectious disease diagnostics

Roby Bhattacharyya

Tools and antibioresistance: Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing


Lunch break


Skin Microbiota and skin infections: What’s new in the Diabetic foot microbiota ?

Jean-Philippe Lavigne

Skin Microbiota and skin infections: Detection of ESKAPE Pathogens and Antimicrobial Resistance from Wound Specimens


Afternoon coffee break


Less conventional clinical metagenomics techniques: Cell-free DNA in clinical metagenomics: where do we stand?

Silke Grumaz

Less conventional clinical metagenomics techniques: Targeted metagenomics for the diagnosis of infectious diseases: from research to the clinical laboratory


Less conventional clinical metagenomics techniques: Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids


Conclusion speech

Jacques Schrenzel

Download the final program here!

Abstract program

The 6th ICCMg Conference welcomes abstracts reporting work that focuses on the diverse aspects of clinical metagenomics such as (and not limited) in silico tools, diagnostic solutions, clinical studies, pathogen discovery 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.


We are delighted to welcome you for this new edition of ICCMg! Due to the uncertainty related to Covid-19 pandemic, this year conference will be organized virtually again. We are happy to offer special registration prices to all interested participants.

FEMS is offering 20 registrations to early career scientists, aged younger than 40 years old. If you would like to apply, you must submit an abstract and send a CV and a cover letter to:
Deadline for applications: 6 September 2021.

Regular admission

CHF 150.-

Student admission

CHF 120.-

One day admission

CHF 90.-


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

The International Conference on Clinical Metagenomics is a very interesting conference for anyone working with clinical metagenomics or the application of next generation sequencing to identification of pathogens or diagnosis of infectious diseases. It is also a great place to network and discuss with other researchers working in related areas.

A very interesting conference for anyone working with clinical metagenomics

Sarah Mollerup

Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen

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

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


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 we offer preferential rates for our participants at the hotel “Mon Repos” which costs between CHF 193,30 and CHF 248,85, depending upon the type of room you choose.

Early bird rates are ONLY valid for individual bookings made before 13th of September 2019.

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.

Geneva is a truly international city and its great history and development blends the advantages of a small city with the services and possibilities of a large metropolitan area. Internationally renown as a conference city, Geneva is an ideal location due to its central setting at the heart of Europe and its multicultural flair, being home to important international organizations such as the United Nations, the World Health Organization or the International Labour Organization.

Combining exceptional history, refined cuisine, entertainment and culture, Geneva offers a great variety of activities. Every year in the summer, the famous Geneva Festival attracts numerous visitors from all over the world.


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.