Geneva | 18-19 October 2018


Be informed about the new field of clinical metagenomics, from concepts to possible applications for patients.

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.

  • Thursday19-10-2017
  • Friday20-10-2017

Welcome speech


From yesterday to tomorrow: past, present and future of sequencing

An overview of the thrilling advances in sequencing during the last decade by Laurent Farinelli, a co-inventor of the DNA sequencing method currently used in Illumina sequencers.


Critical Assessment of Metagenome Interpretation

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark ...


On the importance of databases

Clinical metagenomics relies on bioinformatic tools that dig into various databases. How to cure, update and maintain them? What are the right reference set for clinical studies? Answers from the Swiss Institute of Bioinformatics.


Lunch break

After an introduction to sequencing and bio-informatics, let’s enjoy the buffet and get ready for the afternoon.


Regulatory Challenges and Opportunities in Clinical Metagenomics

Setting up a clinical metagenomic pipeline is not just a scientific issue. Quality is crucial! The point of view from regulatory agencies.


Experience of the development of iDTECT, the first NGS based CE-IVD test for pathogen detection

Setting up a clinical metagenomic pipeline is not just a scientific issue. Quality is crucial! The experience of a clinical metagenomics start-up.


Experience from an academic: QC in clinical metagenomics pipeline

Setting up a clinical metagenomic pipeline is not just a scientific issue. Quality is crucial! The experience of an academic laboratory.


Coffee break

Let’s get a bit of cafeine before the last session.


Clinical metagenomics: our real-life experience

Feedback from a pioneer on validation and implementation of a clinical metagenomic assay for diagnosis of infectious diseases in acutely ill hospitalized patients.


Selected abstract: Rapid metagenomic diagnosis of pneumonia

Background Rapid and accurate diagnosis is critical for the effective management of life threatening infections, such as pneumonia. Current culture based diagnosis has sub-optimal specificity and sensitivity and is too slow to impact on patient management. Shotgun metagenomics sequencing has the potential to change the way we diagnose pneumonia, combining rapidity with comprehensiveness beyond that of current methods. We have ...


CMg of dermohypodermitis

The application of deep sequencing to dermohypodermitis samples: comparison with conventional methods and 16S profiling.


Metagenomics for Rapid Pathogen Detection and Characterization of the Microbiome in Health and Disease

Next-gen sequencing, combined with high-resolution metagenomic analysis, offers a new powerful method for diagnosis of infectious diseases. We applied this in several clinical studies, including a retrospective case control study comprising samples of known and unknown etiology, as well as samples from healthy individuals. The results are promising and demonstrate that microbiome analysis could potentially differentiate healthy, diseased, and asymptomatic ...


ICCMg-SSM and ASM awards

The first ICCMg/SSM and the ASM prizes for the best poster presentations will be awarded. The work awarded for the ICCMg/SSM prize will be presented.


Selected abstract: Virus transmission during kidney transplantation assessed by virome analysis of living donor and recipient

Background Before kidney transplantation, donors and recipients are routinely screened for a number of active or latent viral infections using specific tests. Little is known about other, untested, apathogenic viruses a donor might carry and likely will transmit. Here, we aimed to characterize the viral metagenome of both the donor and the recipient using metagenomic sequencing at time of transplantation ...


Poster session

Let’s discover the ICCMg2 posters, discuss with their authors and network. Wine, beer , other drinks and apetizers will be served.


Dinner at the Vieux Bois restaurant

We will have dinner at the Vieux Bois restaurant, located at a 10-minute walk from ICCMg. Conveniently located next to the United Nations, in the beautiful Ariana’s park and enjoying a summer terrace, Vieux-Bois restaurant welcomes a demanding clientele, including international delegations, politicians, economic leaders and artists. It opened in 1934 under the name “L’Auberge de Mr. Vieux Bois”, honoring ...


Understanding and Combatting Resistome Exchange Across Commensal, Environmental, and Pathogenic Microbes


Wrap up of the NGS/EUCAST consultation

Is next-generation sequencing a realistic approach for inferring an antibiogram from genomic data today? Tomorrow? for all bacteria/antibiotics?


Selected abstract: NGS for characterization of clinical class 1 integrons from hospital effluents

Background Class 1 integrons are bacterial genetic elements widely involved in the spread of antibiotic resistance in the clinical setting. Located on plasmids, they can recruit, express and disseminate antibiotic resistance genes (ARGs) embedded within gene cassettes (GCs). GCs are mobilizable units that constitute the variable part of class 1 integrons. Up to 10 GCs can be present within a ...


Selected abstract: clinical metagenomics in endophthalmitis

Background Endophthalmitis is a complication of eye surgeries and can lead to loss of vision. It is an inflammation that develops in response to microorganisms entering the eye. A rapid determination of the causing agents and their antibiotic resistance would facilitate precise treatments and reduce blindness.   Methods We examine the microbiome of 14 vitreous (intraocular body fluid) samples from ...


Selected abstract: Detection of previously missed pathogens in immunocompromised children with suspected pulmonary infections by a fully-validated metagenomics-based test

Background Pulmonary infections are the most common tissue-invasive infection in immunocompromised patients and can be caused by a wide range of common and opportunistic pathogens. Early etiologic diagnosis and initiation of effective treatment is critical to reduce morbidity and mortality but current tests remain negative in up to 60% of patients. Metagenomic DNA and RNA sequencing provides a hypothesis-free alternative ...


Coffee break

Let’s enjoy a break and get ready for the next session.


Clinical metagenomics in bone and joint infections

How the next-generation sequencing of bone and joint infection samples can support or even replace conventional methods.


Nanopore sequencing of urine samples

How the Nanopore technology allows the ultra-fast sequencing of urine samples and the identification of pathogens and their antibiotic resistance traits.


Clinical metagenomics of hospital-acquired pneumonia

How the deep sequencing of respiratory samples collected from hospital-acquired infections can support/replace conventional methods.


Lunch break

Let’s enjoy the buffet under the incredible glass roof of the Campus Biotech.


So what? Clinical impact of microbiome studies

More than ten years after after the next-generation sequencing revolution and the thrilling advances in the understanding of our microbiota, what are the concrete consequences in medicine that can be expected?


The blood microbiome in health and disease

The blood, in physiological conditions, was thought a sterile environment for decades. Current metagenomics approaches provide a more detailed picture of the blood microbiota in health and disease.


Metagenomics: Think before you speak

Metagenomics generate tremendous amount of data. There is a need for a microbiological expertise to properly mine and interpret this data. I will present few examples illustrating how biological interpretation can be key sometimes to find meaningful metagenomics signals.


Selected abstract: Clinical Metagenomics applied to human mummified remains – Reconstruction of a 5,300-year-old Helicobacter pylori genome from the Iceman’s stomach

The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The H. pylori strains found in most Europeans today (hpEurope) have putatively originated from recombination of the two ancestral populations Ancestral ...


Conclusive speech

Etienne Ruppé closes the conference in wrapping up  the main messages given during ICCMg2.

Abstract program

ICCMg3 welcomes abstracts reporting work that focuses on clinical metagenomics from a broad perspective: infectious diseases, antimicrobial resistance, bio-informatics, microbiota… Submit your abstract here and compete for the first ICCMg prize!

Download the final program here!


You need to purchase regular or student admission in order to participate to the conference dinner.

Regular admission

250 CHF

Student admission

100 CHF

Conference dinner

+50 CHF


For ICCMg3, we kept a high quality program with keynotes given by the current leaders in clinical metagenomics, but also to open slots for oral presentations to selected abstracts.


We are grateful to the corporate and institutional sponsors that support the ICCMg3.

Gold sponsorship

Silver sponsorship

Institutional sponsorship



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


Facing one of Geneva’s most beautiful parks, the Hotel Eden is situated a few steps from the lake and close to the town centre and all the international organisations.

Famous for its warm, welcoming atmosphere, the Hotel Eden is the place to stay in Geneva. All rooms have been recently redecorated. Modern facilities combined with friendly staff, who recognize that hospitality is an art, will ensure that your stay is pleasant and memorable.

Ibis Centre Gare

The Hotel ibis Genève Centre Gare is located in the city center, 219 yds from the station and 3.1 miles from the airport, with the Old Town, Grand Casino theater, international organizations and Lake Geneva within 1.2 miles. This non-smoking hotel has 64 rooms with an air cooling system and free WIFI and 1 room suitable for people with reduced mobility. The bar is open 24 hrs and there is a paying car park 219 yds away. 3.1 miles from the PALEXPO exhibition center. Public transport and & WIFI for guests.

Ibis Centre Nation

The Hotel ibis Genève Centre Nations boasts a perfect city center location, a few minutes from Cornavin train station, international organizations and the Geneva International Conference Centre (CICG). It is less than 15 minutes by public transport from Genève Cointrin international airport and the Palexpo exhibition center and has 216 air-cooling rooms with free WIFI. There is a 24-hour bar and paying car park (subject to availability on arrival). Guests also room with free WIFI. There is a 24-hour bar and paying car park (subject to availability on arrival). Guests also benefit from free public transport.


The hotel Lido benefits from a privileged location right in the heart of the international city of Geneva, a 300m from the beautiful shores of “Lake Geneva” and from the main train station. Lido Hotel has 29 sound proofed rooms. The hotel is since 2009 equipped with solar cells for the warm water production to preserve our environment.

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.