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Geneva | 15-16 October 2020


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.

The Program of ICCMg4 (to give you a glimpse of what ICCMg5 could be)

  • Thursday17-10-2019
  • Friday18-10-2019

Welcome speech: welcome to ICCMg4!


An update on clinical metagenomics tools

The field bioinformatics is constantly evolving and several tools have been developed to cover the different aspects of shotgun metagenomics data analysis. In this presentation I will talk about some of the new tools that can potentially improve the diagnosis of infection through shotgun metagenomics.

Natacha Couto

Culture-Free Metagenomic Deconvolution, Plasmid-Host Association, and Strain Genome Separation Using Hi-C Proximity-Ligation Technology


Artificial Intelligence: From Hype to Hope

Artificial Intelligence has taken the world by storm, and the scientific world has not escaped its impact. In this talk, my goal is to convince  you that the naysayers (“it’s all hype!”) are wrong, and that the cautious scientists (“but it’s still mostly hope”) are right. I’ll also share an outlook on what’s coming in AI, and some strategies of ...

Marcel Salathé

Abstract : Viral metagenomics in the clinical realm: lessons learned from a Swiss-wide proficiency test

Aitana Lebrand

Lunch break

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


Diagnosis of bone and joint infections: the point of view from the clinical metagenomist

Matthew Thoendel

What is the clinician’s interest in improving the etiologic diagnosis of periprosthetic joint infection?

Periprosthetic joint infection (PJI) is a feared complication occuring in 0.5-2% of the patients after knee or hip arthroplasty. The type of surgical management widely depends on the etiologic diagnosis of the pathogen. Almost any bacterial or fungal pathogen may cause PJI. However, in 5-10% of the cases even sophisticated culture techniques remain negative. In addition, in a group of ...

Werner Zimmerli

Abstract : Investigating the utility of MicroDTTect® and rapid metagenomic sequencing for the detection of prosthetic joint infection


Abstract : Sequencing microbial cell-free DNA from the blood identifies pathogens in prosthetic joint infections


Coffee break

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


The making of a miscreant: when healthy biofilms go rogue

Bacteria have co-evolved with humans, adapting not only to genotypic idiosyncrasies, but also to behavioral and lifestyle changes. Together, the human and the microbiome we host  form a ‘holobiont’, with these organisms playing a vital role in maintaining our physiology and health. Moreover, these dynamic communities form ecosystems within various niches in the human body, and by virtue of this ...


Fever of Known Origins: Transforming Infectious Disease Diagnosis by Next Generation Sequencing


Abstract : Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases

Verena Kufner

Abstract : Comprehensive and Fast Next-Generation Sequencing (NGS) Profiling of the Microbiome and Antimicrobial Resistance (AMR) in Clinical Urine Samples

Photo-Dorottya- Nagy-Szakal-iccmg4
Dorottya Nagy-Szakal

ICCMg prizes

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: ICCMg4 award lecture


Poster viewing and discussion around a welcome drink

Let’s discover the ICCMg4 posters, discuss with their authors and network. Wine, beer , other drinks and apetizers will be served.


Walk to the Vieux Bois restaurant


Dinner at the Vieux Bois restaurant

We will have dinner at the Vieux Bois restaurant, located at a 10-minute walk from Campus Biotech. 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”, ...


Strain-resolved large-scale metagenomics


Genome-resolved metagenomics for tracking antibiotic resistant pathogens in patients

Culture-independent genomic approaches, such as metagenomic sequencing, are promising tools that permit direct characterization of pathogens from clinical samples. We have been investigating how metagenomic analysis and bacterial genome reconstruction directly from patient specimens can be applied to improve clinical care, infection control and wider outbreak investigations.

Tim Stinear

Strains Matter: assembling and tracking genomes within metagenomes

Mr. Fremin will discuss the the Bhatt lab’s efforts to illuminate the interplay between the microbial environment and host/clinical factors in human diseases. The Bhatt laboratory develops and applies novel molecular and computational tools to directly reconstruct complete microbial strain genomes from complicated microbiomes, track these strains as they cause infections, and understand how the genes within these genomes are ...

Brayon Fremin Joseph

Coffee break

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


CTMR: A public-private partnership with clinical applications and impact

The Center for Translational Microbiome Research (CTMR) at Karolinska Institutet, Sweden, is a research collaboration between Ferring Pharmaceuticals, Karolinska Institutet, and SciLifeLab. In this talk I will explain the structure of the collaboration, show examples of some of our ongoing research projects, and discuss how such a collaboration is mutually beneficial. I will also briefly describe our pipeline for standardized ...

Fredrik Boulund

Experience from the HUG laboratory

Despite some challenges, clinical metagenomics (CMg) can provide an alternative or supplement to bacterial cultures and other currently available molecular diagnostic tests for pathogen identification. We will present several cases where CMg proved a clear clinical benefit and discuss some challenges that need to be tackled and overcome before implementing CMg in clinical routine.

Vladimir Lazarevic

Accreditation of a clinical metagenomics pipeline

Christophe Rodriguez

The Paris-Genève clinical metagenomics group: preliminary conclusions


Round table about the implementation of clinical metagenomics


Lunch break

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


Precision Detection of Antibiotic Resistant Lower Respiratory Infections with CAS9- Enhanced Metagenomic Sequencing


Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults

Lower respiratory tract infections (LRTIs) are the leading cause of infectious disease-related deaths worldwide yet remain challenging to diagnose because of limitations in existing microbiologic tests. In this talk, I will discuss the development of a metagenomic sequencing-based approach that simultaneously interrogates three core elements of acute airway infections: the pathogen, airway microbiome, and host response. In a prospective cohort ...

Katrina Kalantar

Abstract : Design and evaluation of a targeted enrichment assay capturing Mycobacterium tuberculosis complex DNA in ancient human remains

Heidi Yoko Jäger-Ketikides

Abstract : A look into the past: metagenomic analysis of mummified human remains


Conclusive speech: see you in ICCMg5 !

Jacques Schrenzel closes the conference in wrapping up  the main messages given during ICCMg4.

Jacques Schrenzel

Download the final program here!

Abstract program

ICCMg5 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 second ICCMg prize!


ICCMg4 registration is closed, please visit our website in June 2020 to register in ICCMg5. We are delighted to welcome you for this new edition of ICCMG. You need to purchase regular or student admission in order to participate to the conference dinner. Thank you.

Regular admission


Student admission


Conference dinner



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



For ICCMg4, 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.

Gold sponsorship


Silver sponsorship

BD official Logo

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.