ICCMg 2023

Metagenomics in malaria and non-malarial febrile illnesses

Christian Nsanzabana
Switzerland

Modulation of the microbiota by sweeteners

Rafael Valdes
Israel

Estrogen and Recurrent UTI Shape Urinary Microbiome Structure and Function

Nicole de Nisco
USA

Finding genomes in metagenomes: StrainExpress

Alexander Schönhuth
Germany

Regulation pro/con talk #1: point of view of the industry

Steve Miller
USA

VIRTUAL EVENT
21-22 OCTOBER 2021

Introducing the Human contaminome

Lisa Karstens
USA

Regulation pro/con talk #2: point of view of the academics

Patricia Simner
USA

Presentation

Benoît Chassaing
France

Benchmarking metagenomics: the CAMI2 project

Alice McHardy
Germany

ICCMg 2022

Introduction presentation

Jacques Schrenzel
Switzerland

Metagenome assembly and post-assembly analysis of complex clinical samples

Alexey Gurevich
Germany

The microbiota modulates the efficacy of immunotherapies

Lisa Derosa
France

Identifying probiotics: deciphering mechanisms of colonization resistance

Matthew Sorbara
Canada

Plasma Cell-Free DNA for the Diagnosis of Infectious Diseases: the clinician’s perspective

Bhanu Sinha
Netherlands

Variation and transmission of the human gut microbiota across multiple familial generations

Mireia Valles-Colomer
Italy

Microbiota and haematopoetic cell transplantation

Mette D. Hazenberg
Netherlands

A step aside from clinical metagenomics: the contribution of environmental metagenomics to clinical metagenomics

Joakim Larsson
Sweden

Diagnosis of meningitis by transcriptomic approach based on metagenomic data

Christophe Rodriguez
France

Etiology of upper respiratory tract infection in outpatients before and during the SARS-CoV-2 pandemic

Michael Huber
Switzerland

Gut microbiome associations with host genotype vary across ethnicities and potentially influence cardiometabolic traits

Ulrika Boulund
Netherlands

Does our microbiome travel well? Gut microbiome perturbations precede the onset of Post-Infectious IBS in intercontinental travelers

John Penders
Netherlands

Identification and surveillance of emerging microorganisms circulating in rock pigeons (Columba livia) by a shotgun metagenomics approach

Bryan Jimenez Araya
France

VIRTUAL EVENT
21-22 OCTOBER 2021

Conclusion presentation

Etienne Ruppé
France

Assessment of host response using metatranscriptomics for periprosthetic joint infection diagnosis

Cody Fisher
USA

From probiotics to precision probiotics

Max Nieuwdorp
Netherlands

Microbiome and circadian metabolic diseases

Christoph Thaiss
USA

Clinical Impact of Metagenomic Next-Generation Sequencing of Plasma Cell-Free DNA for the Diagnosis of Infectious Diseases

Catherine Hogan
USA

The Microbiota Vault

Adrian Egli
Switzerland

Microbiota and aging

Hervé Blottière
France

Metagenomique to identify future threats?

Anders Johanes Hansen
Denmark

Highlighting discriminating functional annotations in patients’ gut microbiota through Machine Learning classification applied to functional descriptions of the microbiome

Baptise Ruiz
France

Better interpretability of clinical metagenomics results using Bayesian hierarchical modeling

Alban Ramette
Switzerland

Chronic hepatitis due to a novel human circovirus in a heart-lung transplant patient

Marc Eloit
France

Microbial Diversity in the Vaginal Microbiota and its Link to Pregnancy Outcomes

Sean P Kennedy
France

Pathogen detection by metagenomic next-generation sequencing during neutropenic fever in patients with haematological malignancies

Silke Grumaz
Germany

ICCMg 2021

Introduction presentation

Etienne Ruppé
France

Searching for evidence of microbial nucleic acids in cancer sequencing data

Abraham Gihawi
UK

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

Rémi Gschwind
France

Respiratory infections

Jean-Damien Ricard
France

Transcriptional profiling to accelerate infectious disease diagnostics

Roby Bhattacharyya
USA

Clinical Metagenomic Sequencing for Diagnosis of Infections

Charles Chiu
USA

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

Jean-Pierre Hubaux
Switzerland

Detection of ESKAPE Pathogens and Antimicrobial Resistance from Wound Specimens

Manoj Dadlani
USA

Challenges in bacterial DNA enrichment and quantification in clinical samples

Vladimir Lazarevic
Switzerland

Less conventional clinical metagenomics techniques

Silke Grumaz
Germany

COVID

Darren Smith
UK

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

Jutte de Vries
Netherlands

VIRTUAL EVENT
21-22 OCTOBER 2021

Conclusion presentation

Jacques Schrenzel
Switzerland

Rapid Pathogen Detection by Metagenomic Next-generation Sequencing of Infected Body Fluids

Wei Gu
USA

Rapid respiratory metagenomics using nanopore Flongle sequencing

Justin O’Grady
UK

Resfinder – past, present and future

Frank Moller Aarestrup
Denmark

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

Karel Brinda
USA

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

Samia Hurst
Switzerland

What’s new in the Diabetic foot microbiota?

Jean-Philippe Lavigne
France

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

Evgeny Zdobnov
Switzerland

Respiratory infections

Jean-Damien Ricard
France

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

Laure Flurin
USA

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

Laurence Josset
France

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

Anne Jamet
France

ICCMg 2020

Selected abstract: Use of Whole Genome Sequencing data for a first in silico specificity evaluation of the RT-qPCR assays used for SARS-CoV-2 detection

Mathieu Gand
Belgium

Virological aspects of the SARS-CoV-2

Volker Thiel
Switzerland

Strain evolution and host response in patients

 

Christopher Mason
USA

Application of metagenomic analysis for detection of SARS-CoV-2 and co-infecting microorganisms

Alexander Greninger
USA

Selected abstract: Identification of superinfection and assessment of antimicrobial usage in COVID-19 patients combined with use of metagenomic sequencing: a cohort study in Shanghai

Qing Miao
China

Selected abstract: Advancing the analysis of gut microbiome in critically ill patients using Hi-C technology

 

Alexander Tyakht
Russia

Science communication during COVID-19

Maryn Mckenna
USA

VIRTUAL EVENT
15-16 OCTOBER 2020

Epidemiology of COVID-19 – what we have learned, and do not know yet

 

Bruno Lina
France

Nextstrain, sequencing and the SARS-CoV-2 pandemic

 

Emma Hodcroft
Switzerland

Selected abstract: Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness

Ellen Carbo
Netherlands

Comprehensive detection of human viruses with CARMEN–Cas13

Cameron Myhrvold
USA

Selected abstract: Detection of SARS-CoV-2 in respiratory samples using a metagenomic next-generation sequencing workflow

Gavin Wall
USA

Functional profiling of COVID-19 respiratory tract microbiomes

Laxmi Parida
USA

ICCMg 2019

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

Heidi Yoko Jäger-Ketikides
Italy

Fever of known origins: transforming infectious disease diagnosis by next generation sequencing

Asim Ahmed
USA

Selected abstract: two years of viral metagenomics in a tertiary diagnostics unit: evaluation of the first 105 cases

 

Verena Kufner
Switzerland

Photo-Aitana-Lebrand-iccmg4

Selected abstract: viral metagenomics in the clinical realm: lessons learned from a Swiss-wide proficiency test

Aitana Lebrand
Switzerland

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

Werner Zimmerli
Switzerland

An update on clinical metagenomics tools

 

Natacha Couto
Netherlands

Culture-free metagenomic deconvolution, plasmid-host association and strain genome separation using Hi-C proximity-ligation technology

Ivan Liachko
USA

Selected abstract: Transmission of human-associated microbiota along family and social networks

Thomas Gurry
Switzerland

Conclusive speech

Jacques Schrenzel
Switzerland

GENEVA  
17-18 OCTOBER 2019

Metagenomic detection of antimicrobial resistant respiratory pathogens

 

Chaz Langelier
USA

Selected abstract: Experience from the HUG laboratory

 

Vladimir Lazarevic
Switzerland

Selected abstract: investigating the utility of MicroDTTect® and rapid metagenomic sequencing for the detection of prosthetic joint infection

Alex Trotter
UK

Genome-resolved metagenomics for tracking antibiotic resistant pathogens in patients

Tim Stinear
Australia

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

Matthew Thoendel
USA

Accreditation of a clinical metagenomics pipeline

Christophe Rodriguez
France

The Paris-Genève clinical metagenomic group

 

Etienne Ruppé
France

ICCMg: behind the scenes

ICCMg 2018

A year in clinical bioinformatics

Helena Seth Smith
Switzerland

Selected abstract:

Extensive viral nucleic acid contamination in clinical samples

Maria Asplund
Denmark

Nanopore sequencing: mobile metagenomics at the epicentre of a viral outbreak

Liana Kafetzopoulou
England

https://www.researchgate.net/profile/Liana_Kafetzopoulou

Eran-Segal-ICCMG-Microbiota

Personalizing treatments using microbiome and clinical data

Eran Segal
Israel

Gut microbiota in immuno-oncology; from discovery to clinical trials

Bertrand Routy
Canada

Now moving to the vaginal microbiota and personalized medicine?

Jacques Ravel
USA

picture_YanShao-ICCMG-Congress

Selected abstract:

Caesarean section stunts the gut microbiota and predisposes pathogen colonisation during very early life

Yan Shao
United Kingdom

Next-Generation Sequencing Diagnostics of Sepsis

Silke Grumaz
Germany

Pathogen Detection Using Cell-free DNA in Body Fluids

Wei Gu
USA

christophe-rodriguez-iccmg-

Selected abstract:

Metagenomic Shotgun Sequencing in the Microbiology laboratory: Routine Implementation for complex cases

Christophe Rodriguez
France

ICCMg conclusive speech

Etienne Ruppé
Paris, France

https://www.researchgate.net/profile/Etienne_Ruppe

GENEVA  
18-19 OCTOBER 2018

Practical issues in implementing genomics in routine diagnostic microbiology

John WA Rossen
Netherlands

willem-van-Schaik-International-Conference-of-Clinical-Metagenomics

Challenges and opportunities for whole‐genome sequencing–based surveillance of antibiotic resistance

Willem van Schaik
United Kingdom

How can WGS help in outbreaks? The point of view of the infection prevention and control

Stephan Harbarth
Switzerland

Jennifer-Gardy-International-Conference-of-Clinical-Metagenomics

Lost in translation? Considering user needs in reporting clinical microbial genomics results

Jennifer Gardy
Canada

Symbiosis, an interdisciplinary concept with ethical applications

Beatrice de Montera
France

Real-time phylogenetic analysis of emerging pathogens

Richard Neher
Switzerland

Sébastien-Gagneux-International-Conference-of-Clinical-Metagenomics

Clinical genomics in tuberculosis

Sébastien Gagneux
Switzerland

Selected abstract: Diversity and composition of the microbiome in the lower respiratory tract is associated with lung damage in tuberculosis patients from Tanzania

Monica Ticlla
Switzerland

sarah-morrelup-iccmg-congress

Selected abstract:

Investigation of viruses in human cancers by application of multiple pre-sequencing enrichment methods

Sarah Mollerup
Denmark

ICCMg3 welcome speech

Jacques Schrenzel
Geneva, Switzerland

https://www.researchgate.net/profile/Jacques_Schrenzel

ICCMg 2017

NGS for characterization of clinical class 1 integrons from hospital effluents

Olivier Barraud
Limoges, France
https://www.researchgate.net/profile/Olivier_Barraud

Clinical metagenomics:

our real-life experience

Charles Chiu
San Francisco, USA

https://www.researchgate.net/profile/Charles_Chiu2

From yesterday to tomorrow: past, present and future of sequencing: the next generation sequencing revolution

Laurent Farinelli
Geneva, Switzerland

https://www.researchgate.net/profile/Laurent_Farinelli

The blood microbiota in health and disease

Peter Gyarmati
Peoria, USA

https://www.researchgate.net/profile/Peter_Gyarmati

Critical Assessment of Metagenome Interpretation

Alice McHardy
Brunswick, Germany

Clinical metagenomics in bone and joint infections

Robin Patel
Rochester, USA

Nanopore Sequencing- a step forward in pathogen identification and antibiotic resistance gene profiling of urine samples

Katarzyna Schmidt
Norwich, UK

Regulatory Challenges and Opportunities in Clinical Metagenomics

Kristian Roth
Rockville, USA

Clinical metagenomics of dermohypodermitis and necrotizing fasciitis

Christophe Rodriguez
Créteil, France

Clinical metagenomics of hospital-acquired pneumonia

Sébastien Hauser
Grenoble, France

https://www.researchgate.net/profile/Sebastien_Hauser2

ICCMg conclusive speech

Etienne Ruppé
Paris, France

https://www.researchgate.net/profile/Etienne_Ruppe

GENEVA  
19-20 OCTOBER 2017

Development of a NGS-based CE-IVD test for pathogen detection

Pascale Beurdeley
Paris, France

https://www.researchgate.net/profile/Pascale_Beurdeley

Understanding and combatting resistome exchange across commensal, environmental, and pathogenic microbes

Gautam Dantas
Saint Louis, USA

https://www.researchgate.net/profile/Gautam_Dantas

Can whole genome sequencing replace antibiotic susceptibility testing?

Matthew Ellington
London, UK

https://www.researchgate.net/profile/Matthew_Ellington2

On the importance of curated databases

Philippe Lemercier
Geneva, Switzerland

Metagenomic NGS for pathogen detection:
quality control issues and strategies

Steve Miller
San Francisco, USA

Clinical metagenomics in post-operative endophthalmitis

Sünje Johanna Pamp
Lyngby, Denmark

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

Verena Kufner
Zurich, Switzerland

https://www.researchgate.net/profile/Verena_Kufner

Rapid metagenomic diagnosis of hospital acquired pneumonia

Justin O’Grady
Norwich, UK

Detection of previously missed pathogens  by a fully-validated metagenomics-based test

Robert Schlaberg
Salt Lake City, USA

ICCMg2 welcome speech

Jacques Schrenzel
Geneva, Switzerland

https://www.researchgate.net/profile/Jacques_Schrenzel

ICCMg 2016

Cinical metagenomics in urinary tract infections

Frank M. Aarestrup
Technical University of Denmark

Clinical metagenomics for the diagnosis of acute infectious diseases

Jérôme Bouquet
University of California – San Francisco

Inferring the antibiogram from genomes

Derrick Crook
Public Health England

Clinical metagenomics in immunocompromised patients

Marc Eloit
Institut Pasteur Paris and Pathoquest

From metagenomics to bacterial therapy

Eric Pamer
Memorial Sloan Kettering Cancer Center

Probing the medical microbiome

Georges Weinstock
The Jackson Laboratory for Genomic Medicine

Welcome address

Jacques Schrenzel
Geneva University Hospitals

Conclusive speech

GENEVA  
13-14 OCTOBER 2016

Clinical microbiomics: towards diagnostics and personalised intervention

Peer Bork
European Molecular Biology Laboratory – EMBL

Sequencing of M. tuberculosis directly from sputum

Judith Breuer
University College London

The intestinal microbiota and the link with diseases 

S. Dusko Ehrlich
MetaGenoPolis, INRA Jouy en Josas

Overview of bioinformatics analyses for metagenomics data

Aitana Lebrand
Swisss Institute of Bioinformatics

Using biofilms (and metagenomics) to diagnose colon cancer

Cynthia Sears
Johns Hopkins University School of Medicine

Next Generation Sequencing for metagenomics

Patrick Wincker
Genoscope and CEA, France

Snapshots from the ICCMg 2016