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
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
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
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
Selected abstract:
Metagenomic Shotgun Sequencing in the Microbiology laboratory: Routine Implementation for complex cases
Christophe Rodriguez
France
ICCMg conclusive speech
Etienne Ruppé
Paris, France
GENEVA
18-19 OCTOBER 2018
Practical issues in implementing genomics in routine diagnostic microbiology
John WA Rossen
Netherlands
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
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
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
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
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
From yesterday to tomorrow: past, present and future of sequencing: the next generation sequencing revolution
Laurent Farinelli
Geneva, Switzerland
The blood microbiota in health and disease
Peter Gyarmati
Peoria, USA
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
ICCMg conclusive speech
Etienne Ruppé
Paris, France
GENEVA
19-20 OCTOBER 2017
Development of a NGS-based CE-IVD test for pathogen detection
Pascale Beurdeley
Paris, France
Understanding and combatting resistome exchange across commensal, environmental, and pathogenic microbes
Gautam Dantas
Saint Louis, USA
Can whole genome sequencing replace antibiotic susceptibility testing?
Matthew Ellington
London, UK
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
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
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
