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About

Previously controlled bacterial infections can re-emerge due to antibiotic resistance or vaccine escape. Species of pathogenic bacteria comprise a huge amount of genotypic and phenotypic diversity. Our lab is interested in the diversity, evolution and epidemiology of bacterial pathogens and in the links between the genotypic and phenotypic (ecology, colonization, transmission, virulence, antibiotic resistance, immune response) diversity of the strains within particular species. We focus on three pathogens of high public health importance: the multidrug resistant Klebsiella pneumoniae, which causes various types of infections including urinary tract, respiratory and blood infections; Bordetella pertussis, the agent of whooping cough; and Corynebacterium diphtheriae, the agent of diphtheria. We combine epidemiological surveillance, microbiology, genomics, proteomics, bioinformatics and immunological approaches as well as in-vivo and in-vitro models of infection. We also develop and maintain genomic libraries of bacterial genotypes and strain nomenclatures that facilitate global collaborative surveillance and population biology of bacterial pathogens.

Members

Sylvain Brisse
Head of Structure
Head
Christèle Auguste
Administrative Staff
Julie Toubiana
Deputy Director of National Reference Center
Edgar Badell-Ocando
Deputy Director of National Reference Center
Carla Rodrigues
Deputy Director of National Reference Center
Valérie Bouchez
Research Engineer
Virginie Passet
Technician
Chiara Crestani
Project Manager
Sylvie Bremont
Technician
Marion Barbet
Technician
Nathalie Armatys
Technician
Annie Landier
Technician
Nora Zidane
Research Engineer
Mirko Sadi
PhD Student
Martin Rethoret-Pasty
Research Engineer
José F. Delgado-Blas
Post-doc
Solène Cottis
Project Manager

Former Members

2000
2000
Name
Position
2017
2019
Marina Barros
Post-doc
2017
2019
Melody Dazas
Technician
2017
2019
Sandra Corre
Research Engineer
2017
2019
Leonardo-Gabriel Panunzi
Post-doc
2017
2019
Juan Sebastián López Fernández
Post-doc
2017
2019
Nadine Pouradier
Technician
2017
2019
Pierre Tonnerre
Post-doc
2017
2019
Pauline Leroux
Graduate Student
2016
2022
Sophie Guillot
Deputy-Head NRC Whooping Cough
2020
2023
Sebastien Bridel
Post-doc
2016
2022
Isabelle Moulherat
Assistant
2020
2023
Soraya Matczack
PhD student
2018
2023
Melanie Hennart
PhD Student and post-doc
2016
2023
Annick Carmi-Leroy
Technician
Show all

Courses

10:00
29
Oct 2018
Course

Bacterial strain nomenclatures applied to international epidemiological surveillance: A Theoretical and Hands-on Course

This two-day course will provide participants both theory and hands-on practical exercises on bacterial strain nomenclatures using the core genome MLST concept. Focus will be put on the BIGSdb software tool and database and […]
Biodiversity and Epidemiology of Bacterial Pathogens
Sylvain Brisse
2018-10-29 10:00:00 2018-10-30 17:00:00 Europe/Paris Bacterial strain nomenclatures applied to international epidemiological surveillance: A Theoretical and Hands-on Course This two-day course will provide participants both theory and hands-on practical exercises on bacterial strain nomenclatures using the core genome MLST concept. Focus will be put on the BIGSdb software tool and database and […] 25 Rue du Dr Roux, 75015 Paris, France

Projects

Project
Ongoing
3 Members

The GenEpi-BioTrain programme: Interdisciplinary training in genomic epidemiology and public health bioinformatics

Sylvain Brisse (PI)

This interdisciplinary program, funded by the ECDC, integrates both lectures and hands-on practical sessions provided by various host institutions to enhance surveillance, preparedness, and the ability to respond to outbreaks. Institutes included in the […]
Project
Ongoing
4 Members

PER-SEVERE: Defining the contribution of variable microbial factors and host immunity to pertussis severity

Carla Rodrigues (PI)

Whooping cough is a respiratory disease caused by a bacterium (Bordetella Pertussis) which can, in certain cases and in particular in infants, be severe or even fatal (this is called malignant whooping cough). The […]
Project
Ongoing
8 Members

The SARA project: Surveillance of Antibiotic Resistance in Africa, an integrative project of the Pasteur Network

Sylvain Brisse (PI)

Antibiotic resistance is one of the most serious threats to global health. The consequences for human health are particularly severe in low-resource countries, and in Africa in particular. The SARA project is funded by […]
Project
Ongoing
34 Members

Welcome to the Nanopore User Group at Institut Pasteur webpage

Chiara Crestani (PI)

About the Nanopore User Group: The Nanopore User Group at Institut Pasteur was established in 2019 with the primary goal of fostering collaboration, sharing knowledge, and advancing the application of Oxford Nanopore Technologies (ONT) […]
Project
Ongoing
3 Members

KlebNet: a One Health network bridging science and surveillance on antimicrobial resistant Klebsiella

Sylvain Brisse (PI)

Join us on Google groups! KlebNET e-mail distribution list on Google groups. Please ask for registration, by explaining your interest in Klebsiella research or surveillance and providing your institution, so that the moderators can […]
Project
Ongoing
8 Members

Bordetella and whooping cough: Population Biology and Vaccination

Sylvain Brisse (PI)

Our research on Bordetella ranges from the population biology and epidemiology of various Bordetella species, including Bordetella pertussis (the major agent of whooping cough), to studies of host-pathogen relationships and immunity. Current research lines […]
Project
Ongoing
6 Members

Diphtheria and Corynebacteria: genomics, evolution and epidemiology

Sylvain Brisse (PI)

Our research on Corynebacterium diphtheriae and related bacterial pathogenic species, including Corynebacterium ulcerans,  aims at defining the diversity, evolution and epidemiology of the agents of diphtheria and related infections. We study human and animal clinical […]
Project
Ongoing
7 Members

Population biology of the bacterial pathogen Klebsiella pneumoniae

Sylvain Brisse (PI)

Klebsiella pneumoniae is one of the most urgent threats to public health given its increasing resistance to antimicrobial agents including carbapenems, considered as last-resort antibiotics.  In this project we aim to understand the ecological, epidemiological and […]
Project
Ongoing
15 Members

Genomic taxonomy of bacterial strains: universal nomenclatures for epidemiology and population biology

Sylvain Brisse (PI)

High-throughput sequencing has revolutionized our abilities to track and characterize novel bacterial strains as they emerge and disseminate globally. Genome-based epidemiological typing systems provide ultimate resolution for strain discrimination. Genome sequences may also be […]
Project
Ongoing
3 Members

Bioinformatics of genome sequencing applied to epidemiological surveillance of infectious agents

Sylvain Brisse (PI)

The Institut Pasteur has voluminous activities of microbial strain characterisation, in the context of epidemiological surveillance, biological resource centres collections management, and research. These activities involve National Reference Centers, WHO-collaborative centers, biological resources centers […]

Transversal Project

Drug Discovery & Screening at Institut Pasteur

The Technological Targeted Action Drug Discovery and Screening (ATC-DDS) coordinates projects and collaborations at the Institut Pasteur Paris campus on therapeutic development. It raises awareness for DDS in basic research projects and stimulates intra-campus […]

Emerging Infectious Diseases

Ever since its very early days, the Institut Pasteur has been committed to tackling emerging infections, and its work has left an extraordinary legacy. Many emerging infectious diseases are zoonoses, in which an animal […]

Antimicrobial resistance

Antimicrobial resistance is dramatically increasing worldwide and is becoming one of the most urgent public health threats. There is an urgent need for actions to reverse the curve of antimicrobial resistance dissemination and to […]

LabEx IBEID – Integrative Biology of Emerging Infectious Diseases

Presentation The aim of the Integrative Biology of Emerging Infectious Diseases (IBEID) project, coordinated by Professors Philippe Sansonetti and Pascale Cossart and currently coordinated by Carla Saleh and Philippe Bastin, is to develop a […]

Software

Software
Ongoing
19 Members

BIGSdb-Pasteur

Sylvain Brisse (PI)

BIGSdb-Pasteur is the genomic-based strain taxonomy and nomenclature platform of Institut Pasteur, powered by the BIGSdb software developed at Oxford University. This web platform hosts collections of curated, open or private databases of bacterial […]
Software
Completed
2 Members

JolyTree

Alexis Criscuolo (PI)

JolyTree implements an alignment-ƒree distance-based procedure ƒor inferring phylogenetic trees ƒrom genome contig sequences. For each pair of genomes, a dissimilarity measure is ƒirst computed and next transƒormed to obtain an estimation oƒ the […]

Fundings

Publications

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Contact

Phone: +33 1 45 68  80 05 E-mail: isabelle.moulherat@pasteur.fr Address 25-28 Rue du Docteur Roux 75015, Paris France