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: 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.
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 […]
PER-SEVERE: Defining the contribution of variable microbial factors and host immunity to pertussis severity
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 […]
The SARA project: Surveillance of Antibiotic Resistance in Africa, an integrative project of the Pasteur Network
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 […]
Oxford Nanopore sequencing for detection and surveillance of pathogens
This project intends to share expertise, developments, equipement and bioinformatics tools to apply Oxford Nanopore Technology sequencing to the detection, diagnostic and characterization of pathogens of public health importance. It corresponds to a collaboration […]
KlebNet: a One Health network bridging science and surveillance on antimicrobial resistant Klebsiella
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 […]
Bordetella and whooping cough: Population Biology and Vaccination
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 […]
Diphtheria and Corynebacteria: genomics, evolution and epidemiology
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 […]
Population biology of the bacterial pathogen Klebsiella pneumoniae
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 […]
Genomic taxonomy of bacterial strains: universal nomenclatures for epidemiology and population biology
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 […]
Bioinformatics of genome sequencing applied to epidemiological surveillance of infectious agents
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 […]
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 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, is to develop a structure to anticipate and tackle emerging infectious diseases (EIDs). […]
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 […]
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 […]
Genomic and nomenclature databases of pathogenic bacterial strains
The genomic and nomenclature databases of strains of pathogenic bacterial species are available through the Institut Pasteur BIGSdb portal: http://bigsdb.pasteur.fr. The portal is powered by the Bacterial Isolates Genome Sequence DataBase (BIGSdb) tool developed […]
2022A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings., Nat Microbiol 2022 Dec; 7(12): 2054-2067.
2022Corynebacterium ulcerans as filamentous branching rods., Clin Microbiol Infect 2022 Nov; (): .
2022Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods., Gut Microbes ; 14(1): 2118500.
2022Limited Transmission of Klebsiella pneumoniae among Humans, Animals, and the Environment in a Caribbean Island, Guadeloupe (French West Indies)., Microbiol Spectr 2022 Sep; (): e0124222.
2022A comprehensive resource for Bordetella genomic epidemiology and biodiversity studies., Nat Commun 2022 Jul; 13(1): 3807.
2022Non-toxigenic Corynebacterium diphtheriae in hallux ulceration., J Infect Dev Ctries 2022 Jun; 16(6): 1118-1121.
2022A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains, Mol Biol Evol. 2022 Jun; msac135.
2022Association between the COVID-19 pandemic and pertussis derived from multiple nationwide data sources, France, 2013 to 2020., Euro Surveill 2022 Jun; 27(25): .
2022Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies., Environ Microbiol 2022 May; (): .
2022In Vitro and In Vivo Assessments of Two Newly Isolated Bacteriophages against an ST13 Urinary Tract Infection Klebsiella pneumoniae., Viruses 2022 05; 14(5): .
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