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 use genomics, proteomics, bioinformatics and immunological approaches as well as in-vivo and in-vitro models of infection. We also develop databases of bacterial genotypes and strain nomenclatures that facilitate global collaborative surveillance 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 […]
Rapid diagnostic test of diphtheria
Although the crucial role of diphtheria toxin in severe diphtheria symptoms was discovered more than 100 years ago by Yersin and Roux, a reliable, specific, accurate, affordable and simple method for the detection of […]
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 […]
MedVetKlebs: Klebsiella pneumoniae from ecology to source attribution and transmission control
Klebsiella pneumoniae (hereafter, K. pneumoniae) is a major cause of hospital-acquired infections such as urinary infections, pneumonia, bloodstream infections, infections in newborns and in intensive-care unit patients. Some hypervirulent strains also cause community infections […]
SPARK: Transmission of multidrug resistant Klebsiella clones and genes – a One Health approach
The SPARK (Spread of Population-wide Antibiotic Resistance in Klebsiella) project, funded by the JPIAMR instrument of the European Union H2020 programme, seeks to address the complex issue of transmission of antimicrobial resistance genes and […]
Bordetella and whooping cough: Population Biology and Vaccination
Our research on Bordetella covers the population biology and epidemiology of various Bordetella species, including B. pertussis, the major agent of whooping cough; vaccine improvements; and the impact of vaccination on population evolution. Current […]
Diphtheria and Corynebacteria: genomics, evolution and epidemiology
Our project on Corynebacterium diphtheriae and related bacterial pathogenic species aims at defining the diversity, evolution and epidemiology of the agents of diphtheria. We study clinical isolates from our culture collection of prospectively collected […]
A descriptive analysis of pertussis in 4 different regions of the world Coordinated by Fabien Taieb, physician affiliated with the Center for Translational Science at the Institut Pasteur, responsible for the coordination of the […]
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 databases for bacterial epidemiology, population biology and strain nomenclature
High-throughput sequencing has revolutionized our abilities to track and characterize novel bacterial strains as they emerge and disseminate globally. Genome-based typing systems are being developed to replace or complement classical epidemiological markers and have […]
Bioinformatics developments for whole-genome sequencing of microbial agents for epidemiological surveillance
The PIBnet initiative is a large collaborative program that aims at reinforcing microbial strain collection management and characterization approaches and technologies. It involves National Reference Centers, WHO-collaborative centers, biological resources centers and other microbiological expertise laboratories, together […]
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). […]
JolyTree is a script that 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 […]
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 […]
2020Klebsiella pneumoniae carriage in low-income countries: antimicrobial resistance, genomic diversity and risk factors., Gut Microbes 2020 Sep; 11(5): 1287-1299.
2020Characterization of Klebsiella pneumoniae isolates from a mother-child cohort in Madagascar., J. Antimicrob. Chemother. 2020 Jul; 75(7): 1736-1746.
2020Corynebacterium rouxii sp. nov., a novel member of the diphtheriae species complex, Res. Microbiol. 2020 Feb;.
2020The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples., Appl. Environ. Microbiol. 2020 03; 86(7): .
2020Core/Whole Genome Multilocus Sequence Typing and Core Genome SNP-Based Typing of OXA-48-Producing Klebsiella pneumoniae Clinical Isolates From Spain., Front Microbiol 2019 ; 10(): 2961.
2020Determining Factors for Pertussis Vaccination Policy: A Study in Five EU Countries, Vaccines (Basel) 2020 Jan;8(1).
2019Gene composition as a potential barrier to large recombinations in the bacterial pathogen Klebsiella pneumoniae, Genome Biol Evol 2019 Oct;.
2019Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov., Front Microbiol 2019 ; 10(): 2360.
2019Erratum to “Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov.” [Res Microbiol 170 (3) (2019) 165-170], Res. Microbiol. 2019 Sep - Oct;170(6-7):300.
2019Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization, Microb Genom 2019 Oct;.
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