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.
Post-doc position: Population biology, Evolution and Structural genomics of Bordetella pertussis
We are looking for a young talented researcher to analyse hundreds of genomes of Bordetella pertussis, the agent of whooping cough, to investigate the following aspects: Sublineage emergence and associated genomic features Ongoing temporal […]
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: diversity, 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 use genomics, transcriptomics and proteomics to define the population dynamics […]
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 […]
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 […]
2017Characterization of Post-Translational Modifications and Cytotoxic Properties of the Adenylate-Cyclase Hemolysin Produced by Various Bordetella pertussis and Bordetella parapertussis Isolates, Toxins (Basel) 2017 Sep;9(10).
2017Real-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes, France, Emerging Infect. Dis. 2017 09;23(9):1462-1470.
2017Bordetella holmesii: Lipid A Structures and Corresponding Genomic Sequences Comparison in Three Clinical Isolates and the Reference Strain ATCC 51541, Int J Mol Sci 2017 May;18(5).
2017Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov, Antonie Van Leeuwenhoek 2017 Aug;.
2017The length of poly(C) stretch in the Bordetella pertussis Pfim3 promoter determines the vag or vrg function of the fim3 gene, Microbiology (Reading, Engl.) 2017 Aug;.
2017In-vivo loss of carbapenem resistance by extensively drug-resistant Klebsiella pneumoniae during treatment via porin expression modification, Sci Rep 2017 Jul;7(1):6722.
2017Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts, BMC Genomics 2017 Jul;18(1):525.
2017Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain, Nat Commun 2017 May;8:15483.
2017Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone, Microb Genom 2017 Apr;3(4):e000110.
2017Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae, Environ. Microbiol. 2017 May;19(5):1881-1898.
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