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 […]
Deciphering dormancy in Cryptocococcus neoformans
Cryptococcus neoformans is a sugar-coated yeast that is able to interact closely with numerous organisms in the environment including amebae, paramecium of nematodes. The interaction with these organisms probably shaped its virulence. The ability […]
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 […]
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 […]
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 […]
2023Corynebacterium ramonii sp. nov., a novel toxigenic member of the Corynebacterium diphtheriae species complex., Res Microbiol 2023 Aug; (): 104113.
2023Phages against Noncapsulated Klebsiella pneumoniae: Broader Host range, Slower Resistance., Microbiol Spectr 2023 Jun; (): e0481222.
2023Genomic Epidemiology of Corynebacterium diphtheriae in New Caledonia., Microbiol Spectr 2023 Apr; (): e0461622.
2022Klebsiella MALDI TypeR: a web-based tool for Klebsiella identification based on MALDI-TOF mass spectrometry., Res Microbiol ; 172(4-5): 103835.
2022Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147., Microb Genom 2022 01; 8(1): .
2016Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis, Sci Rep 2016;6:30379.