PIBnet – Pasteur International Bioresources network
The PIBnet program aims at harmonizing microbial strain biobanking and analytical methods deployed within the microbiological expertise laboratories in Paris and throughout the International Network of Institut Pasteur. It is a large collaborative program […]
Bordetella 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 […]
Population biology and epidemiology of Corynebacteria
This project aims at defining the diversity, evolution and epidemiology of Corynebacterium diphtheriae and closely related species. We use genomics, transcriptomics and proteomics to define the population dynamics of strains, of the diphtheria toxin, […]
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 […]
Human and ruminant neurolisteriosis: a comparative study (Swiss National Science Foundation, Sinergia)
Neurolisteriosis is a common and frequently fatal complication of Listeria monocytogenes infection in human and ruminants. It has a high impact on human and animal health, but only little is known about its pathogenesis. […]
Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends of high-throughput sequencing (HTS) reads. AlienTrimmer was developed in order to detect and remove such contaminants. Based on the decomposition of […]
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 […]
2017Real-time whole-genome sequencing for surveillance of Listeria monocytogenes, France, Emerging Infectious Diseases 2017, doi.org/10.3201/eid2309.170336 (in press).
2016Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes, Nat Microbiol 2016 Oct;2:16185.
2016Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1, Nat Microbiol 2016 Oct;1(11):16209.
2016[Pertussis: Where do we stand 10years after the introduction of cocooning vaccination strategy in France?], Gynecol Obstet Fertil 2016 Sep;.
2016Microbiological and molecular characterization of Corynebacterium diphtheriae isolated in Algeria between 1992 and 2015, Clin. Microbiol. Infect. 2016 Aug;.
2016Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 03-8664 Isolated from a Human Throat, Genome Announc 2016;4(4).
2016Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis, Sci Rep 2016;6:30379.
2016Surveillance of pertussis: methods and implementation, Expert Rev Anti Infect Ther 2016 Jul;14(7):657-67.
2016Follow-Up of External Quality Controls for PCR-Based Diagnosis of Whooping Cough in a Hospital Laboratory Network (Renacoq) and in Other Hospital and Private Laboratories in France, J. Clin. Microbiol. 2016 Aug;54(8):2169-71.
2016Draft Genome Sequence of Corynebacterium ulcerans Strain 04-3911, Isolated from Humans, Genome Announc 2016;4(2).
+View full list of publications