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 […]
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
IINCEPTION Goal The Inception’s goal is to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in a range of health issues. Inception program uses Integrative Biology, Social Science […]
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 […]
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). […]
KlebNet: a One Health network bridging science and surveillance on antimicrobial resistant Klebsiella
Klebsiella, particularly Klebsiella pneumoniae (hereafter, collectively called Kp) is an opportunistic pathogen of humans and animals that now tops the ‘urgent threat’ lists of CDC, ECDC and WHO due to high rates of multidrug […]
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 […]
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 […]
2019Carriage of a single strain of non-toxigenic biovar Belfanti () in four patients with cystic fibrosis, J. Clin. Microbiol. 2019 Feb;.
2019Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov, Res. Microbiol. 2019 Feb;.
2019LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe, Microb Genom 2019 Feb;5(2).
2019Whole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella pneumoniae isolates from Austrian rivers and clinical isolates from hospitals, Sci. Total Environ. 2019 Jan;662:227-235.
2018Re-emergence of Corynebacterium diphtheriae, Med Mal Infect 2018 Dec;.
2018Pertussis epidemiology in Tunisian infants and children and characterization of Bordetella pertussis isolates: results of a 9-year surveillance study, 2007 to 2016, J. Med. Microbiol. 2018 Dec;.
2018Identification of and Related Phylogroups by MALDI-TOF Mass Spectrometry, Front Microbiol 2018;9:3000.
2018Complete Genome Sequences of Bordetella pertussis Clinical Isolate FR5810 and Reference Strain Tohama from Combined Oxford Nanopore and Illumina Sequencing, Microbiol Resour Announc 2018 Nov;7(19).
2018Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae, Genome Med 2018 10;10(1):77.
2018Taxonomic status of Corynebacterium diphtheriae biovar Belfanti and proposal of Corynebacterium belfantii sp. nov, Int. J. Syst. Evol. Microbiol. 2018 Dec;68(12):3826-3831.
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