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 aims to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in various health issues (Official website here: https://www.inception-program.fr/en). The inception program uses Integrative Biology, […]
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 and currently coordinated by Carla Saleh and Philippe Bastin, is to develop a […]
PERT-SEVERE II – Impact de l’expression bactérienne et de la réponse immunitaire dans la gravité de la coqueluche
Sorry, this entry is only available in French.
PER-SEVERE: Defining the contribution of variable microbial factors and host immunity to pertussis severity
Whooping cough is a respiratory disease caused by a bacterium (Bordetella Pertussis) which can, in certain cases and in particular in infants, be severe or even fatal (this is called malignant whooping cough). The […]
HoloZcan – Deep Learning Powered Holographic Microscopy for Biothreat Detection on Field
The project is a Research and Innovation Action, its funding originates from the H2020-EU.3.7.5. – Increase Europe’s resilience to crises and disasters budget line, topic : SU-DRS04-2019-2020 – Chemical, biological, radiological and nuclear (CBRN) […]
The SARA project: Surveillance of Antibiotic Resistance in Africa, an integrative project of the Pasteur Network
Antibiotic resistance is one of the most serious threats to global health. The consequences for human health are particularly severe in low-resource countries, and in Africa in particular. The SARA project is funded by […]
Microbial Resource Research Infrastructure (MIRRI-ERIC)
The Microbial Resource Research Infrastructure (MIRRI) is the pan-European distributed Research Infrastructure for the preservation, systematic investigation, provision and valorisation of microbial resources and biodiversity. It currently brings together 50+ microbial domain Biological Resource […]
IS_MIRRI21 – Implementation and Sustainability of Microbial Resource Research Infrastructure for the 21st century
IS_MIRRI21 commenced in February 2020, which was officialised by the successful Kick-Off Meeting conducted on the 25th and 26th of March, 2020 under the coordination of University of Minho (UMINHO) from Portugal. This European […]
Welcome to the Nanopore User Group at Institut Pasteur webpage
About the Nanopore User Group: The Nanopore User Group at Institut Pasteur was established in 2019 with the primary goal of fostering collaboration, sharing knowledge, and advancing the application of Oxford Nanopore Technologies (ONT) […]
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 […]
Bordetella and whooping cough: Population Biology and Vaccination
Our research on Bordetella ranges from the population biology and epidemiology of various Bordetella species, including Bordetella pertussis (the major agent of whooping cough), to studies of host-pathogen relationships and immunity. Current research lines […]
Diphtheria and Corynebacteria: genomics, evolution and epidemiology
Our research on Corynebacterium diphtheriae and related bacterial pathogenic species, including Corynebacterium ulcerans, aims at defining the diversity, evolution and epidemiology of the agents of diphtheria and related infections. We study human and animal clinical […]
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 […]
Bioinformatics of genome sequencing applied to epidemiological surveillance of infectious agents
The Institut Pasteur has voluminous activities of microbial strain characterisation, in the context of epidemiological surveillance, biological resource centres collections management, and research. These activities involve National Reference Centers, WHO-collaborative centers, biological resources centers […]
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 […]
Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends oƒ high-throughput sequencing (HTS) reads. AlienTrimmer was developed in order to detect and remove such contaminants. ßased on the decomposition oƒ […]
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 […]
2023A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence, Peer Community Journal, 2023, 3, pp.e76. ⟨10.24072/pcjournal.307⟩.
2023Corynebacterium ramonii sp. nov., a novel toxigenic member of the Corynebacterium diphtheriae species complex., Res Microbiol 2023 Aug; (): 104113.
2023Emerging Corynebacterium diphtheriae Species Complex Infections, Réunion Island, France, 2015-2020., Emerg Infect Dis 2023 Aug; 29(8): 1630-1633.
2023Genomic features of Klebsiella isolates from artisanal ready-to-eat food production facilities., Sci Rep 2023 Jul; 13(1): 10957.
2023Phages against Noncapsulated Klebsiella pneumoniae: Broader Host range, Slower Resistance., Microbiol Spectr 2023 Jun; (): e0481222.
2023Biological differences between FIM2 and FIM3 fimbriae of Bordetella pertussis: not just the serotype, Microbes and Infection, 2023, pp.105152. ⟨10.1016/j.micinf.2023.105152⟩.
2023Genomic Epidemiology of Corynebacterium diphtheriae in New Caledonia., Microbiol Spectr 2023 Apr; (): e0461622.
2023Corynebacteria of the diphtheriae Species Complex in Companion Animals: Clinical and Microbiological Characterization of 64 Cases from France., Microbiol Spectr 2023 Apr; (): e0000623.
2023Defining genomic epidemiology thresholds for common-source bacterial outbreaks: a modelling study., Lancet Microbe 2023 Mar; (): .
2023Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae., Microb Genom 2023 Feb; 9(2): .
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