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 (Official website here : https://www.inception-program.fr/en). Inception program […]
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). […]
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 […]
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 […]
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 […]
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 […]
2022Characterization of Klebsiella pneumoniae isolated from patients suspected of pulmonary or bubonic plague during the Madagascar epidemic in 2017., Sci Rep 2022 Apr; 12(1): 6871.
2022Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis., Sci Transl Med 2022 Apr; 14(642): eabn3253.
2022Pertussis surveillance results from a French general practitioner network, France, 2017 to 2020., Euro Surveill 2022 Apr; 27(17): .
2022In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes., BMC Genomics 2022 Mar; 23(1): 235.
2022A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality., Genome Res 2022 Mar; (): .
2022Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation., Nat Commun 2022 02; 13(1): 1086.
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): .
2021Emergence and global spread of Listeria monocytogenes main clinical clonal complex., Sci Adv 2021 Dec; 7(49): eabj9805.
2021Cutaneous diphtheria: 3 case-reports to discuss determinants of re-emergence in resource-rich settings., Emerg Microbes Infect 2021 Nov; (): 1-7.
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