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). […]
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 […]
Rapid diagnostic test of diphtheria
Although the crucial role of diphtheria toxin in severe diphtheria symptoms was discovered more than 100 years ago by Yersin and Roux, a reliable, specific, accurate, affordable and simple method for the detection of […]
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 […]
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: 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 isolates […]
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 […]
2021Incidence and severity of pertussis hospitalisations in infants aged less than 1 year in 37 hospitals of six EU/EEA countries, results of PERTINENT sentinel pilot surveillance system, December 2015 to December 2018., Euro Surveill 2021 Jan; 26(4): .
2020High resolution typing of Staphylococcus epidermidis based on cgMLST to investigate the hospital spread of multidrug resistant clones., J Clin Microbiol 2020 Dec; (): .
2020Population genomics and antimicrobial resistance in Corynebacterium diphtheriae., Genome Med 2020 Nov; 12(1): 107.
2020Elizabethkingia anophelis meningitis in a traveler returning from the Americas., Med Mal Infect 2020 Nov; (): .
2020Corynebacterium diphtheriae Infection in Mahajanga, Madagascar: First Case Report., J Trop Pediatr 2020 Oct; (): .
2020Klebsiella pneumoniae carriage in low-income countries: antimicrobial resistance, genomic diversity and risk factors., Gut Microbes 2020 09; 11(5): 1287-1299.
2020Genomic background of the Klebsiella pneumoniae NDM-1 outbreak in Poland, 2012-18., J. Antimicrob. Chemother. 2020 Aug; (): .
2020Low Detection Rate of Bordetella pertussis Using the BioFire FilmArray Respiratory Panel 2plus., Open Forum Infect Dis 2020 Aug; 7(8): ofaa267.
2020Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage., Microb Genom 2020 Aug; 6(8): .
2020Cutaneous ulcers revealing diphtheria: A re-emerging disease imported from Indian Ocean countries?, Ann Dermatol Venereol 2020 Jul; (): .
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