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Related projects (9)

Pasteur MLST: Institut Pasteur genomic taxonomy database of microbial strains

- The Institut Pasteur genomic taxonomy database of microbial strains (“Pasteur MLST”) is a free, publicly-accessible resource that hosts nucleotide sequence-based definitions of microbial strains, along with information on bacterial isolates (provenance data) and their genomic sequences. The Pasteur MLST database provides universal nomenclatures that are largely adopted for important pathogens (Klebsiella, Listeria, …), and represent a unifying language on strains for microbial population biology. - Unified strain taxonomies facilitate the coordinated international surveillance of bacterial pathogens. Several hundred research laboratories and public health agencies worldwide have deposited novel strain types, sequences and provenance data on their bacterial isolates. - Pasteur MLST is powered by the Open source GPL3 BIGSdb web application developed at Oxford University (Keith Jolley & Martin Maiden). ( ). Its evolution in terms of functionality is tightly linked to the developments of the software at Oxford U. Its evolution in terms of contents is managed by dedicated international teams of curators for each bacterial pathogenic species, coordinated by the PasteurMLST team. - The genomic taxonomies hosted at Pasteur MLST represent unique, authoritative resources that are highly valued by the community, as testified by the routine use of Pasteur MLST strain tags (e.g., K. pneumoniae ST258) in the scientific literature. Several labs (National Reference Centers or Units) of Institut Pasteur are coordinating the curation of genomic taxonomies (Klebsiella, Listeria, Corynebacteria, Bordetella, Leptospira, Yersinia, ...). The aim of the project is to obtain support from the C3BI HUB for the maintenance of the BIGSdb instance at Pasteur: deployment, upgrades, installation of API functionality developed by our partner, coping with future IT evolutions, ...

Project status : In Progress

Neonatal acquisition of ESBL-PE in the community of a Low-Income Country

Severe bacterial infections are a leading cause of neonatal deaths, with low income countries (LICs) bearing the highest burden. In LICs, neonatal bacterial infections are mainly caused by Enterobacteriaceae. One important driver of unfavorable outcome in infections caused by these bacteria is multidrug resistance. Of particular concern, extended-spectrum beta-lactamase-producing enterobacteriaceae (ESBL-PE) are resistant to most penicillins and especially cephalosporins (3rd-4th generation). Enterobacteriaceae are known to colonize the digestive tract, which represents the first step for potential neonatal infections. The newborn is exposed at birth and during the first weeks of life to several possible sources of ESBL-PE acquisition, e.g. maternal, health-care facilities, and outside hospitals: parents, others relatives, food and environment. However, the routes of ESBL-PE acquisition in neonates are not well defined. Also, local environments and practices influence strongly the interactions of the infant with its environment. However, practices contributing to the transmission of ESBL-PE to neonates are not well characterized in LICs. The objectives of the project are: a better knowledge of the role of different routes of ESBL-PE transmissions to newborns in the community, and more specifically within a household, to understand local environments and practices that facilitate ESBL-PE transmission in Madagascar In Madagascar, 60 newborns and members of their households will be follow-up for one month. ESBL-PE will be characterized with last generation DNA sequencing methods. To integrate all these data globally, we will develop novel sophisticated analytical approaches combining mathematical modeling and statistics. Also, in-depth interviews will be conducted and mother-newborn pairs will be followed with a participants-observations methodology. Our study aims at identifying and quantifying the role of the different routes of transmission for newborns in the community. With a multidisciplinary approach, it should allow identifying the most acceptable interventions for local population to prevent ESBL-PE acquisition in newborns in Madagascar, where the burden of neonatal infection is huge. Partner : Institut Pasteur in Madagascar

Project status : Pending