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 […]
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 […]
2018Genomic Sequencing of Bordetella pertussis for Epidemiology and Global Surveillance of Whooping Cough, Emerging Infect. Dis. 2018 Jun;24(6):988-994.
2018Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing, MBio 2018 Apr;9(2).
2018Rhinoscleroma pathogenesis: The type K3 capsule of Klebsiella rhinoscleromatis is a virulence factor not involved in Mikulicz cells formation, PLoS Negl Trop Dis 2018 Jan;12(1):e0006201.
2017Description of Klebsiella grimontii sp. nov, Int. J. Syst. Evol. Microbiol. 2018 Jan;68(1):377-381.
2017Molecular and epidemiological characterization of carbapenemase-producing Enterobacteriaceae in Norway, 2007 to 2014, PLoS ONE 2017;12(11):e0187832.
2017Genomic analysis of endemic clones of toxigenic and non-toxigenic Corynebacterium diphtheriae in Belarus during and after the major epidemic in 1990s, BMC Genomics 2017 Nov;18(1):873.
2017Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter, Environ. Microbiol. 2017 Oct;.
2017Real-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes, France, Emerging Infect. Dis. 2017 09;23(9):1462-1470.
2017Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov, Antonie Van Leeuwenhoek 2017 Aug;.
2017Psychrobacter pasteurii and Psychrobacter piechaudii sp. nov., two novel species within the genus Psychrobacter, Int. J. Syst. Evol. Microbiol. 2017 Sep;67(9):3192-3197.
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