A5053494989- Genomics and Phylogenetic Studies
- Aquaculture disease management and microbiota
- Bacterial Identification and Susceptibility Testing
- Antibiotic Resistance in Bacteria
- Microbial infections and disease research
- Myxozoan Parasites in Aquatic Species
- Pneumonia and Respiratory Infections
- Diphtheria, Corynebacterium, and Tetanus
- Bacterial Infections and Vaccines
- Molecular Biology Techniques and Applications
- Microfluidic and Capillary Electrophoresis Applications
- Infective Endocarditis Diagnosis and Management
- Vibrio bacteria research studies
- Mycobacterium research and diagnosis
- Nanopore and Nanochannel Transport Studies
- Enzyme Production and Characterization
- Yersinia bacterium, plague, ectoparasites research
- Bacteriophages and microbial interactions
Institut Pasteur
2020-2024
Université Paris Cité
2022-2024
Université Paris-Saclay
2019-2022
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2020-2022
Université de Versailles Saint-Quentin-en-Yvelines
2018-2022
Centre Île-de-France - Jouy-en-Josas - Antony
2022
Virologie et Immunologie Moléculaires
2018-2020
Abstract Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, precise definition is important basic research for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication population biology epidemiological surveillance. Here, we propose a broadly applicable genomic classification nomenclature approach bacterial strains, using the prominent threat Klebsiella pneumoniae as...
The genus Bordetella includes bacteria that are found in the environment and/or associated with humans and other animals. A few closely related species, including pertussis, human pathogens cause diseases such as whooping cough. Here, we present a large database of isolates genomes develop genotyping systems for B. pertussis clade. To generate database, merge previously existing databases from Oxford University Institut Pasteur, import public repositories, add 83 newly sequenced...
The genus Tenacibaculum encompasses several species pathogenic for marine fish. dicentrarchi and "Tenacibaculum finnmarkense" (Quotation marks denote that have not been validly named.) were retrieved from skin lesions of farmed fish such as European sea bass or Atlantic salmon. They cause a condition referred to tenacibaculosis severe outbreaks important losses reported in Spanish, Norwegian, Chilean farms. We report here the draft genomes T. "T. type strains. These compared with field...
Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features interpret emergence the global C. diphtheriae population framework. Methods: We developed bioinformatics pipeline diphtOscan (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) extract from genomes Corynebacteria species...
Abstract Tenacibaculum maritimum is responsible for tenacibaculosis, a devastating marine fish disease. This filamentous bacterium displays very broad host range and worldwide geographical distribution. We analyzed compared the genomes of 25 T. strains, including 22 newly draft-sequenced from isolates selected based on available MLST data, origin fish. The genome size (~3.356 Mb in average) all strains similar. core composed 2116 protein-coding genes accounting ~75% each genome. These...
Abstract Unified strain taxonomies are crucial for fostering international communication in microbiological research and the epidemiological surveillance of bacterial pathogens. While multilocus sequence typing (MLST) has served as a foundation taxonomy two decades, whole genome sequencing enables more precise classifications significantly improves discriminatory resolution. The core genome-wide extension MLST (known cgMLST) thus holds great promise genotyping classification, but its...
Hydrolytic extracellular enzymes degrading host tissues potentially play a role in bacterial pathogenesis. Flavobacterium psychrophilum is an important pathogen of salmonid fish reared freshwater throughout the world. Diversity among isolates has been described at phenotypic, serological, and genomic levels, but links between these various traits remain poorly understood. Using genome-wide association study, we identified gene encoding novel elastinolytic enzyme F. To formally demonstrate...
Tenacibaculum maritimum is a devastating bacterial pathogen affecting large variety of marine fish species. It responsible for significant economic losses in aquaculture farms worldwide. Different typing methods have been proposed to analyse diversity and population structure. Serological heterogeneity has observed up four different serotypes described so far. However, the underlying molecular factors remain unknown. By combining conventional serotyping genome-wide association study, we...
Abstract Background Diphtheria, caused by Corynebacterium diphtheriae , reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features interpret emergence the global C. population framework. Methods We developed bioinformatics pipeline DIPHTOSCAN (available at https://gitlab.pasteur.fr/BEBP/diphtoscan ) extract from genomes Corynebacteria species complex,...
Abstract Motivation Klebsiella species are increasingly multidrug resistant pathogens affecting human and animal health widely distributed in the environment. Among these, pneumoniae complex (KpSC), which includes seven phylogroups, is an important cause of community hospital infections. In addition, oxytoca (KoSC) also causes infections antibiotic-associated haemorrhagic colitis. The unsuitability used clinical microbiology methods to distinguish within each these complexes leads high rates...
Tenacibaculum maritimum is a devastating bacterial pathogen affecting large variety of marine fish species. It responsible for significant economic losses in aquaculture farms worldwide. Different typing methods have been proposed to analyze diversity and population structure. Serological heterogeneity has observed up four different serotypes described so far. However, the underlying molecular factors remain unknown. By combining conventional serotyping genome-wide association study, we...
Abstract Background The re-emergence of whooping cough and geographic disparities in vaccine escape or antimicrobial resistance dynamics, underline the importance a unified definition Bordetella pertussis strains. Understanding evolutionary adaptations pathogens to humans animals requires comparative studies with environmental bordetellae . Methods We have set-up library genomes by merging previously existing Oxford Pasteur databases, importing from public repositories, developing harmonized...