The Genotyping of Pathogens Pole, the centre for microbial genomics of the Environment and Infectious Risks Research and Expertise Unit, provides skills with genotyping and genomics technologies for the characterization of sensitive pathogens and/or pathogens of public health importance. Our activities include: (1) A high-responsiveness genotyping and sequencing support in case of bioemergency and/or sensitive pathogens (MOTs), and (2) Research and development collaborative projects in the field of molecular epidemiology, genomics, identification and discovery of microbial pathogens, based on leading-edge technologies and bioinformatics. We also develop high-throughput sequencing approaches (Ion torrent and Illumina-based technology) for two major applications: genomic characterization of emerging bacterial and viral strains and detection and/or identification of novel pathogens in complex samples. Genotyping of Pathogens Pole is highly involved in bioinformatics developments for data analysis, mainly focus on high-throughput sequencing for faster and precise characterization, detection and discovery of emerging pathogens. The huge quantity of data generated is administered, sorted and analyzed by the development of specific programs, the use and configuration of existing bioinformatics tools, and their automation. The Genotyping of Pathogens Pole is engaged in quality assurance and obtained the certification according to ISO 9001 norm in 2014.