Genome-wide analysis and characterization of bacterial pathogens are essential tools for infectious diseases analysis and surveillance, identification of clusters of concern and emerging clones. Combined with curated nomenclature reference database, they can provide the international research community and applications to public health surveillance with a common language to better understand and address the challenge of known and emerging bacterial pathogen strains, in particular the antibiotic-resistant bacteria. Next generation Sequencing boosts epidemiological understanding and surveillance of bacterial pathogen strains, by providing (i) accurate identification of pathogenic strain variants through genomic taxonomy and sequence typing based on reference nomenclatures (i.e. BIGSdb-Pasteur), (ii) analysis of sequences of concern (i.e., virulence and antimicrobial resistance mutations) and (iii) characterization of their genetic contexts (e.g., genomic location of sequences of concern on mobile genetic elements such as plasmids). Access to such data enable international research projects in population biology, source tracking, epidemiology, and surveillance of bacterial pathogens, including multidrug resistant, in One Health and Global Health contexts.