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This collection of reviews highlights how genomics has transformed our understanding of virulence, host-adaptation strategies, and the evolution of bacterial pathogens. It details current technologies, including computational tools and functional approaches to genome analysis, with clear illustrations. Key topics covered are genome comparison visualization tools, databases, in silico metabolic reconstructions, function prediction, and interactomics for studying protein-protein interactions. The concepts of pan-genomics and reverse vaccinology are introduced to tackle the challenges posed by bacterial diversity in preventing and treating infectious diseases. The authors examine various bacterial pathogens, discussing the mechanisms behind their evolutionary success. Notable examples of host adaptation include Helicobacter pylori and Mycobacterium tuberculosis, both of which are human-specific and highly persistent. Additional bacteria explored include Escherichia coli, Campylobacter, Pseudomonas, Legionella, Bartonella, Burkholderia, and Staphylococcus. This work offers a comprehensive overview of key aspects and future trends in bacterial pathogenomics, assessing their implications for understanding and treating infectious diseases. Accessible and well-illustrated, it is recommended for researchers in microbiology, genomics, and biotechnology, as well as for educators.