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This Reprint, "Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition", continues the work of our previous edition under the same title. Emerging infectious diseases remain among the most rapidly spreading and impactful global health threats. Alongside these, a wide range of other infectious agents continue to endanger billions of people worldwide, posing urgent and evolving challenges that demand innovative approaches for their detection, characterization, and treatment. In this Reprint, we present nine high-quality articles that explore key aspects of emerging pathogens, including viruses, bacteria, and fungi. These studies provide novel insights into pathogen biology, diagnostic methods, and therapeutic strategies. This Special Issue enhanced our scientific and clinical understanding of the world's most critical infectious threats. Collectively, these efforts aim to drive innovation in global health preparedness and strengthen our response to the ever-evolving landscape of emerging pathogens.