Comparative microbial genomics analysis by high-throughput whole-genome sequencing (WGS) offers exquisite resolution for epidemiological investigations of infectious disease. This approach has revolutionized outbreak detection and monitoring of transmission dynamics of infectious agents and antimicrobial resistance across humans, animals, and environment. The objective of this Research Topic was to assemble articles on genomic epidemiological approaches to identify sources and mechanisms of transmission of infection and antimicrobial resistance. Leading experts discuss advances in fine-tuning the WGS laboratory workflows and bioinformatics for analyzing viral, bacterial, and protozoan genomic data as well as best available WGS data sharing and vizualization tools for infectious disease surveillance and control. The Research Topic consists of 13 articles on public health applications of comparative genomics of key human and zoonotic pathogens, including Original research, Reviews, Systematic Review and Curriculum, instruction, and pedagogy reports.

The ongoing COVID-19 pandemic underlines the crucial need for open access to advanced viral infectious disease surveillance systems that integrate genomic and epidemiological data on epidemic pathogens in real-time. Theys et al. review cutting-edge phylodynamic analysis tools and visualization solutions for translating these data into information for disease control decisions by public health and health policy professionals. They discuss bioinformatics platform use for temporal and spatial visualization through examples for tracking viral disease dissemination across populations and monitoring viral evolution and adaptation.

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