Genomic Epidemiology and Evolution of Antimicrobial Resistance in Low-Resource Settings: A One Health Perspective

Antimicrobial resistance (AMR) research has become a major focus of global health and evolutionary bioinformatics. Despite advances in genomic sequencing and analysis, large disparities remain in the generation and integration of data from low-resource regions, where diagnostic and surveillance systems are often limited. These settings face a high burden of resistant infections, spanning bacterial, viral, and zoonotic pathogens, yet remain underrepresented in global datasets. Genomic epidemiology and population genetics have improved our understanding of how resistant and re-emerging pathogens emerge, spread, and adapt across clinical, community, environmental, and animal reservoirs, but important gaps persist across ecological, epidemiological, and sociogeographic contexts. A One Health framework, integrating human, animal, and environmental health data, is increasingly recognized as essential for capturing the full complexity of AMR dynamics and for building equitable, connected surveillance systems that link molecular evidence with public health action.

This Research Topic aims to bring together original research and critical perspectives on the genomic and evolutionary dynamics of AMR, with particular emphasis on low- and middle-income countries and other underrepresented settings. Contributions are encouraged from genomic, computational, evolutionary, clinical, veterinary, and public health disciplines.

We welcome submissions addressing, but not limited to, the following themes:

• Population genomics and evolutionary dynamics of antimicrobial resistance across bacterial, viral, and zoonotic pathogens
• Mechanisms of resistance evolution and adaptation under antimicrobial pressure

• Transmission networks and phylogenetic tracing of resistant and re-emerging pathogens
• One Health approaches to AMR surveillance across human, animal, and environmental interfaces
• Genomic integration into public health surveillance systems in low-resource settings
• Bioinformatics pipelines and analytical tools tailored to AMR monitoring
• Policy and data-sharing frameworks for equitable and regionally informed genomic surveillance

Article types: Original Research, Review, Methods, Perspective, and Brief Research Report.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Clinical Trial
• Community Case Study
• Data Report
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Clinical Trial
• Community Case Study
• Data Report
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Policy and Practice Reviews
• Policy Brief
• Review
• Systematic Review
• Technology and Code

Keywords: Antimicrobial resistance, genomic epidemiology, One Health, population genomics, low- and middle-income countries, pathogen surveillance, resistance evolution, phylogenetics, zoonotic pathogens, bioinformatics pipelines

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.