Integrating Genomics and Bioinformatics for Pathogen Surveillance and Antimicrobial Resistance in Veterinary Science

Antimicrobial resistance (AMR) is a major global issue that threatens both animal and human health. In veterinary systems, covering livestock and companion animals, resistant pathogens lead to ongoing infections and zoonotic transfer. Traditional surveillance methods often miss the full genetic picture of resistance or its epidemiological links. Recent breakthroughs in genomics and bioinformatics now allow detailed tracking of resistance factors, including mobile genetic elements (MGEs), and how they evolve in animal populations. At the same time, microRNAs (miRNAs) have become promising tools for diagnosis and regulation, affecting pathogen responses. By combining genomic data from multiple species with epidemiological insights, the One Health approach enables thorough monitoring of AMR development, spread, and spillover. Merging these molecular insights with genomic epidemiology provides new ways to understand and control AMR in veterinary settings. This special issue aims to highlight innovative analytical frameworks and data standards for AMR detection and pathogen surveillance in veterinary contexts across animal health, One Health interfaces, and zoonotic transmission.

This Research Topic seeks to showcase integrative approaches that combine genomics and bioinformatics for pathogen surveillance and AMR detection in veterinary medicine. The primary goal is to emphasize applications relevant to animal health, zoonotic risk, and surveillance systems. A special focus will be given to miRNA-based diagnostics and their regulatory roles in antimicrobial resistance, along with bioinformatics tools and workflows that transform complex datasets into actionable insights for disease control and informed decision-making.

To gather further insights in these areas, we welcome articles addressing, but not limited to, the following themes:

• Genomic Epidemiology for Animal Health: Integration of genotypic, phenotypic, and epidemiological data to resolve AMR transmission patterns in animal populations. Studies focusing on strain diversity and genomic markers linked to resistance genes.

• AMR Determinants and Mobile Genetic Elements: Identifying resistance genes and studying the role of mobile genetic elements that enable the transfer of these genes between different bacterial species.

• miRNAs in Diagnostics and Antimicrobial Resistance: Exploring how host and pathogen-derived microRNAs (miRNAs) can act as biomarkers for resistance detection and as regulators that influence antimicrobial response and treatment outcomes in veterinary pathogens.

• Practical Bioinformatics Pipelines and Data Standards: Development, validation of reproducible bioinformatics workflows, metadata frameworks, and data standards to improve comparability, data sharing, and large-scale AMR surveillance in animal health.

• Zoonotic Transmission and One Health Perspectives: Studies examining the circulation of resistance genes among animals and humans, with implications for risk reduction and global monitoring.

We welcome the following article types: Original Research, Methods, Data Reports, Reviews, Systematic Reviews, Mini Reviews, Perspectives, and Opinions.

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
• Data Report
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• ... 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
• Data Report
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Policy Brief
• Review
• Systematic Review
• Technology and Code

Keywords: pathogen genomics, antimicrobial resistance, bioinformatics, surveillance, One Health, whole genome sequencing, outbreak investigation, epidemiology

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.