Leveraging Real-Time Genomic Surveillance to Combat Infectious Diseases and Antimicrobial Resistance

The rapid advancement of genomic technologies has demonstrated unparalleled potential in enhancing the control of infectious diseases and antimicrobial resistance (AMR). Building upon the success of large-scale genome sequencing during the COVID-19 pandemic, particularly with SARS-CoV-2 variant tracking, this Research Topic aims to explore solutions enabling the transformative potential of real-time genomic surveillance in public health and assess its real-world impact across settings. This includes laboratory and digital health solutions facilitating the universal access to production and integration of human and zoonotic pathogen whole genome sequencing (WGS) data within epidemiological surveillance systems to inform healthcare practices, bolster infection prevention and control, shape public health policies, and guide the adaptive development of vaccines and antimicrobial drugs.

The Topic’s overall theme is based on the following lead article published in Frontiers in Science: Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance

We aim to invite research and review articles that focus on seven critical components to enhance and evaluate pathogen genomic surveillance capabilities and health benefits:

1. Universal Access to Pathogen WGS Data: Research on establishing and maintaining universal access to real-time WGS data of pathogens and its application in clinical settings, infection control practices, and public health policy-making. Contributions may explore innovative ways to democratize access to genomic data and the implications for healthcare and policy.

2. Evolutionary Public Health Research: Research on short term evolutionary changes in human and zoonotic pathogens that affect phenotype and impacts pathogen transmissibility, virulence, antigenic profile, diagnostic assay sensitivity and drug susceptibility.

3. Integration of Multidimensional Data: Studies that investigate the integration of diagnostic microbiology data, asymptomatic testing data, pathogen sequence data, clinical data, and epidemiological information into cohesive surveillance programs. Emphasis on how integrated data platforms can enhance the detection, monitoring, and management of infectious diseases and AMR.

4. Cross-Sectorial One Health Collaborations: Insights into the power of collaborative efforts between healthcare, public health, animal health, and environmental surveillance sectors using One Health approaches. Articles may focus on the ecology, transmission pathways of pathogens, and AMR across ecosystems, highlighting successful examples of cross-sectorial integration and coordination.

5. International Collaboration and Standardization: Research addressing the governance of international collaboration, interconnection of surveillance networks, harmonization of laboratory methods, and standardization of surveillance protocols. Focus on the means and global benefits of common nomenclature and reporting standards for pathogen genomic variants and strains.

6. FAIR+E Data Sharing Principles: Studies on the implementation and benefits of responsible data sharing according to FAIR (findability, accessibility, interoperability, and reusability) principles, as well as considering equitable access and benefit sharing between stakeholders (FAIR+E principles). Exploration of the challenges and best practices in data exchange between surveillance networks, databases, and platforms to foster a collaborative environment.

7. Cost-Effectiveness and Implementation Research: Contributions that assess the implementation strategies and cost-effectiveness of genomic surveillance systems for different pathogens and AMR threats across varied settings. This includes economic evaluations, logistical considerations, and strategic frameworks for efficient deployment of these technologies in diverse regions and scenarios.

Objective: Through this collection, we aim to foster a comprehensive understanding of how enhanced genomic surveillance can be mobilized and overcome current hurdles to contain and mitigate health threats posed by infectious diseases and AMR, guided by One Health principles. This Research Topic will emphasize the importance of cross-sectorial collaborations, standardized methodologies, and FAIR+E data sharing to fortify global health security.

We invite researchers and practitioners from diverse fields such as genomics, epidemiology, public health, microbiology, veterinary science, environmental science, and policy-making to contribute their original research, reviews, case studies, and perspectives.

We welcome submissions of various article types, including Original Research, Review, Systematic Review, Community Case Study, Conceptual Analysis, Hypothesis & Theory, Methods, Perspective, Policy Brief, and Policy and Practice Reviews.

Authors are invited to submit a summary of their intended contribution before the 17th of December, though they also have the option to submit a full manuscript directly.

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
• Classification
• Clinical Trial
• Community Case Study
• Conceptual Analysis
• Curriculum, Instruction, and Pedagogy
• Data Report
• Editorial
• ... 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
• Classification
• Clinical Trial
• Community Case Study
• Conceptual Analysis
• Curriculum, Instruction, and Pedagogy
• Data Report
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Policy and Practice Reviews
• Policy Brief
• Review
• Study Protocol
• Systematic Review
• Technology and Code

Keywords: genomic surveillance, real-time genomic surveillance, infectious diseases, antimicrobial resistance

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.