AUTHOR=Struelens Marc J. , Ludden Catherine , Werner Guido , Sintchenko Vitali , Jokelainen Pikka , Ip Margaret 

TITLE=Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance

JOURNAL=Frontiers in Science

VOLUME=Volume 2 - 2024

YEAR=2024

URL=https://www.frontiersin.org/journals/science/articles/10.3389/fsci.2024.1298248

DOI=10.3389/fsci.2024.1298248

ISSN=2813-6330

ABSTRACT=This article advocates for mobilizing pathogen genomic surveillance to contain and mitigate health threats from infectious diseases and antimicrobial resistance (AMR), building upon successes achieved by large-scale genome sequencing analysis of SARS-CoV-2 variants in guiding COVID-19 monitoring and public health responses and adapting a One Health approach. 
Capabilities of laboratory-based surveillance and epidemic alert systems should be enhanced by fostering (i) universal access to real-time whole genome sequence (WGS) data of pathogens to inform clinical practice, infection control, public health policies, and vaccine and antimicrobial drug research and development; (ii) integration of diagnostic microbiology data, data from testing asymptomatic individuals, pathogen sequence data, clinical data, and epidemiological data into surveillance programs; (iii) strengthening cross-sectorial collaborations between healthcare, public health, animal health, and environmental surveillance and research using One Health approaches, towards understanding the ecology and transmission pathways of pathogens and AMR across ecosystems; (iv) international collaborations and interconnection of surveillance networks, harmonization of laboratory methods, and standardization of surveillance methods for global reporting, including on pathogen genomic variant or strain nomenclature; (v) responsible data sharing between surveillance networks, databases and platforms according to FAIR (findability, accessibility, interoperability and reusability) principles; and (vi) research on genomic surveillance system implementation and their cost-effectiveness for different pathogens and AMR threats across different settings. Regional and global One Health policies and governance initiatives should foster the concerted development and efficient utilization of pathogen genomic surveillance to protect the health of humans, animals, and the environment