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

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

25 April 2024 | Marc J. Struelens, Catherine Ludden, Guido Werner, Vitali Sintchenko, Pikka Jokelainen and Margaret Ip
This article advocates for the mobilization of pathogen genomic surveillance to enhance control of infectious diseases and antimicrobial resistance (AMR). Building on the successes of large-scale genome sequencing in SARS-CoV-2 variant monitoring during the COVID-19 pandemic, the authors propose a One Health approach to strengthen public health surveillance. Key recommendations include: 1. **Universal Access to Real-Time Whole Genome Sequencing (WGS)**: Enhancing laboratory-based surveillance and epidemic alert systems by providing universal access to real-time WGS data to inform clinical practice, infection control, public health policies, and vaccine and drug research. 2. **Integration of Data**: Integrating diagnostic microbiology data, asymptomatic testing data, pathogen sequence data, clinical data, and epidemiological data into surveillance programs. 3. **Cross-Sectoral Collaborations**: Strengthening cross-sectoral collaborations between healthcare, public health, animal health, and environmental surveillance using a One Health approach. 4. **International Collaboration**: Promoting international collaboration and interconnection of surveillance networks, harmonizing laboratory methods, and standardizing surveillance methods for global reporting. 5. **Responsible Data Sharing**: Ensuring responsible data sharing between surveillance networks, databases, and platforms according to FAIR (findability, accessibility, interoperability, and reusability) principles. 6. **Research on Genomic Surveillance**: Conducting research on the implementation and cost-effectiveness of genomic surveillance systems for different pathogens and AMR threats. The article highlights the strengths and weaknesses of genomic surveillance during the COVID-19 pandemic, emphasizing the need for continued investments in technical infrastructure, methodological development, training, and public health decision-making. It also discusses the importance of integrating genomic, clinical, and epidemiological data for enhanced surveillance and the design of national genomic surveillance systems. Finally, it underscores the benefits and challenges of pathogen sequencing data sharing, advocating for consensus-based guidelines to ensure responsible data integration and mobilization.This article advocates for the mobilization of pathogen genomic surveillance to enhance control of infectious diseases and antimicrobial resistance (AMR). Building on the successes of large-scale genome sequencing in SARS-CoV-2 variant monitoring during the COVID-19 pandemic, the authors propose a One Health approach to strengthen public health surveillance. Key recommendations include: 1. **Universal Access to Real-Time Whole Genome Sequencing (WGS)**: Enhancing laboratory-based surveillance and epidemic alert systems by providing universal access to real-time WGS data to inform clinical practice, infection control, public health policies, and vaccine and drug research. 2. **Integration of Data**: Integrating diagnostic microbiology data, asymptomatic testing data, pathogen sequence data, clinical data, and epidemiological data into surveillance programs. 3. **Cross-Sectoral Collaborations**: Strengthening cross-sectoral collaborations between healthcare, public health, animal health, and environmental surveillance using a One Health approach. 4. **International Collaboration**: Promoting international collaboration and interconnection of surveillance networks, harmonizing laboratory methods, and standardizing surveillance methods for global reporting. 5. **Responsible Data Sharing**: Ensuring responsible data sharing between surveillance networks, databases, and platforms according to FAIR (findability, accessibility, interoperability, and reusability) principles. 6. **Research on Genomic Surveillance**: Conducting research on the implementation and cost-effectiveness of genomic surveillance systems for different pathogens and AMR threats. The article highlights the strengths and weaknesses of genomic surveillance during the COVID-19 pandemic, emphasizing the need for continued investments in technical infrastructure, methodological development, training, and public health decision-making. It also discusses the importance of integrating genomic, clinical, and epidemiological data for enhanced surveillance and the design of national genomic surveillance systems. Finally, it underscores the benefits and challenges of pathogen sequencing data sharing, advocating for consensus-based guidelines to ensure responsible data integration and mobilization.
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