Collaborative development of open-source outbreak detection tools: Needs, concept and implementation

Abstract

Abstract Issue The early detection of infectious disease outbreaks through surveillance is critical to initiate targeted public health interventions. Automated outbreak detection helps to identify trends and unusual events. Yet, there is no overview of how many EU countries use outbreak detection systems and what factors hindered their implementation. Description of the problem One aim of the Joint Action UNITED4Surveillance (U4S) is to identify EU countries’ requirements for outbreak detection, and based on these, develop and deploy a tool for the timely and accurate detection of outbreaks. Through surveys, interviews and an in-person workshop involving public health experts, we identified uses cases, collected functional and technical requirements for a tool. Subsequently the tool development started in August 2023 as an open-source software process on GitHub. Results Despite high interest, only three of the 21 countries that took part in the survey have implemented outbreak detection tools, even though national surveillance systems offer the potential for their use. Reasons for this are limited resources and low prioritization. Experts identified gastrointestinal diseases as one major potential use case and emphasised the necessity of flexible outputs. Tailored to these requirements, data scientists from five European public health institutes developed an open-source R package for signal detection. The tool generates signals based on national surveillance data and enables the user to analyses these results using a dashboard with flexible exploration and generation of a report. The tool is now being piloted locally by ten European public health authorities and its use will be evaluated. Lessons There is a need to use automated outbreak detection tools for routine surveillance of infectious diseases in EU countries but often lack resources. Projects like U4S can bring together expertise to build sustainable tools and supporting material that can address the identified needs. Key messages • Collaborative and open-source development leads to tools that are well tailored to the needs of the community and foster a high uptake in the usage of these tools. • The tool enhances surveillance and outbreak detection in countries without the capacities to develop and implement outbreak detection methods for their surveillance systems.