Publication: The value of local use cases for expanding pathogen genomics in resource-limited settings (Nature Health, 2026)

The COVID-19 pandemic pushed pathogen genomics from research laboratories into the forefront of public health practice. Sequencing can now trace how and where microbes are spreading, and predict traits like drug resistance. Costs are falling and tools are getting easier to use. However, in many low- and middle-income countries (LMICs), genomics is still often confined to research settings due to still-prohibitive costs and a lack of integration into existing public health systems.

A recent commentary in Nature Health argues that in such settings, genomics delivers the most value when it is applied to specific, local problems with clear routes from data to decisions. That means prioritising focused “use cases” that impact what clinicians or programme managers do. A well-defined use case must link a specific application of sequencing with a defined pathogen or pathogen group and a concrete purpose. Not every disease benefits equally from genomics. The question to ask is: Will the result shift treatment, policy, or response?

Scaling pathogen genomics in resource-limited settings requires navigating technical, logistical, and governance hurdles. Approaches like multi-pathogen platforms to improve efficiency and technological advances such as artificial intelligence can help mitigate some of these challenges. Multi-sectoral collaboration with industry and academia is also critical, to share resources and expertise. Tighter links between research and public health ensure findings translate into policy and practice and that training builds in-country capacity.

Finally, preparedness depends on routine use. Outbreaks are the wrong time to start from scratch. A “warm base” of ongoing, locally relevant sequencing ensures teams can pivot quickly when new threats emerge. Ultimately, by demonstrating that genomics can save lives and resources at the national level, LMICs can build the investment case for systems that are both locally impactful and globally beneficial.