Bridging the bioinformatics gap: tool selection for decentralized AMR genomic surveillance in Africa

Antimicrobial resistance (AMR) poses a significant threat to public health, particularly in low- and middle-income countries where centralized genomic surveillance infrastructure is limited. To support decentralized AMR surveillance in Africa, the SeqAfrica project evaluated bioinformatics tools suitable for Oxford Nanopore Technologies sequencing data. Through two surveys and an expert elicitation workshop, the project assessed over 80 tools, focusing on usability, cost, accessibility, and AMR relevance. Graphical user interface (GUI) based tools were shortlisted for non-bioinformatician use. Terra.bio and EPI2ME emerged as leading candidates due to their user-friendly interfaces and integrated workflows. EPI2ME, which is an Oxford Nanopore Technologies tool, was favored for its offline capability, ease of use, and compatibility with local infrastructure, while Terra.bio offered strong interoperability and cloud-based scalability. The findings underscore the need for standardized, interoperable pipelines, and sustained technical support to ensure effective genomic surveillance in resource-limited settings. SeqAfrica has initiated pilot implementation and collaborative development of EPI2ME-based workflows to enhance AMR monitoring capacity across the African continent.