Supplementary file 1_Bridging the bioinformatics gap: tool selection for decentralized AMR genomic surveillance in Africa.docx

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.

抗菌药物耐药性（Antimicrobial Resistance, AMR）对全球公共卫生构成重大威胁，在集中式基因组监测基础设施匮乏的中低收入国家尤为突出。为支持非洲地区的去中心化抗菌药物耐药性监测工作，SeqAfrica项目针对适配牛津纳米孔技术公司（Oxford Nanopore Technologies）测序数据的生物信息学工具展开了评估。该项目依托两项调研与一场专家征询研讨会，对80余款生物信息学工具进行了评估，评估维度涵盖易用性、成本、可及性以及抗菌药物耐药性相关性。基于图形用户界面（Graphical User Interface, GUI）的工具被纳入非生物信息学专业人员可用的候选名单。Terra.bio与EPI2ME凭借其友好的用户界面与整合式工作流成为领跑候选工具。作为牛津纳米孔技术公司自研工具的EPI2ME，因其支持离线运行、操作简便且适配本地基础设施而更受青睐；而Terra.bio则具备出色的互操作性与基于云平台的可扩展性。本研究结果凸显了构建标准化、互操作性强的分析流程，并提供持续技术支持的必要性，以确保在资源受限地区开展高效的基因组监测工作。SeqAfrica项目已启动基于EPI2ME的工作流的试点部署与协同开发工作，以提升整个非洲大陆的抗菌药物耐药性监测能力。