Contexts, Facilitators, and Barriers to Integrating Portable Genomics for Outbreak Response in Coastal Kenya: A Qualitative Analysis of Participatory Stakeholder Discussions

<ns3:p>Background The Kenyan coast frequently experiences infectious disease outbreaks, but the response is often hindered by limited diagnostic capacity, diagnostic delays, and logistic barriers related to sample transportation and storage. Portable genomic sequencing technology offers the potential to accelerate outbreak investigations and inform timely public health interventions. However, a critical gap remains in understanding stakeholders' needs and level of engagement in integrating this technology within resource-limited settings. Methods We conducted a framework analysis on the stakeholder discussions from a consultative engagement meeting held in Nairobi, Kenya, in July 2024. Twenty-one stakeholders participated in discussions focusing on exploring outbreak response strategies within the respective counties and the potential integration of portable genomic sequencing technologies. The meeting sessions were recorded, and verbatim transcripts were analyzed using qualitative methods with NVivo software. Results Three key aspects of outbreak response were reported to be influenced by the resources available in each county: a) outbreak notification and reporting, b) outbreak management, and c) the sample journey. Participants strongly supported integrating portable sequencing technologies, identifying several key facilitators such as outbreak notification mechanisms, establishing public-private partnerships, and good security within the counties. However, logistical challenges were highlighted, including geographical inaccessibility, poor internet connectivity, power outages, and cultural or religious barriers to sample collection and sequencing. Conclusion Portable genomic sequencing was viewed as a high-value innovation with great potential to transform outbreak management in coastal Kenya. However, its successful integration during outbreaks will require addressing logistical challenges and leveraging existing partnerships and notification systems.</ns3:p>