The PREPARE-TID consortium has successfully developed a comprehensive, end-to-end diagnostic pipeline. Work began with creating novel nucleic acid extraction chemistries and a unique portable, battery-operated extraction instrument designed to process challenging samples like wastewater, blood, and arthropod vectors directly in the field. For pathogen detection, two distinct hardware platforms were developed. The first is the One Health Pod, a versatile, low-cost (€2−5 per sample), point-of-care qPCR platform. It uses pre-loaded cartridges that allow minimally trained personnel to screen for up to 22 different respiratory agents, mosquito- or tick-borne pathogens, and critical antimicrobial resistance (AMR) markers in under an hour. The second is the self-contained Mobile Suitcase Laboratory, a rugged, all-in-one unit for on-site nanopore sequencing, which has been deployed across seven countries. To make field-based genomic analysis accessible, the project developed Lazypipe NP, a user-friendly, offline bioinformatics pipeline that allows non-specialists to perform complex data analysis in real-time. All diagnostic data is integrated into an innovative One Health digital surveillance platform, which combines a mobile app for field data collection with a web dashboard for real-time monitoring and outbreak visualization. The true power of this integrated pipeline was proven in real-world crises. In Sierra Leone, the Mobile Suitcase Laboratory was deployed to respond to an mpox outbreak, reducing diagnostic turnaround time from days to hours. Following Cyclone Chido in Mayotte, a mobile water-testing laboratory was used to rapidly assess water safety, enabling authorities to target interventions effectively.
