Surveilling the genomic epidemiology of malaria in travelers

Despite wide-scale control and elimination efforts, the global decline in malaria has stagnated in recent years. There is a strong need for malaria molecular surveillance in endemic regions to address the threats posed by antimalarial drug and diagnostic resistance, and to strategically prioritize the limited resources for malaria control programs. Meanwhile, non-endemic regions are not only being faced with an increasing number of travel-related malaria cases, in conjunction with adverse clinical outcomes, but also with rare cases of autochthonous transmission. To address these issues, we present the SUrveillance of Molecular epidemiology of Malaria In Travelers (SUMMIT) project. Travelers present an as-of-yet untapped resource of diverse genomic information on the Plasmodium parasite, which allows for close-to-real-time data collection and sharing, as well as the standardization of lab and bioinformatics methodologies. We aim to establish a pioneering platform for the routine systematic surveillance of travel-related malaria, which combines parasite whole-genome sequencing data with epidemiological patient data. The platform will be enabled through a global network of travel clinics (GeoSentinel) and embrace FAIR principles by providing standardized and reproducible bioinformatics analysis and reporting pipelines. These will be built using Nextflow and powered by nf-core's components and best practices. We will leverage this continuously growing and global-spanning resource to monitor the emergence and spread of clinically relevant markers, develop machine learning tools to trace parasite origins, and conduct studies on treatment failure. Our approach is complementary to existing surveillance approaches and strives to increase the geographic, temporal and genetic resolution of the available genomic data and function as a sentinel system to aid preparedness efforts for reactive and coordinated responses to outbreaks. Our ultimate goal is to provide an up-to-date and accessible resource containing actionable data that can facilitate further malaria research, inform case management, prioritize efficacy studies, and aid in surveillance and control efforts. Here, we give an overview of the initial setup of the SUMMIT project, our preliminary findings, and future objectives, paying particular attention to how we will utilize Nextflow pipelines to achieve our goals.