Advancing pathogen genomics in resource-limited settings
Paul Pronyk, Ruklanthi de Alwis, Rebecca J. Rockett, Kerri Basile, Yan Boucher, Vincent Pang, October M. Sessions, Marya Getchell, Tanya Golubchik, Connie Lam, Raymond Lin, Tze Minn Mak, Ben J. Marais, Rick Twee‐Hee Ong, Hannah Clapham, Lin‐Fa Wang, Yorin Cahyorini, Francisco Gerardo M. Polotan, Yuni Rukminiati, Eby Sim, Carl J. E. Suster, Gavin J. D. Smith, Vitali Sintchenko
Abstract
Genomic sequencing has emerged as a powerful tool to enhance early pathogen detection and characterization with implications for public health and clinical decision making. Although widely available in developed countries, the application of pathogen genomics among low-resource, high-disease burden settings remains at an early stage. In these contexts, tailored approaches for integrating pathogen genomics within infectious disease control programs will be essential to optimize cost efficiency and public health impact. We propose a framework for embedding pathogen genomics within national surveillance plans across a spectrum of surveillance and laboratory capacities. We adopt a public health approach to genomics and examine its application to high-priority diseases relevant in resource-limited settings. For each grouping, we assess the value proposition for genomics to inform public health and clinical decision-making, alongside its contribution toward research and development of novel diagnostics, therapeutics, and vaccines.