Advancing pathogen genomics in resource-limited settings

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.

Keywords: emerging infectious diseases; genomics; pathogen genomics; resource-limited settings; surveillance; whole-genome sequencing.

Graphical abstract

Figure 1

Conceptual framework for assessing the value proposition of pathogen genomic surveillance A framework was developed to help policymakers determine the utility of applying genomic surveillance for various pathogens. The framework considers three inter-related components: (1) existing surveillance and laboratory system capacity, (2) pathogen-specific characteristics, and (3) public health, clinical, and research and development utility.

Figure 2

Utility of genomic pathogen surveillance by pathogen grouping based on level of surveillance and laboratory system capacity (A) Existing surveillance and laboratory system capacity determines the overall utility of applying genomic surveillance to various pathogens. The capacity to implement pathogen genomics has been categorized into three tiers: limited, moderate, and high capacity. (B) Areas of public health (light-blue shaded boxes), clinical, and research and development (R&D) (dark-blue shaded boxes) where the utility of pathogen genomics has informed decision-making in moderate and high-capacity settings are shown. These utilities have been applied to a number of high-priority pathogen groupings including (1) tuberculosis, (2) drug-resistant bacteria, (3) respiratory viruses, (4) zoonotic viruses with high spillover risk, (5) arboviruses, (6) novel or emerging pathogens, and (7) environmental surveillance (as a platform).