Infectious diseases cause a substantial global disease burden and mortality despite advances in medical interventions and improved access to healthcare. Low- and middle-income countries (LMICs), including countries in sub-Saharan Africa and Asia, are particularly affected by infectious diseases1. Moreover, it is widely postulated that the actual infectious disease burden in LMICs is underestimated, highlighting an urgent need for improved and robust disease diagnostics and surveillance. Indeed, effective clinical management and prevention of infectious diseases require accurate and timely diagnosis. However, diagnosing infectious diseases remains challenging due to the lack of tests that simultaneously detect all pathogens, further compounded by overlapping, non-disease-specific symptoms such as fever. Additionally, patients may be infected with multiple pathogens simultaneously, further increasing the risk of misdiagnosis. Therefore, innovative and unbiased techniques are required to address these challenges associated with infectious disease diagnostics.
Metagenomics, the sequencing of total genomic DNA in a sample, has emerged as a valuable tool in clinical settings2. This approach enables the simultaneous and accurate detection of multiple pathogens, including pathogens that are uncommon, not well characterized and those not included in standard diagnostic panels. In addition, metagenomics can also detect pathogens with molecular changes leading to diagnostic failure and those that are not easily recoverable based on traditional methods such as microscopy and culture. Since its development, metagenomics has remained a powerful approach for pathogen detection and surveillance, with its application commonly seen in many developed countries2. However, more data are needed on how this technology can be utilized in LMICs, where the burden of infectious diseases is highest. A recently published study in Nature Communications by Oguzie and colleagues highlights the feasibility and potential use cases of metagenomic sequencing for pathogen detection and surveillance in Nigeria. We highlight this paper to showcase the benefits of integrating metagenomics into pathogen surveillance in LMICs, where this approach may be most beneficial.
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