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.

尽管医疗干预措施取得了进步并且获得医疗保健的机会有所改善，但传染病仍给全球带来了巨大的疾病负担和死亡率。低收入和中等收入国家 (LMIC)，包括撒哈拉以南非洲和亚洲国家，尤其受到传染病的影响¹ 。此外，人们普遍认为中低收入国家的实际传染病负担被低估，这凸显出迫切需要改进和健全的疾病诊断和监测。事实上，有效的临床管理和传染病预防需要准确、及时的诊断。然而，由于缺乏同时检测所有病原体的测试，再加上发烧等重叠的非疾病特异性症状，诊断传染病仍然具有挑战性。此外，患者可能同时感染多种病原体，进一步增加误诊风险。因此，需要创新和公正的技术来解决与传染病诊断相关的这些挑战。

宏基因组学，即样本中总基因组 DNA 的测序，已成为临床环境中的宝贵工具² 。这种方法能够同时准确地检测多种病原体，包括不常见、未充分表征和未包含在标准诊断组中的病原体。此外，宏基因组学还可以检测因分子变化而导致诊断失败的病原体，以及那些基于显微镜和培养等传统方法不易恢复的病原体。自发展以来，宏基因组学一直是病原体检测和监测的有力方法，其应用在许多发达国家很常见² 。然而，需要更多数据来了解如何在传染病负担最高的中低收入国家中利用这项技术。 Oguzie 及其同事最近在《自然通讯》上发表的一项研究强调了宏基因组测序在尼日利亚用于病原体检测和监测的可行性和潜在用例。我们强调这篇论文是为了展示将宏基因组学整合到中低收入国家病原体监测中的好处，这种方法可能是最有益的。