High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens—bacteria, fungi, parasites and viruses—including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.

中文翻译：

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人类病原体的混合捕获目标富集：鉴定、进化、生物监测和基因组流行病学

高通量测序 (HTS) 彻底改变了病原体基因组学领域，使得能够从临床和环境样本中直接恢复病原体基因组。然而，病原体核酸常常被宿主核酸淹没，需要深度宏基因组测序来恢复足够的序列用于下游分析（例如鉴定和基因组表征）。为了避免这种情况，混合捕获目标富集 (HC) 能够根据所使用的面板，在多个分歧和分类单元范围内富集病原体核酸。在这篇综述中，我们概述了 HC 在人类病原体（细菌、真菌、寄生虫和病毒）中的应用，包括鉴定、基因组流行病学、抗菌素耐药性基因分型和进化。重要的是，我们探索了 HC 在临床宏基因组学中的适用性，这最终需要更多的工作才能成为可靠​​且准确的临床诊断工具。与此相关，HC 的实用性以 COVID-19 为例，它被用作案例研究来说明 HC 在恢复病原体序列方面的成熟度。当我们揭开 COVID-19 的起源时，人畜共患疾病仍然比以往任何时候都更加重要。因此，本次综述还强调了 HC 在生物监测研究中的作用，这对于我们为下一次大流行做好准备至关重要。我们还发现，虽然 HC 是研究病毒的常用工具，但它在寄生虫和真菌以及细菌中仍未得到充分利用。最后，我们评估了 HC 在真核群体诱饵设计方面的未来以及 HC 与长读长 HTS 相结合的前景。