Long-Read Sequencing for the Rapid Response to Infectious Diseases Outbreaks.

IF 3.1 Q2 MICROBIOLOGY

Current Clinical Microbiology Reports Pub Date : 2025-01-01 Epub Date: 2025-05-15 DOI:10.1007/s40588-025-00247-y

Josephine B Oehler, Kaitlin Burns, Jeffrey Warner, Ulf Schmitz

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引用次数: 0

Abstract

Purpose of review: Long-read sequencing (LRS) has revolutionized pathogen surveillance by enabling real-time, high-fidelity genomic analysis critical for outbreak response. This review synthesizes recent breakthroughs in LRS, evaluating its impact on genomic epidemiology, metagenomics, and public health decision-making while addressing limitations and prospects for integrating LRS into global outbreak surveillance.

Recent findings: Unlike short-read sequencing, LRS-pioneered by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio)-resolves complex genomic structures, antimicrobial resistance determinants, and transmission dynamics with unprecedented accuracy. The portability of some LRS devices has facilitated rapid pathogen identification in field settings, notably during the Ebola and COVID-19 pandemics. Despite advancements in basecalling algorithms and target enrichment, challenges including sequencing errors, computational bottlenecks, and cost barriers remain.

Summary: By critically evaluating recent findings and discussing future directions, this review highlights the importance of leveraging LRS for outbreak preparedness and response, equipping researchers and public health professionals with the knowledge necessary to navigate the complexities of modern infectious disease challenges.

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用于传染病暴发快速反应的长读测序。

综述目的：长读段测序（LRS）通过实现对疫情应对至关重要的实时、高保真基因组分析，彻底改变了病原体监测。本综述综合了LRS的最新突破，评估了其对基因组流行病学、宏基因组学和公共卫生决策的影响，同时探讨了将LRS纳入全球疫情监测的局限性和前景。最近的发现：与短读测序不同，lrs——由牛津纳米孔技术公司（ONT）和太平洋生物科学公司（PacBio）开创——以前所未有的准确性解决了复杂的基因组结构、抗菌素耐药性决定因素和传播动力学。一些LRS设备的便携性有助于在现场环境中快速识别病原体，特别是在埃博拉和COVID-19大流行期间。尽管在基调用算法和目标丰富方面取得了进步，但包括测序错误、计算瓶颈和成本障碍在内的挑战仍然存在。摘要：通过批判性地评估最近的发现和讨论未来的方向，本综述强调了利用LRS进行疫情准备和应对的重要性，为研究人员和公共卫生专业人员提供必要的知识，以应对现代传染病挑战的复杂性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Current Clinical Microbiology Reports MICROBIOLOGY-

CiteScore

7.50

自引率

1.90%

发文量

期刊介绍： Current Clinical Microbiology Reports commissions expert reviews from leading scientists at the forefront of research in microbiology. The journal covers this broad field by dividing it into four key main areas of study: virology, bacteriology, parasitology, and mycology. Within each of the four sections, experts from around the world address important aspects of clinical microbiology such as immunology, diagnostics, therapeutics, antibiotics and antibiotic resistance, and vaccines. Some of the world’s foremost authorities in the field of microbiology serve as section editors and editorial board members. Section editors select topics for which leading researchers are invited to contribute comprehensive review articles that emphasize new developments and recently published papers of major importance, which are highlighted in annotated reference lists. These timely reviews of the literature examine the latest scientific discoveries and controversies as they emerge and are indispensable to both researchers and clinicians. The editorial board, composed of more than 20 internationally diverse members, reviews the annual table of contents, ensures that topics address all aspects of emerging research, and where applicable suggests topics of critical importance to various countries/regions.