Long-Read Sequencing for the Rapid Response to Infectious Diseases Outbreaks
Oehler, Josephine B., Burns, Kaitlin, Warner, Jeffrey, and Schmitz, Ulf (2025) Long-Read Sequencing for the Rapid Response to Infectious Diseases Outbreaks. Current Clinical Microbiology Reports, 12 (1). 10.
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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.
| Item ID: | 87699 |
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| Item Type: | Article (Research - C1) |
| ISSN: | 2196-5471 |
| Keywords: | Genomic epidemiology antimicrobial resistance profiling, Metagenomics, Pathogen identification, Real-time surveillance, Third-generation sequencing |
| Copyright Information: | © The Author(s) 2025. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. |
| Funders: | National Health and Medical Research Council (NHMRC) |
| Projects and Grants: | NHMRC 2028308, NHMRC 1196405 |
| Date Deposited: | 23 Jan 2026 01:46 |
| FoR Codes: | 42 HEALTH SCIENCES > 4202 Epidemiology > 420202 Disease surveillance @ 100% |
| SEO Codes: | 20 HEALTH > 2004 Public health (excl. specific population health) > 200404 Disease distribution and transmission (incl. surveillance and response) @ 100% |
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