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Related Experiment Video

Updated: May 21, 2025

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

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

Josephine B Oehler^1,2, Kaitlin Burns^2,3, Jeffrey Warner^2,3

¹Computational Biomedicine Lab, College of Science and Engineering, James Cook University, 1 James Cook Drive, Townsville, QLD 4811 Australia.

Current Clinical Microbiology Reports

|May 19, 2025

Summary

Long-read sequencing (LRS) offers high-fidelity pathogen genomic analysis for real-time outbreak response. This review covers LRS advancements, applications in epidemiology and public health, and future integration strategies.

Keywords:

Genomic epidemiology antimicrobial resistance profiling Metagenomics Pathogen identification Real-time surveillance Third-generation sequencing

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Area of Science:

Genomic epidemiology
Pathogen surveillance
Bioinformatics

Background:

Long-read sequencing (LRS) provides high-fidelity genomic data crucial for infectious disease outbreak response.
LRS technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), enable detailed analysis of complex genomic structures and antimicrobial resistance.
The portability of LRS devices has been key in field-based pathogen identification during global health crises like Ebola and COVID-19.

Purpose of the Study:

To review recent advancements in long-read sequencing (LRS) technologies and their applications.
To evaluate the impact of LRS on genomic epidemiology, metagenomics, and public health decision-making.
To identify limitations and future prospects for integrating LRS into global outbreak surveillance systems.

Main Methods:

Literature review of recent studies on long-read sequencing in pathogen surveillance.
Synthesis of findings on LRS applications in genomic epidemiology and metagenomics.
Critical evaluation of LRS performance, including accuracy, portability, and limitations.

Main Results:

LRS offers superior resolution of complex genomic features, antimicrobial resistance genes, and transmission dynamics compared to short-read sequencing.
Portable LRS platforms have enabled rapid, on-site pathogen identification during major outbreaks.
Ongoing challenges include sequencing error rates, computational demands, and cost-effectiveness.

Conclusions:

Long-read sequencing is a transformative tool for pathogen surveillance and outbreak response.
Addressing current limitations is essential for maximizing the potential of LRS in global health security.
Leveraging LRS knowledge is vital for researchers and public health professionals facing evolving infectious disease threats.