Submitted to: Frontiers in Cellular and Infection Microbiology
Publication Type: Review Article
Publication Acceptance Date: 3/10/2025
Publication Date: 4/15/2025
Citation: Chaves, M., Hashish, A., Goraichuk, I., Caserta, L.C., Mears, M.C., Gadu, E., Bakre, A.A., Alexander, M.E., Shelkamy, M.M., Nadendla, S., El-Gazzar, M. 2025. Nanopore Sequencing in Veterinary Medicine: From Concepts to Clinical Application. Frontiers in Cellular and Infection Microbiology. 15:1545032. https://doi.org/10.3389/fcimb.2025.1545032.
DOI: https://doi.org/10.3389/fcimb.2025.1545032

Interpretive Summary: The commercial poultry industry contributes significantly to the global protein and nutritional demands of a growing world. However, both bacterial and viral infectious agents can significantly affect bird health and lead to significant losses for commercial poultry operations. Infectious disease outbreaks can lead to devastating economic losses; rapid characterization of these pathogens via sequencing can enable rapid containment and reduce commercial losses. However, current sequencing technologies require specialized equipment, expensive reagents and highly skilled personnel and a considerable time delay to obtain relevant data which precludes their adoption in field settings. Recent developments in third generation sequencing technologies such as the MinION platform from Oxford Nanopore Technologies (ONT), bring rapid, near real-time sequencing to the field and may assist in faster outbreak control for both human and veterinary pathogens. In this review article, we summarize the application of ONT based MinION sequencing in veterinary diagnostics with a focus on poultry infectious diseases. Based on in-house experience and a growing body of literature, ONT MinION sequencing enables rapid sequencing of various avian bacterial and viral pathogens. This review article summarizes the technology, current procedures and applications of this technology for veterinary diagnosis and detection.

Technical Abstract: Oxford Nanopore Technologies (ONT) is a third-generation sequencing platform that provides real-time data generation, portability, and long-read output, making it a valuable tool for veterinary diagnostics. This review explores the use of ONT for detecting viral and bacterial pathogens, antimicrobial resistance profiling, foodborne disease surveillance, and metagenomic analysis. It covers the ONT workflow, from sample preparation to bioinformatics analysis, and compares its advantages with traditional sequencing methods. The review also discusses key challenges, such as error rates, barcode crosstalk, and wet lab complexities, as well as potential future developments and long-term impact in the field of genomics. As ONT technology advances, its role in veterinary diagnostics is expected to expand, improving disease surveillance, outbreak response, and contributions to One Health initiatives.