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Nanopore Sequencing in Veterinary Pathogen Detection: A Review of Technologies and Applications
by
, and
Lei Xu
1,2, 
Leilei Zhao
1,2,
Zeyu Tong
1,2,
Kai Peng
1,2,
Mianzhi Wang
1,2,
Runsheng Li
3,4,5,
Zhiqiang Wang
1,2,6,7,* and
Ruichao Li
1,2,6,7,*
1
Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
2
College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
3
Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen 518057, China
4
Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong 999077, China
5
Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong 999077, China
6
Jiangsu Interdisciplinary Center for Zoonoses and Biosafety, Yangzhou University, Yangzhou 225009, China
7
Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
*
Authors to whom correspondence should be addressed.
Vet. Sci. 2026, 13(3), 216; https://doi.org/10.3390/vetsci13030216
Submission received: 31 December 2025
/
Revised: 12 February 2026
/
Accepted: 23 February 2026
/
Published: 25 February 2026
(This article belongs to the Special Issue Advanced Sequencing and Bioinformatics for Tracking MDR Bacteria in Veterinary and One Health Interfaces)
Simple Summary
Rapid and reliable pathogen detection is critical for animal health, outbreak response, and One Health surveillance. Nanopore sequencing is a portable long-read technology that can generate sequence data in real time, enabling flexible diagnostic strategies ranging from untargeted metagenomics to targeted amplicon sequencing and isolate whole-genome sequencing. In this review, we summarize how nanopore sequencing is being applied to detect viral, bacterial (including antimicrobial resistance), and parasitic pathogens in veterinary settings, and we compare its strengths and limitations with conventional methods such as PCR, culture, microscopy, and serology. We highlight practical workflow considerations from sample processing to data interpretation, discuss where nanopore sequencing can provide added value, and outline current barriers to routine implementation, including standardization, analytical thresholds, biosafety, and regulatory acceptance. We conclude with perspectives on how ongoing improvements in chemistry, basecalling, and enrichment strategies may support more consistent and standardized use in veterinary diagnostics and surveillance.
Abstract
Nanopore-based sequencing has emerged as a revolutionary tool for animal pathogen genomics, offering capabilities unattainable with Sanger and next-generation sequencing (NGS). Despite rapid technical progress, routine veterinary deployment still faces uncertainty in study design, sample preparation, and interpretation thresholds across diverse hosts and sample matrices. Accordingly, this review consolidates recent evidence and provides workflow-oriented guidance for veterinary diagnostics and One Health surveillance. Its portability, ability to generate real-time long-read data, and minimal infrastructure requirements enable rapid, on-site sequencing for veterinary diagnostics and surveillance. This review examines the principles of nanopore sequencing and its advantages over conventional methods, surveying recent applications across viral, bacterial (including antimicrobial resistance, AMR), and parasitic pathogen detection in animals. In viral diagnostics, it facilitates rapid whole-genome sequencing and outbreak tracing in field settings. For bacterial pathogens, it enables near-complete genome assembly and identification of plasmid-borne AMR genes. Emerging studies also demonstrate its utility in parasitology, from high-resolution species identification to whole-genome assemblies. We compare these advancements with traditional diagnostics, highlighting strengths in speed and comprehensiveness while addressing current limitations in accuracy and host-DNA interference. As technology matures through improvements in chemistry and adaptive sampling, nanopore sequencing is poised to transform veterinary pathogen detection and bolster One Health surveillance of emerging zoonoses.
