# Nanopore Sequencing in Veterinary Pathogen Detection: A Review of Technologies and Applications

## TL;DR

Nanopore sequencing is a portable, real-time DNA sequencing tool that is being used to detect pathogens in animals, offering faster and more comprehensive diagnostics compared to traditional methods.

## Contribution

This review consolidates recent applications of nanopore sequencing in veterinary pathogen detection and provides workflow-oriented guidance for its implementation.

## Key findings

- Nanopore sequencing enables rapid whole-genome sequencing of viral pathogens in field settings.
- It facilitates near-complete bacterial genome assembly and identification of AMR genes.
- The technology shows promise in parasitology for high-resolution species identification and genome assembly.

## Abstract

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.

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.