Third-generation nanopore sequencing: advancing real-time pathogen detection and antimicrobial resistance surveillance in food safety applications
Clinical Snapshot
PICO Framework
| P — Population | Food samples and foodborne pathogens requiring microbiological surveillance |
| I — Intervention | Third-generation nanopore sequencing technology |
| C — Comparator | Traditional pathogen detection methods (culture-based, PCR, conventional whole-genome sequencing) |
| O — Outcomes | Detection time, species identification accuracy, antimicrobial resistance gene sensitivity, cost-effectiveness, and diagnostic performance metrics |
Bottom Line
This systematic review of 80 studies suggests nanopore sequencing offers significant advantages for food safety surveillance, reducing pathogen detection time from days to hours with 95-98% accuracy and >90% antimicrobial resistance gene sensitivity. The technology costs $50-200 per sample versus $300-800 for traditional whole-genome sequencing, making it economically viable. Key benefits include real-time results, multiplex detection capabilities, and identification of viable but non-culturable organisms. However, implementation faces challenges including 8-15% error rates in homopolymeric regions and substantial bioinformatics expertise requirements. While promising for transforming food safety surveillance, the technology requires careful validation and quality assurance protocols before widespread clinical adoption. The evidence suggests potential for integration into existing surveillance systems, particularly for outbreak investigation and high-risk food monitoring, but methodological limitations in this review warrant cautious interpretation.
Key Findings
P Value: Not reported in abstract
Effect Size: Species identification accuracy 95-98%, AMR gene sensitivity >90%
Primary Outcome: Detection time reduction to <24 hours versus 3-7 days for conventional methods
Nnt Or Sensitivity: Sensitivity >90% for AMR gene detection, specificity not reported
Confidence Interval: Not reported in abstract
Clinical Application
Moderate - requires significant bioinformatics expertise and infrastructure investment, but cost-competitive at $50-200 per sample Highly relevant for Food Standards Australia New Zealand (FSANZ) surveillance, state health departments, and private food testing laboratories. Could enhance Australia's foodborne disease surveillance capabilities and support export certification requirements Food safety laboratories, public health surveillance systems, outbreak investigation teams
Abstract
Foodborne diseases impact 600 million people annually, causing 420 000 deaths and over $110 billion in economic losses. Conventional pathogen detection methods take 3-7 days and lack sensitivity for low-abundance pathogens and antimicrobial resistance (AMR) genes. This review evaluates nanopore sequencing's potential in food microbiology, analyzing real-time pathogen detection, AMR surveillance, and performance versus traditional methods. A systematic review of 80 studies (2015-2025) revealed nanopore sequencing reduces detection time to <24 hours with 95-98% species identification accuracy and >90% AMR gene sensitivity, at $50-200 per sample versus $300-800 for traditional whole-genome sequencing. It enables multiplex pathogen detection, viable but non-culturable organism identification, and real-time AMR profiling. However, challenges include error rates of 8-15% in homopolymeric regions and the need for bioinformatics expertise. Addressing challenges, including error rates of 8-15% in homopolymeric regions and the need for bioinformatics expertise, requires strategic mitigation approaches. Despite limitations, advances in base-calling and workflows make nanopore sequencing a transformative tool for next-generation food safety surveillance.
References
- 1.Nadeem, M., Rizvi, A. S., Rahman, A., & Murtaza, G. (2026). Third-generation nanopore sequencing: advancing real-time pathogen detection and antimicrobial resistance surveillance in food safety applications. The Analyst. https://doi.org/10.1039/d5an01028d
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