Antimicrobial Resistance (AMR) in the Food Chain: Detection Gaps and Mitigation Strategies

Dear Colleagues,

Antimicrobial resistance (AMR) continues to pose an escalating threat to global public health, with the food chain serving as a key pathway for the transmission of resistant pathogens and antimicrobial resistance genes (ARGs) from animals to humans. This Special Issue explores whether current surveillance and detection methods are sufficiently sensitive and robust to address the full complexity of AMR dynamics across the food production chain, from farm to fork, while also critically evaluating the strategies available to mitigate these risks.

This research topic encompasses studies examining the strengths and limitations of conventional microbiological assays, molecular diagnostics, whole-genome sequencing (WGS), and metagenomic approaches. In particular, we aim to identify gaps in detection thresholds, sample representativeness, and cross-sector data harmonization that currently hinder effective monitoring.

In parallel, this Issue places strong emphasis on mitigation strategies needed to reduce AMR emergence and transmission through the food chain. This includes

• Implementing integrated One Health surveillance systems to link human, animal, and environmental data;
• Reducing antimicrobial use in agriculture and livestock through stewardship programs, regulatory controls, and alternatives such as vaccines, bacteriophages, aptamers, prebiotics and probiotics, essential oils, among other strategies;
• Improving biosecurity and sanitation across all stages of food production and processing;
• Investing in scalable, rapid diagnostic technologies for real-time detection of resistance.

In this context, this publication aims to support the advancement of effective, science-based approaches to AMR monitoring and mitigation. Ultimately, it seeks to inform stronger risk assessment frameworks, support global coordination, and enhance the early detection and control of antimicrobial resistance in the food chain.

Dr. Joana Castro
Dr. António Machado
Guest Editors

Dr. Ricardo Oliveira
Guest Editor Assistant

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