Antimicrobial resistance in the food chain: bridging knowledge gaps for effective detection and control

• Author(s): Gomes, Emílio ; Mesquita, Tomás Gonçalves ; Serra, Patrícia ; Araújo, Daniela ; Almeida, Carina ; Machado, António ; Oliveira, Ricardo ; Castro, Joana
• Date: 2026
• Persistent ID: https://hdl.handle.net/1822/100920
• Origin: RepositóriUM - Universidade do Minho
• Project/scholarship: info:eu-repo/grantAgreement/other/Concurso de Projetos de I&D em Todos os Domínios Científicos - 2022 - ICDT/2022.07654.PTDC/other; info:eu-repo/grantAgreement/other/Concurso de Projetos de IC&DT em Todos os Domínios Científicos 2023/2023.16313.ICDT/other; info:eu-repo/grantAgreement/other/Concurso de avaliação no âmbito do Programa Plurianual de Financiamento de Unidades de I&D (2017/2018) - Financiamento Base/UIDB/00511/2020/other; info:eu-repo/grantAgreement/other/Concurso de avaliação no âmbito do Programa Plurianual de Financiamento de Unidades de I&D (2017/2018) - Financiamento Programático/UIDP/00511/2020/other; info:eu-repo/grantAgreement/other/Concurso para Atribuição do Estatuto e Financiamento de Laboratórios Associados (LA)/LA/P/0045/2020/other
• Subject(s): AMR mitigation strategies; antimicrobial resistance; food chain; food safety; One Health; whole genome sequencing
• Document Type: Journal article
• Language: English
• Contributor(s): Universidade do Minho

Description

Antimicrobial resistance (AMR) poses a critical global public health threat, with the food chain serving as a significant transmission route connecting animals, environment, and humans. This review adopts a One Health perspective to analyze the key drivers of AMR dissemination across animal agriculture, aquaculture and food processing. We evaluate detection methodologies, contrasting the regulatory gold standard of culture-based phenotypic testing with rapid molecular advancements, including Whole Genome Sequencing (WGS), metagenomics, and emerging CRISPR-Cas diagnostics. While molecular tools offer unprecedented speed and resolution, challenges such as matrix interference, the viable but non-culturable (VBNC) state, and the genotype-phenotype disconnect remain. Finally, integrated mitigation strategies are also described, ranging from on-farm antimicrobial stewardship and innovative biofilm control to consumer hygiene practices. It is essential to bridge the technical and regulatory gaps in AMR surveillance in order to develop effective interventions and ensure a safer food system. © 2026 by the authors.