ArticleNature food2023
Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China.
Article in Nature food, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Discovery of dietary polyphenols targeting the autoinducer-2 quorum sensing system of pathogenic bacteria.Gut microbes · 2026Article
- Age- and diet-driven assembly of the gut antibiotic resistome in humans and food-producing animals.Gut microbes · 2026Review
- Combating antimicrobial resistance through multimodal data via artificial intelligence.One health (Amsterdam, Netherlands) · 2026Review
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 2026Review
- Genomic and socioeconomic drivers of antimicrobial resistance forecast to 2050.Cell genomics · 2026Article
- Meat-Borne Bacterial Pathogen Detection: Conventional, Molecular and Emerging AI-Based Strategies.Diagnostics (Basel, Switzerland) · 2026Review
- Article
- Impact of Farm Management Practices onFoods (Basel, Switzerland) · 2026Review
- The role of gut microbiome in antimicrobial resistance transmission between companion animals and livestock: mechanisms, drivers, and One Health implications.Frontiers in microbiology · 2026Review
- From machine learning to digital twin integration for livestock production and research.Frontiers in veterinary science · 2026Review
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- The gut resistome in poultry production: microbial ecology, antibiotic use, and sustainable control approaches.Frontiers in microbiology · 2026Review
- A guide to network analysis, multi-omics integration, and applications in livestock microbiome research.World journal of microbiology & biotechnology · 2025Review
- Leveraging artificial intelligence for One Health: opportunities and challenges in tackling antimicrobial resistance - scoping review.One health outlook · 2025Article
- Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.BMC microbiology · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- What Are the Drivers Triggering Antimicrobial Resistance Emergence and Spread? Outlook from a One Health Perspective.Antibiotics (Basel, Switzerland) · 2025Review
- How AI can help us beat AMR.npj antimicrobials and resistance · 2025Review
- Article
- Next-generation sequencing applications in food science: fundamentals and recent advances.Frontiers in bioengineering and biotechnology · 2025Review
Corrections and comments
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Authors and funding
20 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.
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