This research is part of the European project MASTER (Microbiome Applications for Sustainable food systems through Technologies and EnteRprise) and was led by the researchers Narciso M. Quijada (FFoQSI, now IRTA Salamanca) and Martin Wagner (FFoQSI GmbH, Vetmeduni) and the professors Avelino Álvarez-Ordoñez and José Francisco Cobo Díaz, from the University of León (Spain).
The research focuses on the resistome, the collection of genes that enable bacteria to resist the effects of antibiotics. While it was already known that the food chain can act as a transmission route for antibiotic-resistant bacteria, no study to date had been as broad and detailed as this one.
Spread of resistance genes in food
Using metagenomic sequencing techniques, the team analyzed nearly 2,000 samples from raw materials and food products (such as milk, meat, fish, cheese, and vegetables), as well as surfaces and industrial environments from over 100 European companies – including 18 facilities located in Vorarlberg and Carinthia.
The results reveal that over 70% of known antibiotic resistance genes are present across the food production chain. However, only a subset of these genes is especially prevalent, with notable resistance genes linked to tetracyclines, beta-lactams, aminoglycosides, and macrolides – antibiotic classes that are key to treating human and animal infections. The analysis also identified the main bacterial carriers of these genes, many of which belong to the ESKAPEE group – well known for their role in hard-to-treat hospital infections – including Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae. Other species detected include Staphylococcus equorum and Acinetobacter johnsonii. One particularly significant finding is that nearly 40% of these genes are associated with plasmids – mobile genetic elements that can facilitate gene transfer between bacteria, increasing the risk of resistance spread.
The study also provides evidence on how specific industrial processes and manufacturing conditions can influence the presence and transmission of these genes, opening up new opportunities for improving food production systems. The researchers emphasize that these findings are crucial for designing more effective antibiotic usage strategies in food production and for informing policy decisions to combat the growing challenge of antimicrobial resistance.
The article “The food-associated resistome is shaped by processing and production environments” by Quijada et al. was published in Nature Microbiology.
Scientific contact:
Univ.-Prof. Dipl.ECVPH Dr.med.vet. Martin Wagner
Klinisches Department für Nutztiere und Sicherheit von Lebensmittelsystemen
Veterinärmedizinische Universität Wien (Vetmeduni)
Martin.Wagner@vetmeduni.ac.at