Superbugs on your plate: how antimicrobial resistance spreads through food

From the moment raw ingredients are harvested to when you cook and eat a meal, an invisible process is taking place: the growth of antimicrobial resistance. This happens when microorganisms (bacteria, fungi, and so on) stop responding to antibiotics or disinfectants. Often described as a “silent pandemic”, antimicrobial resistance is currently one of the greatest threats to global health. Antimicrobial compounds are routinely used in intensive livestock farming and aquaculture, both to prevent disease among animals kept in overcrowded conditions and to promote faster growth. While this latter practice is declining thanks to food hygiene and safety legislation, their widespread use has created the ideal environment for resistant microorganisms to emerge and proliferate. This growing trend is highlighted by recent data from the European Food Safety Authority. Their March 2025 report looked at the resistance developed by zoonotic bacteria (which can be transmitted from animals to humans) and indicator bacteria (those used to indirectly study food hygiene and safety). The report highlights high levels of resistance to ciprofloxacin, an antibiotic commonly used in human medicine, in bacteria such as Campylobacter coli. This microorganism is found in both humans and livestock, particularly chickens, turkeys, calves and fattening pigs. Similar resistance has also been detected in certain strains of Salmonella. These findings indicate the urgent need to raise awareness, and to use antimicrobials more cautiously. Read more: Gutter to gut: How antimicrobial-resistant microbes journey from environment to humans Superbugs on your plate Resistant “superbugs” are capable of spreading through a number of vectors – including irrigation water, soil, agricultural produce and processing plants – before ending up on our dinner tables. Recognising this web of connections between the environment, livestock and people is the first step towards devising effective strategies to ensure food safety and global health. A European study, published in Nature Microbiology in June 2025, analysed more than 2,000 samples, including raw materials (such as fresh meat), finished products (such as cheese) and work surfaces from various food industries. During food’s journey from field to fork, more than 70% of antimicrobial resistance – including resistance to antibiotics used in human and veterinary medicine such as penicillin and streptomycin – is transferred between the bacteria present. The study identified the ESKAPE group of bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) as the primary cause of this transmission. The main vehicle of transmission is thought to be S. aureus, as it is present on the skin and mucous membranes of around one third of the population, making it a significant factor in food handling. Exchanging genes So how are the “instructions” for surviving antibiotics or disinfectants shared among microorganisms? The answer is simple: by exchanging genes, as easily as people might swap football cards. This is known as horizontal gene transfer, and works through one of three different mechanisms. In the first, known as transformation, the bacterium takes up free genetic material directly from the environment, much like picking up a note from the ground and putting it in your pocket. Through the second, known as transduction, the gene is transported via a bacteriophage, a bacterial virus that acts like a messenger delivering a letter. And finally, there is conjugation, where two bacteria come into physical contact and, like two computers connected by a cable, pass information directly from one to the other. Read more: Natural GM: how plants and animals steal genes from other species to accelerate evolution As if that weren’t enough, the food industry also faces the problem of polymicrobial biofilm formation. These are clusters of microorganisms adhering to surfaces that are highly resistant to external agents and conventional cleaning and disinfection methods. These biofilms can harbour “persister” species which, despite being unable to multiply, endure over time and constitute real sources of contamination. They can also facilitate the transfer of resistance genes. Biofilms therefore pose a major challenge for current control systems. New technologies in food processing and preservation focus, in part, on combating them through the use of ozone, UV-C light, metallic nanoparticles, cold plasma or even bacteria-specific viruses. Read more: ‘Every blast is an open wound’: how the chaos of war breeds deadly superbugs that spread around the world Plant-based solutions Research focusing on the search for plant-based antimicrobials, such as essential oils, offers a complementary strategy for biofilm control and food preservation. Notable among these compounds are carvacrol (found in oregano and thyme), peppermint essential oil and citral (derived from citrus fruits). In general, these agents are less toxic than conventional antimicrobials, and are less likely to lead to the development of resistance. By effectively reducing biofilms and eliminating the bacteria that form them, they could help to curb the use of antimicrobials and the rise in resistance to these compounds. 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