The food processing chain may be more important in shaping the microbial contaminants on food than variations in on-farm production practices.

Antimicrobial resistance (AMR) is a major threat to our ability to treat common infections. Bacteria develop resistance from exposure to antibiotics and other selection pressures, through the emergence of specific mutations or spread of AMR genes.

This is a problem because AMR genes can move between bacteria, potentially integrating into the genomes of our own gut microbes, or infectious pathogens, making them much harder to treat.

To address the rise of AMR, more controls have been introduced on the use of antibiotics.

Since 2006, UK and EU farmers have not been able to use antibiotics routinely to promote the growth of livestock. Since then, antibiotic use in UK farming has dropped overall, with a 57% decrease in the sales of antibiotics for use in animals between 2014 and 2024 reported by the UK Veterinary Medicines Directorate.

Against this backdrop, the amount of antibiotic exposure animals receive may be influenced by the farming method. Organic livestock production only allows antibiotic use for individual animals to address a specific need, and UK organic regulations prevent metaphylactic antibiotic use as employed in conventional farming, where an entire group of animals can be given antibiotics if a few individuals show signs of a disease.

This, along with differences in stocking density and where livestock are housed and raised, influence exposure to microbes and antibiotics, which can impact the microbial community on the produce.

Various studies have found more AMR genes in bacteria on conventionally produced foods, compared to other production methods, but this isn’t consistent and some studies find no difference at all.

Most research has been concentrated at sampling livestock at slaughter, but the food processing chain, from farm to when the consumer buys it, introduces many different ways in which the microbial community on the food might be affected.

To date, it’s been an open question of whether or not the different food production methods affect the diversity of microorganisms and their antimicrobial resistance, on the food consumers buy in shops and supermarkets.

To answer this question, the Quadram Institute launched a project, led by Sam Mellor, a Norwich Research Park Biosciences Doctoral Training Partnership PhD student funded jointly by the UKRI Biotechnology and Biological Sciences Research Council and the Food Standards Agency.

The project team sampled over 220 pork, beef, lamb, chicken, salmon and leafy greens from retail stores in the UK between 2018 and 2024 and collected the microbial DNA from them.

This DNA was then sequenced to produce a metagenome, which is the total collection of genetic material from a community of organisms. Sequencing like this can uncover the diversity of organisms present and also identify genes carried by those organisms that make them resistant to antimicrobials.

The study relied on being able to discern the microbial DNA from the otherwise overwhelming amount of DNA of the food itself. A method developed in the Quadram Institute by Dr Samuel Bloomfield, that depletes this host DNA, greatly increased the resolution for studying the bacterial DNA.

The team then analysed the composition of the microbiomes on the foods. These microbial communities were predominantly made up of food spoilage bacteria, such as Pseudomonas and Lactococcus, likely to have been picked up or increased during processing, rather than on the farm.

For most of the food commodities, the samples from the different production systems had similar microbial communities. There were some bacteria that were more abundant in either intensive or extensive production that could warrant further analysis, but the majority of these represented only a fraction of the total bacterial population contaminating foods. Overall, the study found that the production method was not a major driver of the microbial diversity on food at the point of retail.

The same was found to be true when the researchers looked at the presence of antimicrobial resistance genes. Neither the diversity nor abundance of AMR genes were associated with production method. This supports the suggestion that food processing or other post farm production practices shape the composition of microbiome on retail food, while the influence of on-farm practices is limited.

“Our findings support the suggestion that food processing, post farm production, shapes the composition of microbiome on retail food, while the influence of on-farm practices is limited” said Sam Mellor from the Quadram Institute.

This survey doesn’t suggest any immediate risks, however the vast majority of the products tested were farmed in the UK.

“There are unanswered questions about the levels of antimicrobial resistance on imported food. Animal husbandry and antimicrobial use in agriculture, as well as organic and free-range farming regulations can vary substantially between different countries, so similar investigations comparing food production abroad may yield different results” commented Sam Mellor.

“We hope that this study could provide a framework for such studies that can be used to extend our understanding of the drivers of AMR on retail foods.”

Reference: Associations between food production methods, antimicrobial resistance gene burden and diversity of microorganisms on retail food using metagenomics, Sam Mellor, Samuel Bloomfield, Raphaëlle Palau, George Savva, John Wain and Alison Mather, Microbial Genomics, DOI: 10.1099/mgen.0.001705