To date, there have been question marks over whether different food production methods, such as organically farmed, free range, and more conventionally intensive methods affect food’s diversity of microorganisms and their antimicrobial resistance (AMR).
A new study led by the Quadram Institute has now found some very interesting results.
What is antimicrobial resistance (AMR)?
Bacteria develop resistance from exposure to antibiotics and other selection pressures through the emergence of specific mutations or the spread of AMR genes.
AMR genes can move between bacteria, potentially integrating into the genomes of our own gut microbes, or infectious pathogens.
This is presents a major risk to public health as it threatens our ability to treat common infections.
How microbial communities on produce is influenced
In 2006, the UK banned the use of antibiotics to encourage growth among livestock.
Since then, antibiotic use in UK farming has seen a sharp drop, with the UK Veterinary Medicines Directorate reporting a 57% fall in the sale of antibiotics for use in animals between 2014 and 2024.
Against this backdrop, the amount of exposure animals receive may be impacted by the farming methods. For example, organic livestock production only allows antibiotic use for individual animals to address a specific need, whereas conventional farming can employ more blanket methods, wherein an entire group of animals are given antibiotics if just a handful show signs of disease.
This, alongside the differences in stocking density and where livestock is housed and raised, affects exposure to microbes and antibiotics, which in turn shape the microbial community on the produce.
While previous studies have found more AMR genes in bacteria on conventionally produced foods compared to other methods, the team at the Quadrum Institute say the results have been inconsistent – with some research showing no difference at all.
Most studies have been concentrated at sampling livestock at slaughter. However, the food processing chain – from farm to retail shelf, can also influence the microbial community in many ways.
What did the new research uncover?
Led by Quadram Institute in collaboration with the UKRI Biotechnology and Biological Sciences Research Council and the Food Standards Agency, researchers have now discovered that consumers’ exposure to AMR microorganisms on UK retail meat and leafy greens is not impacted by the production methods.
In other words, it doesn’t matter if the food was farmed organically or produced through more traditional intensive methods.
For the study, the team sampled more than 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’ – a total collection of genetic material from a community of organisms. This method can uncover the diversity of organisms present and identify genes carried by those organisms that make them resistant to antimicrobials.
Using a method developed by the lead researcher, Dr Samuel Bloomfield of The Quadram Institute, which depletes the host DNA, the team were able to distinguish between the microbial DNA from the food DNA. This greatly increased the resolution for studying the bacterial DNA.
The researchers then examined 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.
The results showed that for most of the food commodities, the samples from different production systems shared similar microbial communities; showing that, overall, the production method was not a major driver of the microbial diversity on food at the point of retail.
When researchers looked at the presence of AMR genes, they found the same. Diversity and abundance of such genes were not linked to production methods.
“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 Mellor.
As this study focused on UK food, Mellor added that further research is needed related to imported produce: “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.”
He hopes the results of this project will lead to a framework for such studies that can be used to extend our understanding of the drivers of AMR on retail foods.