Scientists discover why chicken farms are a breeding ground for antibiotic resistant bacteria

Friday, 05 January 2024

Scientists from the University of Nottingham are one step closer to understanding how bacteria, such as E. coli and Salmonella enterica, share genetic material which makes them resistant to antibiotics.

Antimicrobial resistance (AMR), the capability of organisms to be resistant to treatment with antibiotics and other antimicrobials, is now one of the most threatening issues worldwide. Livestock farms, their surrounding environments and food products generated from husbandry, have been highlighted as potential sources of resistant infections for animals and humans.

In livestock farming, the misuse and overuse of broad-spectrum antimicrobials administered to reduce production losses, is a major known contribution to the large increase and spread of AMR.

In this latest study, scientists provide a significant contribution to demonstrating that different bacteria species, co-existing within the same microbial community (for example, within the chicken gut), are able to share AMR-associated genetic material and end-up implementing similar resistance mechanisms. The discovery has important implications as it affects our understanding of AMR and poses further challenges to the implementation of solutions for surveillance and treatment/control.

This study, published in Nature Communications, looks at two important bacteria found in food animals - Escherichia coli and Salmonella enterica, which both show high levels of drug resistance, are common in farming settings, have high levels of transmissibility to humans and cause food poisoning.

The research is a collaboration between experts from the University’s School of Veterinary Medicine and Science, the China National Centre for Food Safety Risk Assessment, New Hope Liuhe Group Ltd in China and Nimrod Veterinary Products Limited.

Dr Tania Dottorini, from the School of Veterinary Medicine and Science at the University of Nottingham, is the lead researcher on the study. She said: “These species of bacteria can share genetic material both within, and potentially between species, a way in which AMR is spread. That is why understanding the extent to which these bacteria within the same environment, and importantly, the same host, can co-evolve and share their genome could help the development and more efficient treatments to fight AMR.”

Dr Tania Dottorini

The team collected 661 E. coli and Salmonella bacteria isolates from chickens and their environments in 10 Chinese chicken farms and four abattoirs over a two-and-a-half-year period. They carried out a large-scale analysis using conventional microbiology DNA sequencing and data-mining methods powered by machine learning.

This is the first study of its kind where the genomic content of two bacteria species is characterised over such a large scale, using samples collected from the same animals, at the same time and from real-world settings (farms and abattoirs). The main findings indicate that E. coli and Salmonella enterica co-existing in the chicken gut, compared to those existing in isolation, feature a higher share of AMR-related genetic material, implement more similar resistance and metabolic mechanisms, and are likely the result of a stronger co-evolution pathway.

Dr Dottorini says: “The insurgence and spread of AMR in livestock farming is a complex phenomenon arising from an entangled network of interactions happening at multiple spatial and temporal scales and involving interchanges between bacteria, animals and humans over a multitude of connected microbial environments. microbial community.

“Investing in data mining and machine learning technologies capable to cope with large scale, heterogenoeus data is crucial to investigate AMR , in particular when considering the interplay between cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.

“Overall, this work has also demonstrated that the investigation of individual bacterial species taken in isolation may not provide a sufficiently comprehensive picture or the mechanisms underlying insurgence and spread of AMR in livestock farming, potentially leading to an underestimation of the threat to human health.”
Dr Tania Dottorini, from the School of Veterinary Medicine and Science at the University of Nottingham

Story credits

The Full study can be found here.

More information is available from Tania Dottorini at the University of Nottingham in the School of Veterinary Medicine and Science at

Charlotte Anscombe - Media Relations Manager - Faculty of Medicine and Health Sciences
Phone: 0115 748 4417

Notes to editors:

About the University of Nottingham

Ranked 32 in Europe and 16th in the UK by the QS World University Rankings: Europe 2024, the University of Nottingham is a founding member of the Russell Group of research-intensive universities. Studying at the University of Nottingham is a life-changing experience, and we pride ourselves on unlocking the potential of our students. We have a pioneering spirit, expressed in the vision of our founder Sir Jesse Boot, which has seen us lead the way in establishing campuses in China and Malaysia - part of a globally connected network of education, research and industrial engagement.

Nottingham was crowned Sports University of the Year by The Times and Sunday Times Good University Guide 2024 – the third time it has been given the honour since 2018 – and by the Daily Mail University Guide 2024.

The university is among the best universities in the UK for the strength of our research, positioned seventh for research power in the UK according to REF 2021. The birthplace of discoveries such as MRI and ibuprofen, our innovations transform lives and tackle global problems such as sustainable food supplies, ending modern slavery, developing greener transport, and reducing reliance on fossil fuels.

The university is a major employer and industry partner - locally and globally - and our graduates are the second most targeted by the UK's top employers, according to The Graduate Market in 2022 report by High Fliers Research.

We lead the Universities for Nottingham initiative, in partnership with Nottingham Trent University, a pioneering collaboration between the city’s two world-class institutions to improve levels of prosperity, opportunity, sustainability, health and wellbeing for residents in the city and region we are proud to call home.

More news…

Media Relations - External Relations

The University of Nottingham
YANG Fujia Building
Jubilee Campus
Wollaton Road
Nottingham, NG8 1BB

telephone: +44 (0) 115 951 5798