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

Scientists at the University of Nottingham are close to understanding how bacteria, such as E. coli and Salmonella enterica, share the genetic material that makes them resistant to antibiotics.

Antimicrobial resistance (AMR), the ability of organisms to resist treatment with antibiotics and other antimicrobials, is one of the most threatening problems globally today. Livestock farms, their surrounding environments, and livestock-derived food products have been highlighted as potential sources of resistant infections for animals and humans.

In livestock production, the misuse and excessive use of broad-spectrum antimicrobials administered to reduce production losses is a known major contributor to the increase and spread of AMR.

In this latest study, scientists make a significant contribution by demonstrating that different species of bacteria, coexisting within the same microbial community (e.g., in the chicken intestine), are capable of sharing genetic material associated with AMR and end up implementing similar methods. resistance mechanisms. This finding has important implications as it affects our understanding of AMR and poses further challenges for implementing monitoring and processing/control solutions.

This study, published in Natural communicationsexamines two important bacteria found in food animals: Escherichia coli and Salmonella enterica, both of which have high levels of drug resistance, are common in agricultural settings, have high levels of transmissibility to humans, and cause poisoning food.

The research is a collaboration between experts from the University’s School of Veterinary Medicine and Sciences, China’s National Center 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 study’s lead researcher. She said: “These species of bacteria can share genetic material both within and potentially between species, supporting the spread of AMR. This is why understanding to what extent these bacteria within the same environment and, above all, the same host, can co-evolve and share their genome could help in the development and more effective treatments to combat AMR.

The team collected 661 isolates of E. coli and Salmonella bacteria from chickens and their environments at 10 Chinese chicken farms and four slaughterhouses over a period of two and a half years. They performed large-scale analysis using conventional microbiological DNA sequencing and data mining methods powered by machine learning.

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

Dr Dottorini says: “The emergence and spread of AMR in livestock is a complex phenomenon resulting from a tangled network of interactions occurring at multiple spatial and temporal scales and involving exchanges between bacteria, animals and humans across a multitude of connected microbial environments.

“It is crucial to invest in data mining and machine learning technologies capable of processing large-scale heterogeneous data to study AMR, especially when considering the interaction between cohabiting bacteria, in particularly in ecological environments where community-driven resistance selection occurs.

“Overall, this work also demonstrated that investigating individual bacterial species in isolation may not provide a sufficiently comprehensive picture of the mechanisms underlying the occurrence and spread of AMR in livestock production. , potentially leading to an underestimate of the threat to human health.”