Researchers leverage AI for antimicrobial resistance surveillance in livestock in China

21 Aug 2023 --- Using the power of machine learning, UK-based scientists have pointed toward the potential of big data in antimicrobial resistance (AMR) surveillance in livestock production in China. Analysis of chicken farms and abattoirs in the country showed that the technology could protect livestock from microbes that are becoming resistant to antibiotics.

The research was led by Dr. Tania Dottorini, Professor of Bioinformatics at the University of Nottingham, UK. It revealed an “intricate network of correlations” between environments, microbial communities and AMR, suggesting multiple avenues to improving AMR surveillance in livestock production.

“This is an exciting moment. We are ready to invest in new AI-powered AMR integrated surveillance approaches to identify the drivers and the mechanisms underlying the insurgence and spread of AMR and new genetic variants of resistant pathogens across animals, environment, humans and food. This will be groundbreaking,” remarks Dr. Dottorini.

Over 2.5 years, the team surveyed ten large-scale chicken farms and four connected abattoirs in three provinces, covering 461 microbiomes from birds, carcasses and environments in China – one of the largest consumers of antimicrobials.

Using a magnetic bead genomic DNA extraction kit, they performed DNA extraction on feces, barn floor and outdoor soil samples.

The team surveyed ten large-scale chicken farms and four connected abattoirs in three Chinese provinces. (Image credit: University of Nottingham).Antimicrobial impact on livestock
According to the study published in Nature Food, antimicrobial use in poultry production in China is “five times” higher than the international average.

Dr. Dottorini says: “The spread of antimicrobial resistant microorganisms and AMR at the human-animal-environment level and food interface is a major global concern.”

“The transmission of AMR can take place through different routes and pathways and the food chain, either indirectly via food consumption or directly through contaminated food-animal handling and manure or fecal contamination is a relevant one.”

The research underscores that the impact of antibiotics, even at low levels, “alters and expands” the gut resistome in livestock and the microbial community can “shape antimicrobial resistance (AMR) phenotypes.”

The scientists identified 145 “potentially mobile” antibiotic resistance genes (ARGs) shared between chickens and environments across all farms.

Companies are increasingly focusing on using technology to protect livestock sustainably.

The findings show that temperature and humidity influence the core of the chicken gut microbiome.Environmental factors matter too
In many countries, chickens live in sheds without an efficient climate control system, leading to substantial temperature and humidity variations.

The findings show that temperature and humidity influence the core of the chicken gut microbiome containing “clinically high transmissible” ARGs and relevant bacteria, which correlate with antimicrobial usage.

“We have demonstrated how methodologies can be developed that can associate a wide array of microbial species and genes with observable AMR,” notes Dr. Dottorini.

She adds that her team has “assessed how those are associated with the environmental variables of temperature and humidity.”

“Next, we must consider all relevant and interconnected AMR datasets in a 360° approach, which will deepen our understanding and control of AMR spread,” she underscores.

"Metagenomic and ML approaches could be deployed to provide fast and reliable predictions of AMR outbreaks."Metagenomic sequencing- A promising tech
For efficient AMR surveillance in environmental sectors, metagenomic sequencing (MGS) shows promise. However, with few laboratories and countries currently possessing the resources and expertise to use MGS, methodologies must be “standardized and data gaps filled.”

The study states: “With further development, metagenomic and ML approaches could be deployed to provide fast and reliable predictions of AMR outbreaks, emerging pathogens and transmission routes.”

As per the WHO, antimicrobial resistance (AMR) is one of humanity’s top ten global public health threats. AMR “threatens” the effective prevention and treatment of an ever-increasing range of infections caused by bacteria, parasites, viruses and fungi.

Approximately 600 million cases of food-borne disease, resulting in approximately 420,000 deaths, occur worldwide yearly. Within this, nearly 300 million illnesses and 200,000 deaths are caused by diarrheagenic E. coli globally.

Last year, FoodIngredientsFirst shed light on a Nature study highlighting how upcycling can offset competition between livestock and aquaculture fodder production and the F&B industry.

By Insha Naureen

To contact our editorial team please email us at editorial@cnsmedia.com