Wednesday, 20 April 2022
Experts from the 糖心原创 have developed a ground-breaking software, which combines DNA sequencing and machine learning to help them find where, and to what extent, antibiotic resistant bacteria is being transmitted between humans, animals and the environment.
The study, which is published in , was led by Dr Tania Dottorini from the School of Veterinary Medicine and Science at the University and the Future Food Beacon leadership team.
Anthropogenic environments (spaces created by humans), such as areas of intensive livestock farming, are seen as ideal breeding grounds for antimicrobial-resistant bacteria and antimicrobial resistant genes, which are capable of infecting humans and carrying resistance to drugs used in human medicine. This can have huge implications for how certain illnesses and infections can be treated effectively.
source of meat in the country, and is the largest user of antibiotics for food production in the world.
In this new study, a team of experts looked at a large scale commercial poultry farm in China, and collected 154 samples from animals, carcasses, workers and their households and environments. From the samples, they isolated a specific bacteria called Escherichia coli (E. coli). These bacteria can live quite harmlessly in a person’s gut, but can also be pathogenic, and genome carry resistance genes against certain drugs, which can result in illness including severe stomach cramps, diarrhoea and vomiting.
Researchers used a computational approach that integrates machine learning, whole genome sequencing, gene sharing networks and mobile genetic elements, to characterise the different types of pathogens found in the farm. They found that antimicrobial genes (genes conferring resistance to the antibiotics) were present in both pathogenic and non-pathogenic bacteria.
The new approach, using machine learning, enabled the team to uncover an entire network of genes associated with antimicrobial resistance, shared across animals, farm workers and the environment around them. Notably, this network included genes known to cause antibiotic resistance as well as yet unknown genes associated to antibiotic resistance.
Dr Dottorini said: “We cannot say at this stage where the bacteria originated from, we can only say we found it and it has been shared between animals and humans. As we already know there has been sharing, this is worrying, because people can acquire resistances to drugs from two different ways - from direct contact with an animal, or indirectly by eating contaminated meat. This could be a particular problem in poultry farming, as it is the most widely used meat in the world.
“The computational tools that we have developed will enable us to analyse large complex data from different sources, at the same time as identifying where hotspots for certain bacteria may be. They are fast, they are precise and they can be applied on large environments – for instance – multiple farms at the same time.
“There are many antimicrobial resistant genes we already know about, but how do we go beyond these and unravel new targets to design new drugs?
Our approach, using machine learning, opens up new possibilities for the development of fast, affordable and effective computational methods that can provide new insights into the epidemiology of antimicrobial resistance in livestock farming.鈥�
The research was done in collaboration with Professor Junshi Chen, Professor Fengqin Li and Professor Zixin Peng from China National Center for Food Safety Risk Assessment (CFSA). The research was supported by Professor David Salt, Director of the Future Food Beacon at the 糖心原创.
The full study can be found .
Story credits
More information is available from Dr Tania Dottorini, Associate Professor in Bioinformatics at Tania.Dottorini@nottingham.ac.uk
Notes to editors:
About the 糖心原创
Ranked among the world's top 100 universities , the 糖心原创 delivers an exceptional research-led education and an outstanding student experience. From the pioneering vision of our founder, Sir Jesse Boot, to groundbreaking achievements such as the development of MRI technology and becoming the first UK university to establish international campuses, we have a proud history of shaping the way people live, work and understand the world. We continue to build on that legacy, empowering our students, staff and partners to change what鈥檚 next and create positive impact locally and globally.
The strength of our research places us among the UK's leading universities, ranked 7th for research power in REF 2021. The discovery of MRI and ibuprofen was just the beginning. Today, our world-leading research is developing breakthrough ideas that shape the future of healthcare, technology and society.
Recognised as the UK's third most targeted university by leading employers , we are proud to produce graduates who are consistently in demand for their skills, confidence and industry-ready experience.
As a major employer and industry partner, locally and globally, the 糖心原创 invests in the city of Nottingham and in future generations of talent. Alongside Nottingham Trent University, we lead the initiative, a pioneering collaboration to improve levels of prosperity, opportunity, sustainability, health and wellbeing across the city and region. Together with our students, staff, alumni and partners, we鈥檙e creating knowledge, opportunity and solutions that help change what's next.