Genome sequencing at the Quadram Institute has helped uncover information about the UK population of Campylobacter, the most common bacterial cause of gastroenteritis.

The new study from the Food Standards Agency’s PATH-SAFE programme was led by the Ineos Oxford Institute for antimicrobial research (IOI) with the University of Oxford Department of Biology and the Moredun Research Institute. The Quadram Institute’s considerable expertise and experience in sequencing Campylobacter genomes and optimised sequencing procedures underpinned the research.

Based on genome sequence data generated by the Quadram Institute, the researchers found 4 out of 5 Campylobacter infections are associated with poultry meat. Resistance to some classes of antibiotics has also increased.

The study highlights where more research and interventions are needed, and the why it remains important that consumers practice good hygiene and thoroughly cook poultry meat before eating.

Genome sequencing and analysis indicate that resistance to some antimicrobials is increasing. These data show that more action is needed and could point to where targeted interventions would be most effective in reducing the number of cases of food poisoning caused by Campylobacter.

If you’ve ever had bacterial gastroenteritis, the chances are it was caused by Campylobacter, as these bacteria are responsible for over three times more cases of disease than all other bacteria combined. You wouldn’t be alone; Campylobacter causes around 300,000 cases of disease in the UK each year. This not only affects personal and public health, it also causes economic losses of around £700million.

For most, infection causes unpleasant but not dangerous symptoms that usually clear up within a week. Some cases however can lead to more severe, long-term conditions, and immune-compromised people, the very young or elderly may be more vulnerable. Treatment for severe cases usually relies on antibiotics, but these are becoming less effective as the bacteria develop resistance to them.

Studies and surveillance of Campylobacter’s sources and spread have helped us understand these bacteria and how they interact with their environment, and the food chain. This includes an ongoing 22-year study using samples of Campylobacter isolated from patients in Oxfordshire.

The results of this study from the University of Oxford broadly reflect the situation across the UK. This continuity over time provides a basis for comparison for a newly published survey supported by the Pathogen Surveillance in Agriculture, Food, and the Environment (PATH-SAFE) programme, which is led by the Food Standards Agency and funded by HM Treasury through the Shared Outcomes Fund.

The aims were to characterise transmission routes in the agrifood chain, from the farm to the dinner plate. and determine the current levels of antimicrobial resistance in UK Campylobacter strains, which haven’t been assessed since 2019.

This information was obtained by reading the whole genome sequence of samples of Campylobacter obtained from patients in the Oxfordshire study. The team also collected samples from farmed chickens, as well as other sources that hadn’t been well sampled before, including cattle, sheep, deer, horses, and wild birds.

Analysing these sequences identifies not just the species or strain, but also specific lineages with information about how related they are, to allow tracing of likely contamination routes. Whole genome sequencing also identifies where strains carry known genes that confer resistance against different antimicrobials.

The sequencing was handled by the Quadram Institute’s team. In total, they  generated the genome sequence of over 4,000 different Campylobacter samples, providing the data on the current situation with Campylobacter in the UK.

The findings confirm that chicken is the predominant source of human disease caused by Campylobacter, accounting for over 80% of cases. However, all of the other sources, from pet chickens to starlings and deer had potential to cause disease in humans. This demonstrates the complex ‘One Health’ nature of the Campylobacter problem, which recognises the integration of environmental, animal and human health.

Analysis of the presence of antimicrobial genes in the sequenced genomes showed that compared to the previous study resistance to two classes of antibiotics, fluoroquinolones and tetracycline, has increased in samples obtained from infected patients. The levels of resistance vary across different Campylobacter lineages. Some prevalent chicken-associated lineages showed lower AMR levels; in other closely related strains resistance to fluoroquinolones and tetracycline was close to 100%. Resistance to other antibiotics, the macrolides and aminoglycosides, has however stayed low.

The reasons for increased resistance to some antibiotics is unclear. Antimicrobial use on farms has significantly reduced since 2012, and the study’s authors recommend investigations into why resistance is persisting.

Overall this study demonstrates the value of whole genome sequencing and detailed analysis, as it provides a better picture of the spread of different Campylobacter strains, across the food chain, which will allow more targeted and effective interventions, as well as helping detect new sources.

Farmers, vets, regulatory bodies and scientists are working together to reduce the levels of contamination on chicken, and it is only through their combined efforts that progress will be made.

Consumers can also play a role in ensuring their food is safe, and the advice to them remains the same. Campylobacter is killed by thorough cooking, so poultry meats should always be properly cooked. And good hygiene practices are needed to prevent contamination from raw meat during storage and preparation.

Check the Food Standards Agency webpage for more information and advice on reducing the risk from Campylobacter in the home.

Reference: Genomics of Antimicrobial Resistant Campylobacter Transmission Through UK Agri-Food Systems, Food Standards Agency, University of Oxford, The Moredun Institute, The Quadram Institute, Frances Colles, Ben Pascoe, Kasia Parfitt, Keith Jolley, James Bray, Margaret Varga, Sophie MacKay, Alistair Witheford, Ava McCarthy Kerrigan, Madison Goforth, Alice Bradbury, Samuel Sheppard, Martin Maiden, Eleanor Watson, Scott Hamilton, David Baker, Cara-Jane Moss, Nicol Janecko. DOI: https://doi.org/10.46756/001c.147190