Genomics of Antimicrobial Resistant Campylobacter Transmission Through UK Agri-Food Systems

and the Singleton Hospital in Swansea for providing Campylobacter isolates from human disease.We also thank industry members and farmers for providing samples from livestock and poultry, and pet owners for providing samples from backyard chickens. Lay Summary Lay SummaryCampylobacter is the most common cause of bacterial food poisoning in the UK.Although infection in humans is rarely fatal and usually resolves without treatment after 5-7 days, antibiotics may be needed for severe cases, people with a poorly functioning immune system, the young or the elderly.Disease caused by Campylobacter is a major burden to public health and causes economic loss in excess of £700 million (Daniel et al., 2020) each year in the UK.Furthermore, the problem is worsening as existing treatments for severe infections are becoming less effective with the rise of antimicrobial resistance (AMR).Indeed, Campylobacter were designated 'high priority' pathogens on the 2017 WHO watch list 1 for antimicrobial resistance (Veltcheva et al., 2025).Campylobacter has been removed from the 2024 WHO Bacterial Pathogen Priority List which may give the false impression that Campylobacter related disease or AMR has fallen.1In this study, we determined the current levels of AMR amongst Campylobacter isolated from clinical patients ('human disease isolates') in Oxfordshire, which, as part of an ongoing 22-year study, have been previously shown to mirror national trends.We also included a small number of human disease isolates from Wales.In order to improve the accuracy of methods to predict the source of human infection, we tested Campylobacter isolates cultured from potential sources that are underrepresented in national culture collections (for example, wild birds, cattle, sheep, horses, deer, free-range chicken and chicken breeder flocks).We DNA sequenced each of the Campylobacter isolates to identify genes that predict antibiotic resistance.In addition, DNA sequence data was used to improve modelling approaches to predict the sources of human infection and to assess potential risk of spread ('spillover') of antimicrobial resistant Campylobacter from agriculture to the environment.This study period covers the COVID-19 lockdowns (2020-2021), representing a natural experiment assessing the impact of restrictions affecting eating out, social gatherings and foreign travel.We continued to develop automated methods to identify antibiotic resistance genes, and to enhance typing methods to improve outbreak detection for human infection.Data were stored and analysed using PubMLST, a publicly available database which provides definitive naming systems for Campylobacter genes and variants for the global research community.Key findings from the project are that resistance to two classes of antibiotics called 'fluoroquinolones' and 'tetracycline' with different modes of action has increased amongst human disease isolates since our last study in 2015-2018.Within the Campylobacter jejuni species, there are three closely related genetic lineages that have resistance approaching 100% to these antibiotics, and further research is needed to understand their high prevalence despite significant reduction of antimicrobial use on farms.The COVID-19 lockdowns with restricted eating out and travel did not impact the numbers or genotype distribution of Oxfordshire human infection.More than 80% of human disease is predicted to come from chicken, though it was not possible to determine precise routes of infection (e.g., undercooked meat versus cross contamination in the kitchen, home prepared versus commercially prepared food and takeouts, imported versus UK meat), and further research is recommended. Executive Summary Executive SummaryCampylobacter (principally the species Campylobacter coli and Campylobacter jejuni) is the most common cause of bacterial gastroenteritis in the UK.Although human campylobacteriosis in healthy individuals is rarely fatal and usually self-limiting, the disease is a major burden to public health and causes economic loss in excess of £700 million.Campylobacter infection may also lead to sequellae such as Guillain Barré Genomics of Antimicrobial Resistant Campylobacter Transmission Through UK Agri-Food … FSA Research and Evidence Nine C. coli isolates were resistant to fluoroquinolones, tetracycline and aminoglycosides but not macrolides, and one human disease C. coli isolate was resistant to all of the antimicrobial classes tested in this study.Unlike human disease, no Agri-Food isolates were resistant to all of the antimicrobial classes tested in this study.