The foodborne emergence and epidemiology of Clostridium difficile in Ireland

The purpose of this project was to investigate the prevalence and virulence of Clostridioides difficile in the food chain in Ireland and to understand its potential as a foodborne pathogen. Firstly, this thesis investigated the prevalence of C. difficile at the farm, abattoir and retail level. Results showed decreasing prevalences from farm (32%) to retail (3%). However, all isolates were toxigenic and high concentrations of the bacterium (4.3-6.8 log10 CFU/g) were detected in ready to eat foods. A more in-depth characterisation of the food chain isolates was then carried out. It determined the large prevalence of the hypervirulent ribotype 078 and a variant (RT078/4), as well as multidrug resistance to 3-5 antibiotics in 65% of the tested isolates. The study also investigated C. difficile’s spore viability in meats, salads and dairy products after chilling and cooking temperatures. It concluded that spore concentrations remain intact after chilled or frozen storage and/or sous vide cooking, however a treatment of 40 min at 80°C in spiked meats resulted in statistically significant reductions in spore concentrations (p<0.05) of 1.0-1.5 log10 CFU/g. In addition, C. difficile spore germination and outgrowth in consumer foods was studied at 25°C and 37°C for 10 days. Results showed spore germination and growth in chicken at 37°C, with a maximum growth of 2.5 log10 CFU/g by day 6. Due to the high prevalence of these bacteria found in leafy vegetables, the prevalence and toxigenicity of C. difficile recovered from spinach fields in Ireland was further investigated. C. difficile was detected in 3.3% of spinach and 10% of soil samples collected and toxigenic ribotypes were detected in both sources, including RT078 and RT126 in spinach leaves. Moreover, genomic characterisation showed a broad range of antibiotic resistance and toxin genes. Finally, this thesis examined the chemical and microbial factors that might influence C. difficile’s prevalence in soil. It was concluded that, in our study, chemical and physical parameters of the soil had a higher impact than the microbial factors on the prevalence of C. difficile.