The molecular epidemiology and ecology of Campylobacter in the UK

Campylobacter is a major Public Health problem in the UK, responsible for more than 50,000 recorded cases of gastroenteritis annually. This thesis examines the molecular epidemiology of clinical campylobacteriosis in Oxfordshire over a one-year period, considering the distribution of Campylobacter jejuni and Campylobacter coli clonal complexes, the relationship between clonal complex and ciprofloxacin resistance and the relationship between travel-associated campylobacteriosis and Campylobacter genotype. The clinical picture is related back to the molecular epidemiology of Campylobacter isolated from retail poultry and the prevalence of resistance to antimicrobial substances. A widespread but non-random distribution of antibiotic resistance phenotypes among Campylobacter Sequence Types is indicative of the importance of horizontal transfer of resistant genes as well as clonal expansions of resistant genotypes. Continuing backwards along the food production chain the molecular epidemiology of Campylobacter amongst livestock and farmyard commensals is considered. A study of Campylobacter in rats reveals considerable genetic diversity, and three distinct clades of 'rat-associated' Campylobacter. The use of whole genome sequence data here allows a higher resolution study of the population structure of Campylobacter, identifying a major split in the ST-45 clonal complex. The potential to use next generation sequence data to improve the attribution of clinical campylobacteriosis cases to animal host source is investigated. Whole genome sequencing reveals that there is insufficient differentiation between populations of Campylobacter isolated from farm animals. Throughout this thesis data from conventional MLST and from next generation sequencing of whole genomes are compared and the relative benefits considered.