An Investigation into the Epidemiology and Genetic Relatedness of pig and human Clostridioides difficile isolates in Ireland

Abstract

Historically, Clostridioides difficile (C. difficile) has been associated with nosocomial diarrheal illness in older, immunocompromised patients, particularly in those on long-term antibiotics. However, cases of C. difficile infection are increasingly being reported among community and younger patients with no recent hospitalisation. Strains of C. difficile that are associated with higher virulence and more severe CDI have been found in food animals, such as pigs, which suggests the potential role for foods as a source of community-associated CDI. In addition, prophylactic antibiotics are regularly used in pig rearing, which could lead to the emergence of antimicrobial resistance. Additionally, C. difficile has also been widely isolated from the environment, particularly from soil and water. The objective of this study was to understand the recent shift in C. difficile epidemiology by exploring the impact that pigs may have on the dissemination of C. difficile. This project included a longitudinal study from birth to slaughter was conducted on pig farms in Ireland with varied levels of in-feed antibiotic use. The most prevalent strains found in pig samples are associated with more severe CDI and infections in the community. This suggests the potential for C. difficile to be transmitted through the food chain. Moreover, a whole genome sequencing analysis was carried out to investigate if there were any genetic relationships between C. difficile isolates from pigs and humans. It was clear from the results of this analysis that C. difficile sequence type 11 isolates from pigs and humans were closely related, and subsequently a large part of this study focused on characterising the genotype and phenotype of the isolates belonging to this sequence type. Additional sequence files for human C. difficile sequence type 11 isolates were obtained to elucidate if there was a relationship between pigs, different hospitals, and the environment. Resistance determinants for tetracycline were found in a high proportion of sequence type 11 C. difficile genomes. Tetracycline use in agriculture, coupled with selective pressure and international dissemination through the food chain, may explain the heightened prevalence of sequence type 11 in humans. The formation of a complex network of C. difficile isolates suggested that transmission between pigs, humans and the environment is possible. This epidemiological link highlights the necessity of a "One Health" approach, and that the dissemination of C. difficile may not be confined by geographical regions or populations. This thesis contributes valuable insights into the prevalence, characteristics, and epidemiology of C. difficile in animals and humans, and emphasises the potential implications for public health and food safety. The application of whole genome sequencing is superior to routine typing methodologies for exploring the epidemiology of C. difficile, impacting outbreak investigation, understanding phylohistory, and phylogeography of C. difficile.