Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.

Health care and neoliberalism in Ireland: withholding the gift and corrupting the social contract

The health of a nation tells much about the nature of a social contract between citizen and state. The way that health care is organised, and the degree to which it is equitably accessible, constitutes a manifestation of the effects of moments and events in that country's history. Using four case studies, this thesis uses a historical genealogical approach to explain the evolution of Ireland's particular version of health care provision. The total social fact of the gift relationship, central to all human relations, will be used to form a theoretical and conceptual framework on which to build an analysis of Ireland's health and welfare conditions. Additionally, social contract theory will enable an examination of the role of solidarity in relation to social expectations around health care provision. Through the analysis of these cases, the complex matrix of the influential forces that have shaped current conditions are exposed and revealed, enabling a critical understanding of the extent of acquiescence to the inequitable system that arguably exists. The vulnerability of citizens in need of care to the external and global effects of market forces and neoliberalism, therefore, becomes central to any argument for state-provided health and welfare. The hegemony of such forces can be seen to influence the manner in which the idea of individual self-reliance, in place of collective solidarity, is conceptualised and subsequently infiltrated into a range of aspects of the social world. For example, the particular discourse of the market and of economic concerns succeeds in shaping understandings of responsibilities around central areas of health and welfare. Similarly the 'possessor principle' can be seen to be misplaced within the context of health and social care, but yet has become normalised within this discourse. Within this matrix of complex influencing factors, the welfare state struggles to impose a balance between market values and social values. Responsibilities of the state to support and compensate its citizens for the ills of the market have become devalued, as the core values of classical liberalism have become distorted beyond recognition, leaving instead bare neoliberal concerns. This thesis traces the genealogical origins of this transition within the recent history of Irish health care and thereby reveals the embedding of individualism in place of solidarity, the on going reneging of the social contract and the corruption of the gift relationship.

Diphtheria, the public health response and the origins of the childhood immunisation programme in Ireland

In common with most countries, the childhood immunisation programme in Ireland was founded on a successful public health response to diphtheria. The success of the antidiphtheria public health intervention in Ireland has meant that no case of the disease has been recorded in the state for almost fifty years. This is a significant achievement considering that diphtheria continues to appear annually in many European states, albeit in much reduced numbers on former years. For parents and children of nineteenth, and early twentieth-century Ireland, diphtheria represented the ‘most dreaded disease of childhood’, however, for their modern day counterparts diphtheria is no more than an obscure disease mentioned in leaflets promoting the benefits of childhood immunisation. In Ireland, diphtheria has been consigned to history, and so too have the horrors and mass fatalities once associated with it. But how was this achieved? Was active immunisation received with open arms by public health authorities, the wider medical community, and the general public? This study tackles these questions by undertaking the first historical examination of the issues which underpin the origins of active immunisation in Ireland. It explores the driving forces that shaped the national childhood immunisation programme, and those that opposed them. In addition, it examines the complex social implications attendant on the introduction of this mass public health intervention in an Irish context.