A study of the bacterial ecology of a chocolate ingredient production environment and characterisation of Salmonella species a zoonotic food-borne bacteria of importance to this food industry

Full length 16S rRNA amplicon-mediated sequencing was used to describe and analyse the core microbiome of the swabbed samples taken from a variety of locations within this chocolate production environment. Results from this study provided a species-specific description of the core microbiome of these samples. <br>56 Salmonella isolates were chosen and analysed phenotypically and by whole-genome sequencing. Phenotypic experiments relevant to assessing their colonising potential, were conducted to characterise this selection of Salmonella.

A bioinformatics pipeline was applied to confirm species identification, identify key virulence factors, evaluate antimicrobial resistance genotypes and calculate average nucleotide identity. An analysis of the AMR genotypes detected in silico identified 19 different antimicrobial classes and which largely confirmed the AST tests carried out. Salmonella infections using two distinct host models -Galleria mellonella and mice was investigated.

Data obtained provides valuable insights into categorising different Salmonella at crucial points during the infection process, such as the onset of mortality and potential variations in susceptibility among individual larvae, arising from these infections. Subsequently, the immune responses were evaluated using ELISA for five key cytokines namely-KC, IL-6, IL-1β, IL-17, and MCP-1.<br><br><i>Thesis embargoed until 31 December 2029.</i>