A long (sequence) read: high throughput bacterial sequencing

The project will investigate Campylobacter and Salmonella isolates from diarrhoeal stool specimens by applying high throughput HMW DNA extraction and long read sequencing technologies. Sequence data will be analysed with informatic methods and interpreted by comparison with publicly available data at national and global levels to understand the local strains, mobile elements and antimicrobial resistance determinants in circulation.
The project will also address the challenge of processing stool for HMW DNA extraction prior to long read metagenomic analysis. The aim is to significantly improve the number and quality of metagenomic assembled genomes (MAGs) from Campylobacter and Salmonella positive stools over what would be achieved with short read sequences. The MAGs will provide insight into 1) the presence and genomic location of antimicrobial resistance (AMR) determinants; 2) characterisation of virulence factors; and 3) population level comparisons through strain level typing, which will indicate method viability as an option for outbreak detection.