Enrichment Testing
Aims:
The most suitable broth, conditions, and enrichment time for recovery of Salmonella and Campylobacter for metagenomic sequencing.
Plate count method & qPCR
Host DNA depletion
Aims:
Adaption of Bloomfield et al saponin-neutrase based host DNA depletion method, using alternative consumables, to reduce chicken DNA
Alternative consumables
Sample processing to remove chicken tissue
DNA extraction
Aims:
Assess the most suitable DNA extraction kit for long-read sequencing of chicken rinse samples
DNA extraction kits tested
Further testing of DNA extraction kits
Final assessment of the method
Aims:
ONT MinION sequencing run using spiked chicken rinse samples to assess the final developed method
