The PhD
YEAR 1
Method development for metagenomic Nanopore sequencing of pathogens from retail poultry. Stages include:
Enrichment of pathogens
Host-DNA depletion
DNA extraction for Nanopore
Nanopore library preparation
YEAR 2
Application of the developed method to the poultry processing line. Sampling at different points in the processing line.
Poultry processing sampling
Changes through slaughter process
Nanopore sequencing
Data analysis - metagenomics
YEAR 3
Application of the developed method to retail samples from supermarkets.
Retail poultry sampling
Nanopore sequencing
Data analysis - metagenomics
Pathogen presence