Abstract

Food contamination with pathogens is a major burden on our society. In the year 2019, foodborne pathogens caused 137 hospitalisations in Germany (BVL 2019). Globally, they affect an estimated 600 million people a year and impact socioeconomic development at different levels. These outbreaks are mainly due to Salmonella spp. followed by Campylobacter spp. and Noroviruses, as studied by the Food safety - World Health Organization (WHO).

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• What are the preprocessing steps to prepare ONT sequencing data for further analysis?
• How to identify pathogens using sequencing data?
• How to track the found pathogens through all your samples datasets?

Learning Objectives

• Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore data
• Preprocess the sequencing data to remove adapters, poor quality base content and host/contaminating reads
• Perform taxonomy profiling indicating and visualizing up to species level in the samples
• Identify pathogens based on the found virulence factor gene products via assembly, identify strains and indicate all antimicrobial resistance genes in samples
• Identify pathogens via SNP calling and build the consensus gemone of the samples
• Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees and heatmaps