This document specifies the minimum requirements for generating and analysing whole genome sequencing (WGS) data of bacteria obtained from the food chain. This process can include the following stages:
a) handling of bacterial cultures;
b) axenic genomic DNA isolation;
c) library preparation, sequencing, and assessment of raw DNA sequence read quality and storage;
d) bioinformatics analysis for determining genetic relatedness, genetic content and predicting phenotype, and bioinformatics pipeline validation;
e) metadata capture and sequence repository deposition;
f) validation of the end-to-end WGS workflow (fit for purpose for intended application).
This document is applicable to bacteria isolated from:
— products intended for human consumption;
— products intended for animal feed;
— environmental samples from food and feed handling and production areas;
— samples from the primary production stage.