Microbiology of the food chain — Whole genome sequencing for typing and genomic characterization of bacteria — General requirements and guidance

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.