Guidelines for Dry-Lab Quality Control Metrics and Acceptance Thresholds in Short-Read WGS of zoonotic and indicator bacteria

Foreword

The working group (WG) has been established by the European Commission with the aim to promote the use
of NGS across the EURLs' networks, build NGS capacity within the European Union (EU) and ensure liaison
with the work of the EURLs and the work of EFSA and ECDC on the NGS mandate sent by the Commission.
The WG includes all the EURLs operating in the field of the microbiological contamination of food and feed
and this document represents a deliverable of the WG and is meant to be diffused to all the respective
networks of National Reference Laboratories (NRLs).

Intro

Whole genome sequencing (WGS) enables rapid, cost-effective and high-throughput
characterisation of microbial genomes. It is increasingly used in diagnostics and surveillance of
foodborne and indicator bacteria. Common applications of WGS include (i) species identification,
(ii) antimicrobial resistance (AMR) gene and associated mutation detection, (iii) virulence gene
detection, (iv) serotype-associated genes detection and (v) outbreak investigations.

To ensure reliability and cross-laboratory comparability, implementation of standardised WGS
protocols and rigorous quality control (QC) are essential. Relevant standards for both wet and dry
components of WGS, as well as metadata management are included in EN ISO 23418:2022
“Microbiology of the Food Chain – WGS for typing and genomic characterization of bacteria -
General requirements and guidance”, ISO 20397-1:2022 “Biotechnology – Massively parallel
sequencing, Part 1: Nucleic acid and library preparation” and ISO 20397-2:2021 “Biotechnology –
Massively parallel sequencing, Part 2: Quality evaluation of sequencing data”.

This guidance document focus on dry lab QC for short-read WGS data of zoonotic and indicator
bacteria and is intended to support National Reference Laboratories (NRLs) and official laboratories
by defining QC criteria and accepted thresholds to the zoonotic and indicator bacteria covered by
the European Union Reference Laboratories (EURLs) that are part of the Inter EURLs Working Group
on NGS (Inter-EURLs WG on NGS). It describes measurable parameters for the dry-lab component
and explains how their values affect downstream analyses and reporting.

This document serves as a reference for laboratories to enhance their WGS data quality and,
consequently, the accuracy of zoonotic and indicator bacteria identification and characterisation.