ISO 23418:2022 PDF

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

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Title (English):

ISO 23418:2022

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

Document status:: Active
Format:: Electronic (PDF)
Number of pages:: 45
Publication date:: June 9, 2022
Edition:: ISO IS 23418 edition 1 version 1
ICS:: 07.100.30

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Description (English):

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.

Technical details

Technical committee: ISO/TC 34/SC 9 - Microbiology
SKU: ISO 23418:2022

Abstract

Overview

ISO 23418:2022 - Microbiology of the food chain provides general requirements and guidance for using whole genome sequencing (WGS) to type and genomically characterize bacteria associated with the food chain. Published in 2022, this standard defines minimum requirements for generating, analysing and stewarding bacterial WGS data from samples including food, animal feed, environmental surfaces and primary production. It is technology‑agnostic (applicable to current NGS platforms) and focuses on laboratory best practices, bioinformatics, metadata capture and end‑to‑end validation.

Key topics and technical requirements

End‑to‑end workflow stages: handling of bacterial cultures; axenic genomic DNA isolation; library preparation, sequencing, raw read quality assessment and storage; bioinformatic analysis; metadata capture and sequence repository deposition; and validation of the complete WGS workflow.
Laboratory operations: guidance on sample preparation, isolate handling, DNA extraction, use of controls, sequencing practices, data storage and laboratory management systems.
Bioinformatics: requirements for software and pipelines used to determine genetic relatedness, detect genes/targets, predict phenotype, and generate phylogenies. Specific analysis approaches referenced include SNP analysis, MLST (cgMLST/wgMLST) and k‑mer distance analysis.
Quality and documentation: recommended QC metrics, logging, metrics and log file retention to ensure reproducible results and transparent reporting.
Metadata and repositories: structured metadata fields, interoperability guidance (including ontology slim integration), and practices for depositing sequences in repositories to support traceability and data reuse.
Validation & verification: validation of laboratory methods, bioinformatics pipelines and the full end‑to‑end WGS workflow to demonstrate fitness‑for‑purpose and ongoing verification procedures.

Practical applications and target users

ISO 23418:2022 is intended for:

Public health and food testing laboratories performing pathogen surveillance and outbreak investigations.
Food industry quality and safety teams using WGS for environmental monitoring, source tracking and supplier verification.
Third‑party testing providers offering WGS services to food/feed companies.
Bioinformatics developers and LIMS vendors implementing metadata standards and pipeline validation.
Regulatory agencies and accreditation bodies assessing laboratory competence.

Typical applications include outbreak detection and source attribution, antimicrobial resistance and virulence gene surveillance, supply‑chain traceability, and continuous improvement of food safety controls.

Related standards (if applicable)

ISO 23418 complements other ISO microbiology and laboratory management guidance by focusing specifically on bacterial WGS processes, data stewardship and validation for the food chain. It also links practical laboratory and bioinformatics practice with metadata interoperability to support public sequence deposition and cross‑laboratory comparison.

Related standards

Mentioned in the description and other ISO standards

Abstract

Overview

Key topics and technical requirements

End‑to‑end workflow stages: handling of bacterial cultures; axenic genomic DNA isolation; library preparation, sequencing, raw read quality assessment and storage; bioinformatic analysis; metadata capture and sequence repository deposition; and validation of the complete WGS workflow.
Laboratory operations: guidance on sample preparation, isolate handling, DNA extraction, use of controls, sequencing practices, data storage and laboratory management systems.
Bioinformatics: requirements for software and pipelines used to determine genetic relatedness, detect genes/targets, predict phenotype, and generate phylogenies. Specific analysis approaches referenced include SNP analysis, MLST (cgMLST/wgMLST) and k‑mer distance analysis.
Quality and documentation: recommended QC metrics, logging, metrics and log file retention to ensure reproducible results and transparent reporting.
Metadata and repositories: structured metadata fields, interoperability guidance (including ontology slim integration), and practices for depositing sequences in repositories to support traceability and data reuse.
Validation & verification: validation of laboratory methods, bioinformatics pipelines and the full end‑to‑end WGS workflow to demonstrate fitness‑for‑purpose and ongoing verification procedures.

Practical applications and target users

ISO 23418:2022 is intended for:

Public health and food testing laboratories performing pathogen surveillance and outbreak investigations.
Food industry quality and safety teams using WGS for environmental monitoring, source tracking and supplier verification.
Third‑party testing providers offering WGS services to food/feed companies.
Bioinformatics developers and LIMS vendors implementing metadata standards and pipeline validation.
Regulatory agencies and accreditation bodies assessing laboratory competence.

ISO 23418:2022 PDF

Technical details

Abstract

Overview

Key topics and technical requirements

Practical applications and target users

Related standards (if applicable)

Related standards

Abstract

Overview

Key topics and technical requirements

Practical applications and target users

Related standards (if applicable)

Related standards

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