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BS EN ISO 23418:2022

BS EN ISO 23418:2022

$198.66

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

Published By Publication Date Number of Pages
BSI 2022 58
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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.

PDF Catalog

PDF Pages PDF Title
2 undefined
5 European foreword
Endorsement notice
10 Foreword
11 Introduction
12 1 Scope
2 Normative references
3 Terms and definitions
17 4 Principle
4.1 General
4.2 Laboratory operation: sample preparation and sequencing
18 4.3 Bioinformatics analysis
4.3.1 General
4.3.2 SNP analyses
4.3.3 MLST analyses
4.3.4 Kmer distance analysis
4.4 Metadata formats and sequence repository deposition
19 4.5 Validation and verification of WGS workflow
5 General laboratory guidance
5.1 Bacterial isolation and DNA extraction
5.2 Laboratory environment
5.3 Standard operating procedures and nonconforming work
5.4 Laboratory information management system
5.5 Laboratory competence
20 6 Laboratory operations
6.1 Sample preparation and storage
6.2 Bacterial isolates
6.3 DNA isolation
6.4 Library preparation and sequencing
6.4.1 Library preparation
21 6.4.2 DNA sequencing
6.4.3 Use of controls
6.4.4 Assessing raw read data quality
6.4.5 Sample and data storage and retention
22 7 Bioinformatic data analysis
7.1 Requirements for software and bioinformatic pipelines used for data analysis
7.2 Logging and documentation
7.3 Quality assessments
23 7.4 SNP analyses
7.5 MLST analyses (cgMLST and wgMLST)
24 7.6 Target gene detection
7.7 Phylogenetic tree or dendrogram generation
7.8 Metrics and log files
7.9 Interpreting and reporting the results of bioinformatics analyses
7.9.1 Interpreting results from bioinformatics pipelines
25 7.9.2 Reporting genomic analysis results
8 Metadata
8.1 General
8.2 Metadata interoperability and future-proofing
8.2.1 General
8.2.2 Ontologies
8.2.3 ISO WGS Slim
26 8.3 Formatting metadata using this document
8.4 Metadata associated with sample collection
27 8.5 Metadata associated with the isolate
28 8.6 Metadata associated with the sequence
30 9 Sequence repositories
31 10 Validation and verification
10.1 Validation
10.1.1 General
32 10.1.2 Validation of laboratory operations
10.1.3 Validation of the bioinformatics pipeline
33 10.1.4 Validation of the end-to-end workflow
10.2 Verification
10.2.1 General
10.2.2 Verification of laboratory operations
10.2.3 Verification of the bioinformatics pipeline
35 Annex A (informative) Development of quality metrics and use of controls
40 Annex B (informative) Laboratory contact information fields
42 Annex C (informative) Geographic location of sample collection fields
43 Annex D (informative) Isolate passage history fields
44 Annex E (informative) Antibiogram results and methods fields
46 Annex F (informative) Virulence factor detection and methods fields
47 Annex G (informative) Sequence quality control metrics
48 Annex H (informative) Metadata specification
51 Annex I (informative) Instructions for ontology slim integration by software developers
55 Bibliography

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BS EN ISO 23418:2022
$198.66