{"id":401720,"date":"2024-10-20T04:57:43","date_gmt":"2024-10-20T04:57:43","guid":{"rendered":"https:\/\/pdfstandards.shop\/product\/uncategorized\/bs-en-iso-234182022\/"},"modified":"2024-10-26T08:47:13","modified_gmt":"2024-10-26T08:47:13","slug":"bs-en-iso-234182022","status":"publish","type":"product","link":"https:\/\/pdfstandards.shop\/product\/publishers\/bsi\/bs-en-iso-234182022\/","title":{"rendered":"BS EN ISO 23418:2022"},"content":{"rendered":"

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: \u2014    products intended for human consumption; \u2014    products intended for animal feed; \u2014    environmental samples from food and feed handling and production areas; \u2014    samples from the primary production stage.<\/p>\n

PDF Catalog<\/h4>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
PDF Pages<\/th>\nPDF Title<\/th>\n<\/tr>\n
2<\/td>\nundefined <\/td>\n<\/tr>\n
5<\/td>\nEuropean foreword
Endorsement notice <\/td>\n<\/tr>\n
10<\/td>\nForeword <\/td>\n<\/tr>\n
11<\/td>\nIntroduction <\/td>\n<\/tr>\n
12<\/td>\n1 Scope
2 Normative references
3 Terms and definitions <\/td>\n<\/tr>\n
17<\/td>\n4 Principle
4.1 General
4.2 Laboratory operation: sample preparation and sequencing <\/td>\n<\/tr>\n
18<\/td>\n4.3 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 <\/td>\n<\/tr>\n
19<\/td>\n4.5 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 <\/td>\n<\/tr>\n
20<\/td>\n6 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 <\/td>\n<\/tr>\n
21<\/td>\n6.4.2 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 <\/td>\n<\/tr>\n
22<\/td>\n7 Bioinformatic data analysis
7.1 Requirements for software and bioinformatic pipelines used for data analysis
7.2 Logging and documentation
7.3 Quality assessments <\/td>\n<\/tr>\n
23<\/td>\n7.4 SNP analyses
7.5 MLST analyses (cgMLST and wgMLST) <\/td>\n<\/tr>\n
24<\/td>\n7.6 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 <\/td>\n<\/tr>\n
25<\/td>\n7.9.2 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 <\/td>\n<\/tr>\n
26<\/td>\n8.3 Formatting metadata using this document
8.4 Metadata associated with sample collection <\/td>\n<\/tr>\n
27<\/td>\n8.5 Metadata associated with the isolate <\/td>\n<\/tr>\n
28<\/td>\n8.6 Metadata associated with the sequence <\/td>\n<\/tr>\n
30<\/td>\n9 Sequence repositories <\/td>\n<\/tr>\n
31<\/td>\n10 Validation and verification
10.1 Validation
10.1.1 General <\/td>\n<\/tr>\n
32<\/td>\n10.1.2 Validation of laboratory operations
10.1.3 Validation of the bioinformatics pipeline <\/td>\n<\/tr>\n
33<\/td>\n10.1.4 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 <\/td>\n<\/tr>\n
35<\/td>\nAnnex A (informative) Development of quality metrics and use of controls <\/td>\n<\/tr>\n
40<\/td>\nAnnex B (informative) Laboratory contact information fields <\/td>\n<\/tr>\n
42<\/td>\nAnnex C (informative) Geographic location of sample collection fields <\/td>\n<\/tr>\n
43<\/td>\nAnnex D (informative) Isolate passage history fields <\/td>\n<\/tr>\n
44<\/td>\nAnnex E (informative) Antibiogram results and methods fields <\/td>\n<\/tr>\n
46<\/td>\nAnnex F (informative) Virulence factor detection and methods fields <\/td>\n<\/tr>\n
47<\/td>\nAnnex G (informative) Sequence quality control metrics <\/td>\n<\/tr>\n
48<\/td>\nAnnex H (informative) Metadata specification <\/td>\n<\/tr>\n
51<\/td>\nAnnex I (informative) Instructions for ontology slim integration by software developers <\/td>\n<\/tr>\n
55<\/td>\nBibliography <\/td>\n<\/tr>\n<\/table>\n","protected":false},"excerpt":{"rendered":"

Microbiology of the food chain. Whole genome sequencing for typing and genomic characterization of bacteria. General requirements and guidance<\/b><\/p>\n\n\n\n\n
Published By<\/td>\nPublication Date<\/td>\nNumber of Pages<\/td>\n<\/tr>\n
BSI<\/b><\/a><\/td>\n2022<\/td>\n58<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"featured_media":401728,"template":"","meta":{"rank_math_lock_modified_date":false,"ep_exclude_from_search":false},"product_cat":[124,2641],"product_tag":[],"class_list":{"0":"post-401720","1":"product","2":"type-product","3":"status-publish","4":"has-post-thumbnail","6":"product_cat-07-100-30","7":"product_cat-bsi","9":"first","10":"instock","11":"sold-individually","12":"shipping-taxable","13":"purchasable","14":"product-type-simple"},"_links":{"self":[{"href":"https:\/\/pdfstandards.shop\/wp-json\/wp\/v2\/product\/401720","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pdfstandards.shop\/wp-json\/wp\/v2\/product"}],"about":[{"href":"https:\/\/pdfstandards.shop\/wp-json\/wp\/v2\/types\/product"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/pdfstandards.shop\/wp-json\/wp\/v2\/media\/401728"}],"wp:attachment":[{"href":"https:\/\/pdfstandards.shop\/wp-json\/wp\/v2\/media?parent=401720"}],"wp:term":[{"taxonomy":"product_cat","embeddable":true,"href":"https:\/\/pdfstandards.shop\/wp-json\/wp\/v2\/product_cat?post=401720"},{"taxonomy":"product_tag","embeddable":true,"href":"https:\/\/pdfstandards.shop\/wp-json\/wp\/v2\/product_tag?post=401720"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}