EN ISO 23418:2022

Microbiology of the food chain - Whole genome sequencing for typing and genomic characterization of bacteria - General requirements and guidance (ISO 23418:2022)

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.

Mikrobiologie der Lebensmittelkette - Gesamtgenomsequenzierung zur Typisierung und genomischen Charakterisierung von Bakterien - Allgemeine Anforderungen und Leitfaden (ISO 23418:2022)

Dieses Dokument legt die Mindestanforderungen für die Generierung und Analyse von Daten der Gesamtgenomsequenzierung (WGS) für Bakterien, die aus der Lebensmittelkette gewonnen wurden, fest. Dieser Prozess kann die folgenden Phasen umfassen:
a)   Umgang mit Bakterienkulturen;
b)   keimfreie Isolierung der genomischen DNA;
c)   Vorbereitung der genomischen DNA Bibliothek, Sequenzierung und Beurteilung der Read-Qualität von Rohdaten und deren Speicherung;
d)   bioinformatische Analyse zur Bestimmung der genetischen Verwandtschaft, des genetischen Gehalts und zur Vorhersage des Phänotyps sowie Validierung der bioinformatischen Pipeline;
e)   die Erfassung von Metadaten und die Hinterlegung von Sequenzdaten in Repositorien;
f)   Validierung des Gesamt-WGS-Workflows (gebrauchstauglich für die beabsichtigte Anwendung).
Dieses Dokument ist anwendbar auf Bakterien, die isoliert wurden aus:
—   Produkten, die für den menschlichen Verzehr vorgesehen sind;
—   Produkten, die als Futtermittel vorgesehen sind;
—   Umgebungsproben aus Bereichen, in denen Lebensmittel und Futtermittel gehandhabt und hergestellt werden;
—   Proben aus dem Bereich der Primärproduktion.
WARNHINWEIS — Zum Schutz der Gesundheit des Laborpersonals ist es unerlässlich, dass der Umgang mit Bakterienkulturen nur in Laboratorien mit geeigneter Ausstattung und unter der Leitung eines qualifizierten Mikrobiologen erfolgt und dass bei der Entsorgung allen inkubierten Materials mit äußerster Vorsicht vorgegangen wird. Personen, die dieses Dokument anwenden, sollten mit der üblichen Laborpraxis vertraut sein. Dieses Dokument erhebt nicht den Anspruch, alle gegebenenfalls zutreffenden Sicherheitsaspekte im Zusammenhang mit seiner Anwendung zu behandeln. Es liegt in der Verantwortung des Anwenders, angemessene Sicherheits- und Schutzmaßnahmen zu treffen.

Microbiologie de la chaîne alimentaire - Séquençage de génome entier pour le typage et la caractérisation génomique des bactéries - Exigences générales et recommandations (ISO 23418:2022)

Le présent document spécifie les exigences minimales pour générer et analyser des données de séquençage de génome entier (WGS) de bactéries provenant de la chaîne alimentaire. Ce processus peut comprendre les étapes suivantes:
a) manipulation des cultures bactériennes;
b) isolement de l’ADN génomique axène;
c) préparation de la librairie, séquençage et évaluation de la qualité et du stockage des lectures de séquences brutes d’ADN;
d) analyse bioinformatique visant à déterminer la parenté génétique et le contenu génétique, à prédire le phénotype et à valider le pipeline bioinformatique;
e) capture des métadonnées et dépôt dans des bases de données de séquences;
f) validation du processus de WGS de bout en bout (adapté à l’application prévue).
Le présent document est applicable aux bactéries isolées à partir de ce qui suit:
—    des produits destinés à la consommation humaine;
—    des produits destinés à l’alimentation animale;
—    des échantillons environnementaux prélevés dans des zones de production et de manipulation de produits alimentaires et d’aliments pour animaux;
—    des échantillons de production primaire.

Mikrobiologija v prehranski verigi - Sekvenciranje celotnega genoma za tipizacijo in genomsko karakterizacijo bakterij - Splošne zahteve in smernice (ISO 23418:2022)

Ta mednarodni standard določa minimalne zahteve za ustvarjanje in analizo podatkov o sekvenciranju celotnega genoma (WGS), pridobljenih iz bakterij, ki se prenašajo s hrano. Te zahteve se uporabljajo za vse platforme ali kemijske postopke sekvenciranja. Ta proces lahko vključuje naslednje faze:
• ravnanje z bakterijskimi kulturami;
• izolacija genomske DNA;
• oblikovanje knjižnice sekvenciranja, sekvenciranje in ocena kakovosti odčitavanja in shranjevanja neobdelanih sekvenc DNK;
• bioinformacijska analiza, vključno z metodami, kot so visokokakovostna analiza polimorfizma posameznega nukleotida (hqSNP), tipizacija na osnovi zaporedij lokusov osrednjega in celotnega genoma (cgMLST, wgMLST) ter validacija bioinformacijskih algoritemskih procesov za obdelavo neobdelanih podatkov o sekvenciranju; in
• zajemanje metapodatkov in shranjevanje sekvenc v repozitorij.

General Information

• Status: Published
• Publication Date: 21-Jun-2022
• Withdrawal Date: 30-Dec-2022
• ICS: 07.100.30 - Food microbiology
• Technical Committee: CEN/TC 463 - Microbiology of the food chain
• Drafting Committee: CEN/TC 463 - Microbiology of the food chain
• Current Stage: 6060 - Definitive text made available (DAV) - Publishing
• Start Date: 22-Jun-2022
• Completion Date: 22-Jun-2022
• Directive: 882/2004 - Regulation (EC) No 882/2004 of the European Parliament and of the Council of 29 April 2004 onofficial controls performed to ensure the verification of compliance with feed and food law, animal health and animal welfare rules
• Ref Project: SIST EN ISO 23418:2022 - Microbiology of the food chain - Whole genome sequencing for typing and genomic characterization of bacteria - General requirements and guidance (ISO 23418:2022)

Standards Content (Sample)

SLOVENSKI STANDARD
01-september-2022
Mikrobiologija v prehranski verigi - Sekvenciranje celotnega genoma za tipizacijo
in genomsko karakterizacijo bakterij - Splošne zahteve in smernice (ISO
23418:2022)
Microbiology of the food chain - Whole genome sequencing for typing and genomic
characterization of bacteria - General requirements and guidance (ISO 23418:2022)
Mikrobiologie der Lebensmittelkette - Gesamtgenomsequenzierung zur Typisierung und
genomischen Charakterisierung von Bakterien - Allgemeine Anforderungen und
Leitfaden (ISO 23418:2022)
Microbiologie de la chaîne alimentaire - Séquençage de génome entier pour le typage et
la caractérisation génomique des bactéries - Exigences générales et recommandations
(ISO 23418:2022)
Ta slovenski standard je istoveten z: EN ISO 23418:2022
ICS:
07.100.30 Mikrobiologija živil Food microbiology
2003-01.Slovenski inštitut za standardizacijo. Razmnoževanje celote ali delov tega standarda ni dovoljeno.

EN ISO 23418
EUROPEAN STANDARD
NORME EUROPÉENNE
June 2022
EUROPÄISCHE NORM
ICS 07.100.30
English Version
Microbiology of the food chain - Whole genome
sequencing for typing and genomic characterization of
bacteria - General requirements and guidance (ISO
23418:2022)
Microbiologie de la chaîne alimentaire - Séquençage de Mikrobiologie der Lebensmittelkette - Vollständige
génome entier pour le typage et la caractérisation Genomsequenzierung zur Typisierung und
génomique des bactéries - Exigences générales et genomischen Charakterisierung von Bakterien in
recommandations (ISO 23418:2022) Lebensmitteln - Allgemeine Anforderungen und
Leitfaden (ISO 23418:2022)
This European Standard was approved by CEN on 20 May 2022.

CEN members are bound to comply with the CEN/CENELEC Internal Regulations which stipulate the conditions for giving this
European Standard the status of a national standard without any alteration. Up-to-date lists and bibliographical references
concerning such national standards may be obtained on application to the CEN-CENELEC Management Centre or to any CEN
member.
This European Standard exists in three official versions (English, French, German). A version in any other language made by
translation under the responsibility of a CEN member into its own language and notified to the CEN-CENELEC Management
Centre has the same status as the official versions.

CEN members are the national standards bodies of Austria, Belgium, Bulgaria, Croatia, Cyprus, Czech Republic, Denmark, Estonia,
Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Norway,
Poland, Portugal, Republic of North Macedonia, Romania, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland, Turkey and
United Kingdom.
EUROPEAN COMMITTEE FOR STANDARDIZATION
COMITÉ EUROPÉEN DE NORMALISATION

EUROPÄISCHES KOMITEE FÜR NORMUNG

CEN-CENELEC Management Centre: Rue de la Science 23, B-1040 Brussels
© 2022 CEN All rights of exploitation in any form and by any means reserved Ref. No. EN ISO 23418:2022 E
worldwide for CEN national Members.

Contents Page
European foreword . 3

European foreword
This document (EN ISO 23418:2022) has been prepared by Technical Committee ISO/TC 34 "Food
products" in collaboration with Technical Committee CEN/TC 463 “Microbiology of the food chain” the
secretariat of which is held by AFNOR.
This European Standard shall be given the status of a national standard, either by publication of an
identical text or by endorsement, at the latest by December 2022, and conflicting national standards
shall be withdrawn at the latest by December 2022.
Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. CEN shall not be held responsible for identifying any or all such patent rights.
This document has been prepared under a Standardization Request given to CEN by the European
Commission and the European Free Trade Association.
Any feedback and questions on this document should be directed to the users’ national standards
body/national committee. A complete listing of these bodies can be found on the CEN website.
According to the CEN-CENELEC Internal Regulations, the national standards organizations of the
following countries are bound to implement this European Standard: Austria, Belgium, Bulgaria,
Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Iceland,
Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Norway, Poland, Portugal, Republic of
North Macedonia, Romania, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland, Turkey and the
United Kingdom.
Endorsement notice
The text of ISO 23418:2022 has been approved by CEN as EN ISO 23418:2022 without any modification.

INTERNATIONAL ISO
STANDARD 23418
First edition
2022-06
Microbiology of the food chain —
Whole genome sequencing for typing
and genomic characterization of
bacteria — General requirements and
guidance
Microbiologie de la chaîne alimentaire — Séquençage de génome
entier pour le typage et la caractérisation génomique des bactéries —
Exigences générales et recommandations
Reference number
ISO 23418:2022(E)
ISO 23418:2022(E)
© ISO 2022
All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of this publication may
be reproduced or utilized otherwise in any form or by any means, electronic or mechanical, including photocopying, or posting on
the internet or an intranet, without prior written permission. Permission can be requested from either ISO at the address below
or ISO’s member body in the country of the requester.
ISO copyright office
CP 401 • Ch. de Blandonnet 8
CH-1214 Vernier, Geneva
Phone: [phone]
Email: [e-mail]
Website: www.iso.org
Published in Switzerland
ii
ISO 23418:2022(E)
Contents Page
Foreword .v
Introduction . vi
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Principle . 6
4.1 General . 6
4.2 Laboratory operation: sample preparation and sequencing . 6
4.3 Bioinformatics analysis . 7
4.3.1 General . 7
4.3.2 SNP analyses . 7
4.3.3 MLST analyses . 7
4.3.4 Kmer distance analysis . 7
4.4 Metadata formats and sequence repository deposition . 7
4.5 Validation and verification of WGS workflow . 8
5 General laboratory guidance . 8
5.1 Bacterial isolation and DNA extraction . 8
5.2 Laboratory environment . 8
5.3 Standard operating procedures and nonconforming work . 8
5.4 Laboratory information management system . 8
5.5 Laboratory competence. 8
6 Laboratory operations . .9
6.1 Sample preparation and storage . 9
6.2 Bacterial isolates . 9
6.3 DNA isolation . 9
6.4 Library preparation and sequencing . 9
6.4.1 Library preparation . 9
6.4.2 DNA sequencing . 10
6.4.3 Use of controls . 10
6.4.4 Assessing raw read data quality . 10
6.4.5 Sample and data storage and retention . 10
7 Bioinformatic data analysis .11
7.1 Requirements for software and bioinformatic pipelines used for data analysis . 11
7.2 Logging and documentation . 11
7.3 Quality assessments . 11
7.4 SNP analyses .12
7.5 MLST analyses (cgMLST and wgMLST) .12
7.6 Target gene detection .13
7.7 Phylogenetic tree or dendrogram generation. 13
7.8 Metrics and log files .13
7.9 Interpreting and reporting the results of bioinformatics analyses .13
7.9.1 Interpreting results from bioinformatics pipelines .13
7.9.2 Reporting genomic analysis results . 14
8 Metadata .
...