SIST EN ISO 23418:2022
(Main)Microbiology of the food chain - Whole genome sequencing for typing and genomic characterization of bacteria - General requirements and guidance (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
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: +41 22 749 01 11
Email: copyright@iso.org
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 .14
8.1 General . 14
8.2 Metadata interoperability and future-proofing . 14
8.2.1 General . 14
8.2.2 Ontologies . 14
8.2.3 ISO WGS Slim . 14
8.3 Formatting metadata using this document . 15
8.4 Metadata associated with sample collection . 15
iii
ISO 23418:2022(E)
8.5 Metadata associated with the isolate . 16
8.6 Metadata associated with the sequence . 17
9 Sequence repositories .19
10 Validation and verification .20
10.1 Validation . 20
10.1.1 General .20
10.1.2 Validation of laboratory operations . 21
10.1.3 Validation of the bioinformatics pipeline . 21
10.1.4 Validation of the end-to-end workflow . 22
10.2 Verification . . 22
10.2.1 General .22
10.2.2 Verification of laboratory operations . 22
10.2.3 Verification of the bioinformatics pipeline .22
Annex A (informative) Development of quality metrics and use of controls .24
Annex B (informative) Laboratory contact information fields .29
Annex C (informative) Geographic location of sample collection fields .31
Annex D (informative) Isolate passage history fields .32
Annex E (informative) Antibiogram results and methods fields .33
Annex F (informative) Virulence factor detection and methods fields .35
Annex G (informative) Sequence quality control metrics .36
Annex H (informative) Metadata specification .37
Annex I (informative) Instructions for ontology slim integration by software developers .40
Bibliography . 44
iv
ISO 23418:2022(E)
Foreword
ISO (the International Organization for Standardization) is a worldwide federation of national standards
bodies (ISO member bodies). The work of preparing International Standards is normally carried out
through ISO technical committees. Each member body interested in a subject for which a technical
committee has been established has the right to be represented on that committee. International
organizations, governmental and non-governmental, in liaison with ISO, also take part in the work.
ISO collaborates closely with the International Electrotechnical Commission (IEC) on all matters of
electrotechnical standardization.
The procedures used to develop this document and those intended for its further maintenance are
described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the
different types of ISO documents should be noted. This document was drafted in accordance with the
editorial rules of the ISO/IEC Directives, Part 2 (see www.iso.org/directives).
Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. ISO shall not be held responsible for identifying any or all such patent rights. Details of
any patent rights identified during the development of the document will be in the Introduction and/or
on the ISO list of patent declarations received (see www.iso.org/patents).
Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.
For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO’s adherence to
the World Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT), see
www.iso.org/iso/foreword.html.
This document was prepared by Technical Committee ISO/TC 34, Food products, Subcommittee SC 9,
Microbiology, in collaboration with the European Committee for Standardization (CEN) Technical
Committee CEN/TC 463, Microbiology of the food chain, in accordance with the Agreement on technical
cooperation between ISO and CEN (Vienna Agreement).
Any feedback or questions on this document should be directed to the user’s national standards body. A
complete listing of these bodies can be found at www.iso.org/members.html.
v
ISO 23418:2022(E)
Introduction
Next generation sequencing (NGS) provides rapid, economical and high-throughput access to
microbial whole genome sequences and is being applied to an expanding number of problems in food
microbiology. Whole genome sequences are representations of the biological potential of the sequenced
organism at single base resolution. Whole genome sequencing (WGS) offers significant advantages over
existing technologies (e.g. serotyping, pulsed field gel electrophoresis, antibiotic resistance phenotype)
for many applications. WGS-based analyses are used by public health laboratories to detect outbreaks,
and to detect mutations, genes and other genetic features to characterize virulence and survival
potential. Within the food industry, there is interest in using whole genome sequences to characterize
bacterial isolates from ingredients and environmental surfaces, to better understand their origin and
ecology, and to update procedures to reduce risk. Some companies have developed, or are developing,
the capacity to collect and analyse whole genome sequence data. Others are turning to third-party
laboratories to perform these services, as they have done for other microbiological analyses.
This document provides guidance for both the laboratory and bioinformatic components of whole
genome sequences and associated metadata for bacterial foodborne microorganisms sampled along
the food chain (e.g. ingredients, food, feed, production environment). Although microbiology of the
food chain includes viruses and fungi, this document is only intended for bacteria. This document is
intended to be applicable to all currently available next generation DNA sequencing technologies. It
may be applied to analysis of whole genome sequence data with proprietary, open-source or custom
software. It is not intended to specify sequencing chemistries, analytical methods or software. This
document defines laboratory, data and metadata stewardship practices to ensure that analyses are
clearly reported, transparent and open to inquiry. This document is for use by laboratories to develop
their management systems for quality and technical operations. Laboratory customers and regulatory
authorities can also use it in confirming or recognizing the competence of laboratories. This document
can also be applied in other domains (e.g. environment, human health, animal health).
vi
INTERNATIONAL STANDARD ISO 23418:2022(E)
Microbiology of the food chain — Whole genome
sequencing for typing and genomic characterization of
bacteria — General requirements and guidance
WARNING — In order to safeguard the health of laboratory personnel, it is essential that
handling of bacterial cultures is only undertaken in properly equipped laboratories, under the
control of a skilled microbiologist, and that great care is taken in the disposal of all incubated
materials. Persons using this document should be familiar with normal laboratory practice.
This document does not purport to address all safety aspects, if any, associated with its use. It is
the responsibility of the user to establish appropriate safety and health practices.
1 Scope
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.
2 Normative references
There are no normative references in this document.
3 Terms and definitions
For the purposes of this document, the following terms and definitions apply.
ISO and IEC maintain terminology databases for use in standardization at the following addresses:
— ISO Online browsing platform: available at https:// www .iso .org/ obp
— IEC Electropedia: available at https:// www .electropedia .org/
ISO 23418:2022(E)
3.1
adapter sequence
DNA with a known sequence that is added to the end of a DNA library fragment to facilitate the
sequencing process (e.g. annealing to a flow cell)
3.2
annotation
process of identifying genes and other features on genome assemblies (3.4)
3.3
antibiogram
summary of antimicrobial susceptibility testing results performed for a specific microorganism,
usually represented in tabular form
3.4
assembly
output from process of aligning and merging sequencing reads (3.38) into larger contiguous sequences
(contigs (3.10))
3.5
base calling
process of assigning nucleotides and quality scores to positions in sequencing reads (3.38)
3.6
bioinformatics
collection, storage and analysis of biological data including sequences
3.7
bioinformatics pipeline
individual programs, scripts or pieces of software linked together, where output from one program is
used as input for the next step in data processing
3.8
carryover-contamination
sample contamination linked to previous experiments, transferred to the current analysis (e.g.
carryover-contamination from amplification products in prior polymerase chain reaction (PCR)
experiments to the current PCR analysis, or carryover-contamination of previously sequenced samples
from one sequencing run to another)
3.9
Chemical Entities of Biological Interest Ontology
ChEBI
ontology (3.35) for describing small chemical compounds
3.10
contig
contiguous stretch of DNA sequence that results from the assembly (3.4) of smaller, overlapping DNA
sequence reads (3.38)
3.11
controlled vocabulary
finite set of values that represent the only allowed values for a data item
[SOURCE: ISO 11238:2018, 3.18, modified — Note 1 to entry deleted.]
3.12
coverage
number of times that a given base position is read in a sequencing run
Note 1 to entry: The number of reads (3.38) that cover a particular position.
ISO 23418:2022(E)
[SOURCE: ISO 20397-2:2021, 3.6, modified — Admitted term “coverage depth” deleted.]
3.13
cross-contamination
contamination of a sample (bacterial isolate (3.23) or DNA) with other samples during the preparation
of a sequencing run
3.14
DNA sample
portion of DNA extracted from the processed sample
3.15
draft assembly
de novo genome assembly (3.4) consisting of contigs (3.10) with no implied order, typically generated
using whole genome shotgun sequencing with a short-read technology
3.16
Environment Ontology
EnvO
ontology (3.35) for describing environmental features and habitats
3.17
FoodEx2 Ontology
FoodEx2
standardized food classification and description system developed by the European Food Safety
Authority (EFSA)
3.18
Food Ontology
FoodOn
ontology (3.35) for describing food products, animal feed and food processing
3.19
Gazetteer Ontology
GAZ
ontology (3.35) for describing geographical locations
3.20
index
oligonucleotide sequences used in the process of library preparation to tag or barcode DNA from
specific samples, so that multiple samples (i.e. multiple libraries (3.25)) can be combined (multiplexed)
in a pool of libraries and analysed in a single sequencing reaction
3.21
International Nucleotide Sequence Database Collaboration
INSDC
initiative operated by the DNA Database of Japan (DDBJ), the European Molecular Biology Laboratory,
European Bioinformatics Institute (EMBL-EBI) and the National Center for Biotechnology Information
(NCBI)
3.22
International Organization for Standardization whole genome sequencing slim
ISO WGS Slim
ontology (3.35) slim containing interoperable fields and terms pertaining to the use of WGS (3.49) for
microbiology of the food chain
3.23
isolate
population of bacterial cells in pure culture derived from a single strain (3.45)
ISO 23418:2022(E)
3.24
kmer
possible sequence of length k that is contained in a whole genome sequence
3.25
library
collection of genomic DNA fragments from a single isolate (3.23) intended for determining genome
sequence(s)
Note 1 to entry: A collection of libraries, each of a single isolate, is called a “pool of libraries” and is loaded on a
sequencer to be analysed. This multiplexing of libraries would still provide the result for a single isolate if unique
indices are used for each individual single isolate’s library preparation.
Note 2 to entry: A library of mixed DNA, i.e. originating from a mixture of multiple species, can be made. However,
this is not within the scope of this document as this refers to metagenomics sequencing.
3.26
management system
quality, administrative and technical systems that govern the operations of an organization
Note 1 to entry: For the purposes of this document, “organization” refers to the laboratory.
3.27
mapping
use of software to align sequencing reads (3.38) to reference sequences
3.28
metadata
data that defines and describes other data
[SOURCE: ISO/IEC 11179-1:2015, 3.2.16]
3.29
minimal data for matching
MDM
information required to describe the sample source and provenance of a genomic sequence, as defined
[1]
by the Global Microbial Identifier , and implemented by the International Nucleotide Sequence Database
Collaboration (3.21)
3.30
multi-locus sequence typing
MLST
method of genomic analysis that identifies nucleotide variants within predefined sets of loci
Note 1 to entry: Originally used for seven loci, it is now also applied to either core genome loci for cgMLST or
whole genome loci for wgMLST.
3.31
N50
length (N) such that sequence contigs (3.10) of N or longer include half the bases in the assembly (3.4)
3.32
NCBITaxon
automatic translation of the National Center for Biotechnology Information (NCBI) taxonomy database
into obo/owl
3.33
NG50
length (N) of DNA such that sequence contigs (3.10) of N or longer include half the bases in the genome
ISO 23418:2022(E)
3.34
Open Biological and Biomedical Ontology Foundry
OBO Foundry
collection of ontologies (3.35) created by a collective of ontology developers that are committed to
collaboration and adherence to shared principles
3.35
ontology
controlled vocabulary (3.11) arranged in a hierarchy, where the terms are connected by logical
relationships
3.36
ontology slim
set of ontology fields and terms annotated as part of a particular collection, often for a specific purpose,
which may be extracted to create a file distinct from the original ontology (3.35)
3.37
Phred sequence quality score
Q
measure of the probability (P) that a base is incorrectly assigned at a given position in the sequence
expressed as:
QP=−10 lg
Note 1 to entry: A score of Q30 indicates that there is a 1 in 1 000 chance that a base is incorrectly assigned (i.e.
the base call is 99,9 % accurate).
3.38
read
nucleotide sequence inferred from a fragment of DNA or RNA
3.39
sequence repository
database in which whole genome sequencing (3.49) datasets are stored and managed
Note 1 to entry: A public repository allows unrestricted access to the data, while a private or federated repository
restricts access to the data.
3.40
sequencing replicate
sequencing a different colony from the same isolate (3.23) obtained from the same sample
material, to assess biological variation
3.41
sequencing replicate
resequencing of the same biological sample or library (3.25) to assess sequence variation
due to instrumentation and protocol
3.42
serotype
classification scheme based on the antigenic protein detection or sequence-based detection of genes
encoding bacterial surface molecules
3.43
single nucleotide polymorphism
SNP
single nucleotide variant (3.44) that passes a particular quality or frequency threshold
ISO 23418:2022(E)
3.44
single nucleotide variant
SNV
differences between the nucleotides at the same genomic position of two or more isolates (3.23)
3.45
strain
descendants of a single isolation in pure culture, usually derived from a single initial colony on a solid
growth medium
Note 1 to entry: A strain may be considered an isolate (3.23) or group of isolates that may be distinguished from
other isolates of the same genus and species by phenotypic and genotypic characteristics.
Note 2 to entry: See Reference [2].
3.46
validation
establishment of the performance characteristics of a method and provision of objective evidence that
the performance requirements for a specified intended use are fulfilled
[SOURCE: ISO 16140-1:2016, 2.81]
3.47
validated data entry
automated process ensuring that data entered into a repository are correct
3.48
verification
demonstration that a validated method functions in the user’s hands according to the method’s
specifications determined in the validation study and is fit for its intended purpose
[SOURCE: ISO 16140-3:2021, 3.21, modified — Note 1 to entry deleted.]
3.49
whole genome sequencing
WGS
process of determining the DNA sequence of an organism’s genome using total genomic DNA as input
4 Principle
4.1 General
WGS analyses of bacteria along the food and feed chain consists of culturing the pure bacterial isolate,
DNA isolation performed in a microbiological laboratory, sequencing steps conducted in an appropriate
sequencing environment and bioinformatics analysis performed in a distinct computational
environment.
NOTE The microbiology laboratory, the sequencing facility and the bioinformatics facility can be the same
organization.
4.2 Laboratory operation: sample preparation and sequencing
Sample preparation and sequencing should include the following steps:
a) Information about the isolates being sequenced, including barcodes for multiplexed samples, is
entered into the appropriate record systems, such as a laboratory information management system
(LIMS) or sample description worksheets, or both.
b) Pure isolates (identified at least to the genus level and ideally to the species level) are cultured and
genomic DNA is extracted.
ISO 23418:2022(E)
c) DNA sequencing libraries are prepared from quality controlled genomic DNA (see Table A.1 for
guidance on DNA quantity and quality metrics). This process should include:
1) DNA fragmentation, if required for the applied sequencing technology;
2) ligation of indices and adapters, consistent with the applied sequencing technology’s protocols;
3) quantification, normalization and quality control of the resulting library;
4) pooling of libraries in the case of multiplexed sequencing runs.
d) Libraries (i.e. pool of libraries) are sequenced.
e) Quality metrics produced by the sequencing instrument are ideally recorded for each run to allow
monitoring of the performance.
4.3 Bioinformatics analysis
4.3.1 General
Pipelines for bioinformatics analysis may focus on in silico predictions of phenotype (e.g. virulence) or
detecting clusters of genetically similar isolates (i.e. same strain, sequence type or serotype). Pipelines
based on comparative approaches may be used to detect the presence and states of markers in raw and
assembled sequencing data to make in silico strain (e.g. sequence type) and phenotype predictions.
Sequence data for multiple isolates may be analysed using SNP, MLST or kmer distance analysis
methods to identify clusters of closely related bacteria. Results from these analyses may be used to infer
relationships between isolates, which may be illustrated with phylogenetic trees and dendrograms.
4.3.2 SNP analyses
For SNP analyses, reads are mapped to a reference sequence or reads are assembled into contigs that
are compared. To determine SNPs, SNVs are quality-filtered to identify SNP positions.
4.3.3 MLST analyses
For MLST analyses, reads are assembled or mapped. Alleles are identified, quality-filtered and compared
to a cgMLST or wgMLST database.
4.3.4 Kmer distance analysis
Sequence data for multiple isolates may be analysed using kmer distance methods to identify clusters
of related bacteria. Kmer analyses have the advantage of being very fast but have some limitations,
notably in terms of precision (i.e. they are applicable in species determination, but not recommended
for detailed source tracking analysis of closely related strains).
4.4 Metadata formats and sequence repository deposition
Metadata records shall be created and safely stored for all sequences. Sequence data and corresponding
metadata should be consistently formatted and documented. These metadata may be shared solely at
the discretion of the metadata owner. Sequence data and its corresponding metadata shall be subject
to security considerations, cost and benefits, intellectual property rights, confidential business
information, contract restriction or other binding written agreements.
NOTE Licensing or a privacy policy, or both, can be applied to metadata or sequence data, or both, to protect
private or proprietary information.
[3]
To promote data stewardship best practices , this document provides optional metadata reporting
formats which are harmonized to a community data standard (e.g. MDM or OBO Foundry ontologies).
These formats and standards facilitate reproducibility and common understanding of terminology. An
ISO 23418:2022(E)
ISO WGS Slim was created to format and provide values for the recommended metadata fields. WGS and
selected metadata may be transferred (uploaded) to a publicly accessible database.
4.5 Validation and verification of WGS workflow
The entire WGS workflow shall be validated to provide assurance that the methods are fit for intended
use.
NOTE More details on the validation and verification of the WGS workflow are given in Clause 10 and Table 4.
5 General laboratory guidance
5.1 Bacterial isolation and DNA extraction
Bacterial isolation and DNA extraction should be performed in a general microbiological laboratory
adapted to work with the specific bacteria, including pathogens. For sequencing library preparation
that involves DNA amplification using polymerase chain reaction (PCR), pre- and post-PCR steps should
be carried out in different or segregated areas of the laboratory to avoid carryover-contamination.
5.2 Laboratory environment
Air movements, vibration, temperature and humidity can interfere with the performance of many
sequencers and should be considered in the placement of the equipment in the laboratory. Laboratories
should consult the sequencer manufacturer’s site preparation guide for specific guidance.
5.3 Standard operating procedures and nonconforming work
Laboratories should maintain and adhere to standardized operating procedures (SOPs), workflow
documents, reagent inventory controls and equipment maintenance logs. SOPs should include
procedures for using positive and negative controls for the DNA extraction, sequence library
preparation and sequencing steps. SOPs should include procedures for monitoring operations for run
quality and errors (sample misidentification or cross-contamination).
In the case of sample misidentification or contamination, the root cause of errors in sequencing shall be
investigated:
a) ensuring that runs containing misidentified samples, or samples contaminated with multiple
strains, are not used for bioinformatics analysis for sample interpretation or uploaded to databases;
b) implementing measures to maintain quality and prevent recurrence of errors.
5.4 Laboratory information management system
Sample information shall be captured using a LIMS or similar system of documenting and tracking
information.
5.5 Laboratory competence
Laboratories should maintain records documenting training, education and proficiency for individuals
performing sequencing and bioinformatics analysis, and sample retention policy.
The laboratory should monitor its performance for WGS analysis by comparison with results of other
laboratories, where available and appropriate. This monitoring should be planned and reviewed and
include, but not be limited to, one of the following, ideally annually:
a) participation in a proficiency testing programme;
b) participation in interlaboratory comparisons other than proficiency testing;
ISO 23418:2022(E)
c) verification of the analytical process by introducing “blind” samples or samples whose
characteristics are not known by the operator.
Data (e.g. sequence data, run metrics, result reports provided by the organizing institution) from
these monitoring activities should be analysed, used to control and, if applicable, used to improve the
laboratory’s activities. If the results of the analysis of data from these monitoring activities are found
to be outside predefined criteria, appropriate actions should be taken t
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