CEN/TC 463 - Microbiology of the food chain

This document specifies the general principle and the technical protocol for the validation of identification methods of microorganisms for microbiology in the food chain. As there is no reference method, no method comparison study can be run. Therefore, this document provides a protocol to evaluate the performance characteristics and validate the method workflow using well-defined strains. When required, an additional identification method can be used.
This document is applicable to the validation of identification methods of microorganisms that are used for the analysis of isolated colonies from:
—     products intended for human consumption;
—     products for feeding animals;
—     environmental samples in the area of food and feed production and handling;
—     samples from the primary production stage.
Identification methods only validated in accordance with this document cannot be used instead of confirmation described in:
—     the reference method;
—     an alternative method validated in accordance with ISO 16140-2;
—     an alternative method validated in accordance with ISO 16140-6.
In these instances, the identification method is validated in accordance with ISO 16140-6 method that is used as a confirmation method.
This document is applicable to bacteria and fungi. Some clauses can be applicable to other (micro)organisms, which can be determined on a case-by-case basis.

This document specifies the general requirements for the in vitro amplification of nucleic acid sequences (DNA or RNA).
This document is applicable to the testing for microorganisms and viruses from the food chain using the polymerase chain reaction (PCR). This document, or parts of it, is applicable to other fields of PCR diagnostics based on a case-by-case evaluation.
The minimum requirements laid down in this document are intended to ensure that comparable and reproducible results are obtained in different laboratories.
This document has been established for microorganisms from the food chain and is applicable to:
—     products intended for human consumption;
—     products for feeding animals;
—     environmental samples in the area of food and feed production and handling;
—     samples from the primary production stage.

This document specifies general requirements and gives guidance on microbiological examinations.
It is applicable to:
—     the implementation of specific horizontal or vertical International Standards developed by ISO/TC 34/SC 9 or ISO/TC 34/SC 5 for detection or enumeration of microorganisms, named hereafter “specific standards”;
—     good laboratory practices for microbiology laboratories testing samples from the food chain;
—     guidance for microbiological laboratories testing samples from the food chain on the technical requirements for conforming to ISO/IEC 17025.
The requirements of this general standard supersede corresponding ones in existing specific standards.
Additional instructions for examinations using the polymerase chain reaction (PCR) are specified in ISO 22174.
This document is applicable to examinations for bacteria, yeasts and moulds and can be used, if supplemented with specific guidance, for parasites and viruses. It does not apply to examinations for toxins or other metabolites (e.g. amines) from microorganisms.
This document is applicable to microbiology of the food chain, from primary production stage to food and animal feed products, including the premises where the food or feed production and handling takes place. It is also applicable to the microbiological examination of water where water is used in food production or is regarded as a food in national legislation.

This document specifies the detection of Clostridium (C.) perfringens.
This document is applicable to:
—     products intended for human consumption;
—     products intended for animal feeding;
—     environmental samples in the area of food and feed production and handling;
—     samples from the primary production stage.
This horizontal method was originally developed for the examination of all samples belonging to the food chain. Based on the information available at the time of publication of this document, this method is considered to be fully suited to the examination of all samples belonging to the food chain. However, because of the large variety of products in the food chain, it is possible that this horizontal method is not appropriate in every detail for all products. Nevertheless, it is expected that the required modifications are minimized so that they do not result in a significant deviation from this horizontal method.
NOTE          Interlaboratory studies with a small number of participating laboratories (<10) were conducted for the following food categories:
—      ready-to-eat, ready-to-reheat meat products;
—      eggs and egg products (derivates);
—      ready-to-eat, ready-to-reheat fishery products;
—      processed fruits and vegetables;
—      infant formula and infant cereals (with probiotics);
—      multi-component foods or meal components.
It has also been validated with a small number of participating laboratories for the following other category:
—      environmental samples (food or feed production).
Since the method is not commonly used for samples in the primary production stage, this category was not included in the interlaboratory study. Therefore, no performance characteristics were obtained for this category. The method has not been validated for the category ‘pet food and animal feed’, as the test samples used for the interlaboratory study were already naturally contaminated with C. perfringens. Given the limited number of participating laboratories in the interlaboratory studies, the calculated performance characteristics can be used as indicative values of the method performance. For detailed information on the validation, see Clause 11 and Annexes C to F.

This document specifies the enumeration of Clostridium (C.) perfringens by colony-count technique.
This document is applicable to:
—    products intended for human consumption;
—    products for feeding animals;
—    environmental samples in the area of food and feed production and handling;
—    samples from the primary production stage.
NOTE            This method has been validated in an interlaboratory study for the following food categories:
—     ready-to-eat, ready-to-reheat meat products;
—     eggs and egg products (derivates);
—     processed fruits and vegetables;
—     infant formula and infant cereals;
—     multi-component foods or meal components.
It has also been validated for the following other categories:
—     pet food and animal feed;
—     environmental samples (food or feed production).
As this method has been validated for at least five food categories, this method is applicable for a broad range of food. For detailed information on the validation, see Clause 11 and Annex C. Since the method is not commonly used for samples in the primary production stage, this category was not included in the interlaboratory study. Therefore, no performance characteristics were obtained for this category.
This horizontal method was originally developed for the examination of all samples belonging to the food chain. Based on the information available at the time of publication of this document, this method is considered to be fully suited to the examination of all samples belonging to the food chain. However, because of the large variety of products in the food chain, it is possible that this horizontal method is not appropriate in every detail for all products. Nevertheless, it is expected that the required modifications are minimized so that they do not result in a significant deviation from this horizontal method.
This technique is suitable for, but not limited to, the enumeration of microorganisms in test samples with a minimum of 10 colonies counted on a plate. This corresponds to a level of contamination that is expected to be higher than 10 cfu/ml for liquid samples or higher than 100 cfu/g for solid samples.

This document gives technical requirements and guidance on the establishment or revision of standardized reference methods used for the analysis of microorganisms in:
—    products intended for human consumption;
—    products for feeding animals;
—    environmental samples in the area of food and feed production and handling;
—    samples from the primary production stage.
This document specifies the technical stages of the establishment of a new standardized reference method and of the revision of an existing standardized reference method. It includes, in particular, requirements and guidance on the validation of the selected method.
This document is intended to be implemented in particular by ISO/TC 34/SC 9 and its corresponding structure at CEN level, which is CEN/TC 463.

Inclusion of methods for molecular confirmation and identification of thermotolerant Campylobacter spp. and change of the performance testing of culture media

Inclusion of methods for molecular confirmation and identification of thermotolerant Campylobacter spp. and change of the performance testing of culture media

This document specifies the enumeration of sulfite-reducing Clostridium spp. by the colony-count technique.
This document is applicable to:
—    products intended for human consumption;
—    products for feeding animals;
—    environmental samples in the area of food and feed production and handling;
—    samples from the primary production stage.
NOTE      This method has been validated in an interlaboratory study for the following food categories:
—    ready-to-eat, ready-to-reheat meat products;
—    eggs and egg products (derivates);
—    processed fruits and vegetables;
—    infant formula and infant cereals;
—    multi-component foods or meal components.
It has also been validated for the following other categories:
—    pet food and animal feed;
—    environmental samples (food or feed production).
As this method has been validated for at least five food categories, this method is applicable for a broad range of food. For detailed information on the validation, see Clause 11 and Annex C. Since the method is not commonly used for samples in the primary production stage, this category was not included in the interlaboratory study. Therefore, no performance characteristics were obtained for this category.
This horizontal method was originally developed for the examination of all samples belonging to the food chain. Based on the information available at the time of publication of this document, this method is considered to be fully suited to the examination of all samples belonging to the food chain. However, because of the large variety of products in the food chain, it is possible that this horizontal method is not appropriate in every detail for all products. Nevertheless, it is expected that the required modifications are minimized so that they do not result in a significant deviation from this horizontal method.
This technique is suitable for, but not limited to, the enumeration of microorganisms in test samples with a minimum of 10 colonies counted on a plate. This corresponds to a level of contamination that is expected to be higher than 10 cfu/ml for liquid samples or higher than 100 cfu/g for solid samples.

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.

This document specifies protocols for conducting microbiological challenge tests for growth studies on vegetative and spore-forming bacteria in raw materials and intermediate or end products.
The use of this document can be extended to yeasts that do not form mycelium.

This document specifies requirements for the installation, maintenance, temperature calibration and temperature performance testing of standard thermal cyclers and real-time thermal cyclers. It is applicable to the detection of microorganisms as well as any other applications in the food chain using polymerase chain reaction (PCR)-based methods.
This document has been established for food testing, but is also applicable to other domains using thermal cyclers (e.g. environmental, human health, animal health, forensic testing).

This document specifies a horizontal method for the enumeration of coagulase-positive staphylococci by counting the colonies obtained on a solid medium (rabbit plasma fibrinogen agar medium) after aerobic incubation at 34 °C to 38 °C (see Reference [10]).
This document is applicable to:
—    products intended for human consumption;
—    products intended for animal feeding;
—    environmental samples in the area of food and feed production and handling;
—    samples from the primary production stage.
This horizontal method was originally developed for the examination of all samples belonging to the food chain.
Because of the large variety of products in the food chain, it is possible that this horizontal method is not appropriate in every detail for all products. Nevertheless, it is expected that the required modifications are minimized so that they do not result in a significant deviation from this horizontal method.
Based on the information available at the time of publication of this document, this method is particularly suitable for the examination of fermented products or other products containing technological microbiota based on Staphylococcus spp. (e.g. S. xylosus) (such as cheeses made from raw milk and certain raw meat products) likely to be contaminated by:
—     staphylococci forming atypical colonies on a Baird-Parker agar medium;
—     background microbiota that can obscure the colonies being sought.
Nevertheless, both ISO 6888-1 and this document are given equivalent status.

This document specifies a horizontal method for the enumeration of coagulase-positive staphylococci by counting the colonies obtained on a solid medium (Baird-Parker medium)[10] after aerobic incubation at 34 °C to 38 °C and coagulase confirmation.
This document is applicable to:
—    products intended for human consumption;
—    products intended for animal feeding;
—    environmental samples in the area of food and feed production, handling, and
—    samples from the primary production stage.
This horizontal method was originally developed for the examination of all samples belonging to the food chain.
Because of the large variety of products in the food chain, it is possible that this horizontal method is not appropriate in every detail for all products. Nevertheless, it is expected that the required modifications are minimized so that they do not result in a significant deviation from this horizontal method.
Based on the information available at the time of publication of this document, this method is not considered to be (fully) suited to the examination of fermented products or other products containing technological flora based on Staphylococcus spp (e.g. S. xylosus) (such as cheeses made from raw milk and certain raw meat products) likely to be contaminated by:
—    staphylococci forming atypical colonies on a Baird-Parker agar medium;
—    background flora that can obscure the colonies being sought.
Nevertheless, both this document and ISO 6888-2 are given equivalent status.

This document specifies a method for the detection of Anisakidae L3 larvae commonly found in marine and anadromous fishes. The method is applicable to fresh fish and/or frozen fish, as well as lightly processed fish products, such as marinated, salted or smoked. It is also suitable for visceral organs as a confirmatory method for a visual inspection scheme.
The artificial digestion method[4][5][6] is applicable to quantifying parasitic infections by estimating the number of parasites in the fish musculature and, when applied to fresh fish or lightly processed fish products (never frozen before processing), determining the viability of Anisakidae L3, which can be present.
This method does not apply to determining the species or genotype of detected parasites. Final identification is made by morphological and/or molecular methods.

This document specifies a method for the detection of Anisakidae L3 larvae commonly found in marine and anadromous fishes. The method is applicable to fresh fish and/or frozen fish, as well as lightly processed fish products, such as marinated, salted or cold smoked.
This method is applicable to quantifying parasitic infections by estimating the number of parasites in the fish musculature.
This method does not apply to determining the species or genotype of detected parasites. Final identification is made by morphological and/or molecular methods.

This document specifies the protocol for the verification of reference methods and validated alternative methods for implementation in the user laboratory.
This document is applicable to the verification of methods used for the analysis (detection and/or quantification), confirmation and typing of microorganisms in:
—     products intended for human consumption;
—     products intended for animal feeding;
—     environmental samples in the area of food and feed production, handling;
—     samples from the primary production stage.
This document is, in particular, applicable to bacteria and fungi. Some clauses can be applicable to other (micro)organisms or their metabolites, to be determined on a case-by-case basis.
The technical protocols for the verification of validated qualitative methods and validated quantitative methods are described in Clauses 5 and 6. The technical protocol for the verification of validated alternative confirmation and typing methods is described in Clause 7. The protocols for the verification of non-validated reference methods are described in Annex F.

This document specifies the general principles and the technical protocols for single-laboratory validation of methods for microbiology in the food chain. The protocols in this document only validate the method for the laboratory conducting the study.
This document is applicable to single-laboratory validation of:
—     methods used in the analysis (detection or quantification) of microorganisms in:
—     products intended for human consumption;
—     products intended for animal feeding;
—     environmental samples in the area of food and feed production, handling;
—     samples from the primary production stage;
—     methods for the confirmation or typing of microorganisms. This validation will replace only the confirmation or typing procedure of a specified method (see Annex G).
This document is, in particular, applicable to bacteria and fungi. Some clauses can be applicable to other (micro)organisms or their metabolites, to be determined on a case-by-case basis.
Single-laboratory validation is required if an interlaboratory validation in accordance with ISO 16140-2 is not appropriate. Possible applications are:
—     validation of an in-house method;
—     method evaluation study in the validation process of a reference method in accordance with ISO 17468;
—     extension of the scope of an ISO 16140-2 validated method, e.g. category extension or test portion size;
—     modifications of existing methods.
Single-laboratory validation is the second step in the standardization of a reference method (see ISO 17468). It is only applicable to methods that are fully specified with regard to all relevant parameters (including tolerances on temperatures and specifications on culture media) and that have already been optimized.

This document specifies the general principles and the technical protocols (based on orthogonal, factorial studies) for the validation of non-proprietary methods for microbiology of the food chain.
This document is applicable to the validation of methods used for the analysis (detection or quantification) of microorganisms in:
—     products intended for human consumption;
—     products intended for animal feeding;
—     environmental samples in the area of food and feed production, handling;
—     samples from the primary production stage.
This document is, in particular, applicable to bacteria and fungi. Some clauses can be applicable to other (micro)organisms or their metabolites, to be determined on a case-by-case basis.
This document specifies protocols for the validation against a reference method for both quantitative and qualitative methods. This document also provides a protocol for the validation of quantitative methods without a reference method. Qualitative methods cannot be validated without a reference method in accordance with this document.
NOTE    ISO 16140-2 specifies the general principle and the technical protocol for the validation of alternative, mostly proprietary, methods against a reference method.
This document is only applicable to the validation of methods that are fully specified with regard to all relevant parameters (including tolerances on temperatures and specifications on culture media) and that have already been optimized.
Methods that have been validated in accordance with this document can be used by the laboratories of the specified population of laboratories.

This document specifies rules for the preparation of samples of milk and milk products and their suspensions for microbiological examination when the samples require a different preparation from the general methods specified in ISO 6887-1.
This document excludes the preparation of samples for both enumeration and detection test methods where preparation details are specified in the relevant International Standards.
This document is intended to be used in conjunction with ISO 6887-1.
This document is applicable to:
a)   milk and liquid milk products;
b)   dehydrated milk products;
c)   cheese and cheese products;
d)   casein and caseinates;
e)   butter;
f)    milk-based ice-cream;
g)   milk-based custard, desserts and sweet cream;
h)   fermented milks, yogurt, probiotics milk products and sour cream;
i)     dehydrated milk-based infant foods, with or without probiotics.

This document specifies the general principle and the technical protocol for the validation of alternative confirmation methods for microbiology in the food chain. This document compares the result of the alternative confirmation method against the confirmation procedure of a reference method or, if needed, a reference confirmation method (e.g. whole genome sequencing).
This document is applicable to the validation of alternative confirmation methods used for the analysis (detection or quantification) of isolated microorganisms in:
—          products intended for human consumption;
—          products intended for animal feeding;
—          environmental samples in the area of food and feed production, handling;
—          samples from the primary production stage.
Validated alternative confirmation methods can be used to replace (partly or completely) the confirmation procedure described in:
—          the reference method;
—          an alternative method validated in accordance with ISO 16140-2 only if one of the isolation agars specified in the validation study of the alternative confirmation method is used.
This document is also applicable to the validation of alternative typing methods, where the reference method can be, for example, a serological method (e.g. serotyping of Salmonella) or a molecular method (e.g. typing of Shiga toxin-producing E. coli).
This document is, in particular, applicable to bacteria and fungi. Some clauses can be applicable to other (micro)organisms, to be determined on a case-by-case basis.
Validation studies in accordance with this document are primarily intended to be performed by organizations or expert laboratories involved in method validation, but can also be used by a single laboratory, especially when performing in-house validation under certain conditions (see ISO 16140-4).

This document specifies requirements and gives guidance for the estimation and expression of measurement uncertainty (MU) associated with quantitative results in microbiology of the food chain.
It is applicable to the quantitative analysis of:
—          products intended for human consumption or the feeding of animals;
—          environmental samples in the area of food production and food handling;
—          samples at the stage of primary production.
The quantitative analysis is typically carried out by enumeration of microorganisms using a colony-count technique. This document is also generally applicable to other quantitative analyses, including:
—           most probable number (MPN) techniques;
—          instrumental methods, such as impediometry, adenosine triphosphate (ATP) and flow cytometry;
—          molecular methods, such as methods based on quantitative polymerase chain reaction (qPCR).
The uncertainty estimated by this document does not include systematic effects (bias).

This document specifies a method for detection of hepatitis A virus (HAV) and norovirus genogroups I (GI) and II (GII), from test samples of foodstuffs [(soft fruit, leaf, stem and bulb vegetables, bottled water, bivalve molluscan shellfish (BMS)] or surfaces using real-time RT-PCR.
This method is not validated for detection of the target viruses in other foodstuffs (including multi-component foodstuffs), or any other matrices, nor for the detection of other viruses in foodstuffs, surfaces or other matrices.

This document specifies protocols for conducting microbiological challenge tests for growth studies on vegetative and spore-forming bacteria in raw materials and intermediate or end products.
The use of this document can be extended to yeasts that do not form mycelium.

This document specifies requirements and gives guidelines for the organization of proficiency testing (PT) schemes for microbiological examinations of
a)   foods and beverages,
b)   feeding animals,
c)   environmental samples from food and feed production and handling, and
d)   primary production stages.
This document is also applicable to the microbiological examination of water where water is either used in food production or is regarded as a food in national legislation.
This document relates to the technical organization and implementation of PT schemes, as well as the statistical treatment of results of microbiological examinations.
This document is designed for use with ISO/IEC 17043 and ISO 13528, and deals only with areas where specific or additional details are necessary for PT schemes dealing with microbiological examinations for the areas specified in the first paragraph.

This document specifies horizontal methods for sampling techniques using contact plates, stick swabs, sponges and cloths on surfaces in the food chain environment in order to detect and enumerate culturable microorganisms such as pathogenic or non-pathogenic bacteria or yeasts and moulds.
NOTE       The term "environment" means any item in contact with the food product or likely to represent a contamination or recontamination source; for example, material, premises or operators.
This document does not apply to the validation of cleaning and disinfection procedures.
This document does not apply to sampling techniques for primary production samples, which are covered by ISO 13307. Sampling techniques for carcasses are covered by ISO 17604. Sampling techniques for analysis of noroviruses and hepatitis A viruses are covered by ISO 15216-1.
This document does not give advice on sampling frequency, the number of sampling points, or the need to rotate sampling points, as these are chosen on a case-by-case basis.

ISO 21872-1:2017 specifies a horizontal method for the detection of enteropathogenic Vibrio spp., which causes human illness in or via the intestinal tract. The species detectable by the methods specified include Vibrio parahaemolyticus, Vibrio cholerae and Vibrio vulnificus.
ISO 21872-1:2017 is applicable to the following:
-      products intended for human consumption and the feeding of animals;
-      environmental samples in the area of food production and food handling.

ISO 21528-1:2017 specifies a method, with enrichment, for the detection of Enterobacteriaceae. It is applicable to
-      products intended for human consumption and the feeding of animals, and
-      environmental samples in the area of primary production, food production and food handling.
This method is applicable
-      when the microorganisms sought are expected to need resuscitation by enrichment, and
-      when the number sought is expected to be below 100 per millilitre or per gram of test sample.
A limitation on the applicability of ISO 21528-1:2017 is imposed by the susceptibility of the method to a large degree of variability (see Clause 11).
NOTE       Enumeration can be carried out by calculation of the most probable number (MPN) after incubation in liquid medium. See Annex A.

ISO 10272-1:2017 specifies a horizontal method for the detection by enrichment or direct plating of Campylobacter spp. It is applicable to
-      products intended for human consumption,
-      products intended for animal feeding,
-      environmental samples in the area of food and feed production, handling, and
-      samples from the primary production stage such as animal faeces, dust, and swabs.

ISO 19343:2017 specifies a high performance liquid chromatography (HPLC) method to analyse histamine in fish and fishery products (fish sauces, fish maturated by enzyme in brine, etc.) intended for human consumption.

ISO 10272-2:2017 specifies a horizontal method for the enumeration of Campylobacter spp. It is applicable to
-      products intended for human consumption,
-      products intended for animal feeding,
-      environmental samples in the area of food and feed production, handling, and
-      samples from the primary production stage such as animal faeces, dust, and swabs.

ISO 21528-2:2017 specifies a method for the enumeration of Enterobacteriaceae. It is applicable to
-      products intended for human consumption and the feeding of animals, and
-      environmental samples in the area of primary production, food production and food handling.
This technique is intended to be used when the number of colonies sought is expected to be more than 100 per millilitre or per gram of the test sample.
The most probable number (MPN) technique, as included in ISO 21528‑1, is generally used when the number sought is expected to be below 100 per millilitre or per gram of test sample.

ISO 19020:2017 specifies a screening method for the detection of staphylococcal enterotoxins SEA, SEB, SECs, SED and SEE in foodstuffs. It consists of two main steps: a) extraction followed by a concentration based on dialysis principle; and b) an immunoenzymatic detection using commercially available detection kits.
ISO 19020:2017 is applicable to the screening of staphylococcal enterotoxins SEA to SEE in products intended for human consumption.
Other staphylococcal enterotoxins such as types SEG, SEH, SEI, SER, SES and SET can also cause illness. Due to the lack of commercially available detection kits, ISO 19020:2017 is applicable only to types SEA to SEE, but may apply to other types of toxins, subject to validation of the method.

ISO 11290-1:2017 specifies a horizontal method for
-      the detection of L. monocytogenes, and
-      the detection of Listeria spp. (including L. monocytogenes).
ISO 11290-1:2017 is applicable to
-      products intended for human consumption and for the feeding of animals, and
-      environmental samples in the area of food production and food handling.