ISO/TC 34/SC 9 - Microbiology

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 (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 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 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 ISO 6888-1 and this document 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 a method for the direct enumeration of potentially enteropathogenic V. parahaemolyticus (tdh and/or trh positive) and/or the enumeration of total V. parahaemolyticus in seafood.

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 horizontal method for the enumeration of psychrotrophic microorganisms that are able to grow and form colonies on a solid agar culture medium after aerobic incubation at 6,5 °C. 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. NOTE Annex B specifies a rapid method for the estimated enumeration of psychrotrophic microorganisms in raw and pasteurized milk.

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 16649-1:2018 specifies a horizontal method for the enumeration of β-glucuronidase-positive Escherichia coli by colony-count technique after resuscitation using membranes and incubation at 44 °C on a solid medium containing a chromogenic ingredient for detection of the enzyme β-glucuronidase[9][10][13][14][17][18][19][20]. It is applicable to - products intended for human consumption, - products intended for feeding animals, - environmental samples in the area of food production and food handling, and - samples from the primary production stage such as animal faeces, dust, and swabs.

ISO 13722:2017 specifies a method for the enumeration of viable Brochothrix spp. by means of a colony-count technique. ISO 13722:2017 is especially applicable to meat and meat products, but is also suitable for the examination of the following: - other 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.

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 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 10272-1:2017 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 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 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 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.

ISO 11290-2:2017 specifies a horizontal method for - the enumeration of L. monocytogenes, and - the enumeration of Listeria spp. (including L. monocytogenes). ISO 11290-2:2017 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.

ISO 10273:2017 specifies a horizontal method for the detection of Y. enterocolitica associated with human disease. It is applicable to - products intended for human consumption and the feeding of animals, and - environmental samples in the area of food production and food handling.

ISO 22964:2017 specifies a horizontal method for the detection of Cronobacter spp. Subject to the limitations discussed in the introduction, this document is applicable to - food products and ingredients intended for human consumption and the feeding of animals, and - environmental samples in the area of food production and food handling.

ISO 6887-1:2017 defines general rules for the aerobic preparation of the initial suspension and of dilutions for microbiological examinations of products intended for human or animal consumption. ISO 6887-1:2017 is applicable to the general case and other parts apply to specific groups of products as mentioned in the foreword. Some aspects might also be applicable to molecular methods where matrices can be associated with inhibition of the PCR steps and consequently affect the test result. ISO 6887-1:2017 excludes preparation of samples for both enumeration and detection test methods where preparation instructions are detailed in specific International Standards.

ISO 6887-2:2017 specifies rules for the preparation of meat and meat product samples and their suspension for microbiological examination when the samples require different preparation from the methods described in ISO 6887‑1. ISO 6887‑1 defines the general rules for the preparation of the initial suspension and dilutions for microbiological examination. ISO 6887-2:2017 excludes preparation of samples for both enumeration and detection test methods where preparation details are specified in the relevant International Standards. ISO 6887-2:2017 is applicable to the following fresh, raw and processed meats, poultry and game and their products: - refrigerated or frozen; - cured or fermented; - minced or comminuted; - meat preparations; - mechanically separated meat; - cooked meats; - dried and smoked meats at various degrees of dehydration; - concentrated meat extracts; - excision and swab samples from carcasses. ISO 6887-2:2017 excludes the sampling of carcasses (see ISO 17604) and preparation of samples from the primary production stage (see ISO 6887‑6).

ISO 6887-4:2017 specifies rules for the preparation of samples and dilutions for the microbiological examination of specific food products not covered in other parts of ISO 6887, which deal with more general categories. This document covers a wide range of miscellaneous products, but does not include new products brought on to the market after publication. ISO 6887‑1 defines the general rules for the preparation of the initial suspension and dilutions for microbiological examination. ISO 6887-4:2017 excludes preparation of samples for both enumeration and detection test methods when preparation details are specified in the relevant International Standards. ISO 6887-4:2017 is applicable to the following products: - acidic (low pH) products; - hard and dry products; - dehydrated, freeze-dried and other low aw products (including those with inhibitory properties); - flours, whole cereal grains, cereal by-products; - animal feed, cattle cake, kibbles and pet chews; - gelatine (powdered and leaf); - margarines, spreads and non-dairy products with added water; - eggs and egg products; - bakery goods, pastries and cakes; - fresh fruit and vegetables; - fermented products and other products containing viable microorganisms; - alcoholic and non-alcoholic beverages; - alternative protein products.

ISO 6887-3:2017 specifies rules for the preparation of fish and fishery product samples and their suspension for microbiological examination when the samples require a different preparation from the methods described in ISO 6887‑1. ISO 6887‑1 defines the general rules for the preparation of the initial suspension and dilutions for microbiological examination. ISO 6887-3:2017 includes special procedures for sampling raw molluscs, tunicates and echinoderms from primary production areas. NOTE 1 Sampling of raw molluscs, tunicates and echinoderms from primary production areas is included in this document, rather than ISO 13307, which specifies rules for sampling from the terrestrial primary production stage. ISO 6887-3:2017 excludes preparation of samples for both enumeration and detection test methods where preparation details are specified in the relevant International Standards (e.g. ISO/TS 15216‑1 and ISO/TS 15216‑2 for determination of hepatitis A virus and norovirus in food using real-time RT-PCR). ISO 6887-3:2017 is intended to be used in conjunction with ISO 6887‑1. It is applicable to the following raw, processed or frozen fish and shellfish and their products (see Annex A for classification of major taxa): a) Raw fishery products, molluscs, tunicates and echinoderms including: - whole fish or fillets, with or without skin and heads, and gutted; - crustaceans, whole or shelled; - cephalopods; - bivalve molluscs; - gastropods; - tunicates and echinoderms. b) Processed products including: - smoked fish, whole or prepared fillets, with or without skin; - cooked or partially cooked, whole or shelled crustaceans, molluscs, tunicates and echinoderms; - cooked or partially cooked fish and fish-based multi-component products. c) Raw or cooked frozen fish, crustaceans, molluscs and others, in blocks or otherwise, including: - fish, fish fillets and pieces; - whole and shelled crustacean (e.g. flaked crab, prawns), molluscs, tunicates and echinoderms. NOTE 2 The purpose of examinations performed on these samples can be either hygiene testing or quality control. However, the sampling techniques described in this document relate mainly to hygiene testing (on muscle tissues).

ISO 15216-1:2017 specifies a method for the quantification of levels of HAV and norovirus genogroup I (GI) and II (GII) RNA, from test samples of foodstuffs (soft fruit, leaf, stem and bulb vegetables, bottled water, BMS) or food surfaces. Following liberation of viruses from the test sample, viral RNA is then extracted by lysis with guanidine thiocyanate and adsorption on silica. Target sequences within the viral RNA are amplified and detected by 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, food surfaces or other matrices.

ISO 6579-1:2017 specifies a horizontal method for the detection of Salmonella. It 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; - samples from the primary production stage such as animal faeces, dust, and swabs. With this horizontal method, most of the Salmonella serovars are intended to be detected. For the detection of some specific serovars, additional culture steps may be needed. For Salmonella Typhi and Salmonella Paratyphi, the procedure is described in Annex D. The selective enrichment medium modified semi-solid Rappaport-Vassiliadis (MSRV) agar is intended for the detection of motile Salmonella and is not appropriate for the detection of non-motile Salmonella strains.

ISO 18465:2017 describes the quantitative analysis of the emetic toxin cereulide using high performance liquid chromatography (HPLC) or ultra performance liquid chromatography (UHPLC) connected to a tandem mass spectrometer (LC-MS/MS). ISO 18465:2017 is applicable to the analysis of the toxin in products intended for human consumption.

ISO 16140-2:2016 specifies the general principle and the technical protocol for the validation of alternative, mostly proprietary, methods for microbiology in the food chain. Validation studies according to ISO 16140-2:2016 are intended to be performed by organizations involved in method validation. It is applicable to the validation of methods 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, and - samples from the primary production stage. It is in particular applicable to bacteria and fungi. Some clauses of ISO 16140-2:2016 could be applicable to other (micro) organisms or their metabolites on a case-by-case-basis. In the future, guidance for other organisms (e.g. viruses and parasites) will be included in ISO 16140:2016 (all parts).

ISO 16140-1:2016 defines general terms and definitions relating to method validation of microbiology in the food chain. It is applicable to the validation of methods 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, and - samples from the primary production stage.

ISO 17468:2016 gives technical requirements and guidance on the establishment or revision of standardized reference methods for the analysis (detection or quantification) of microorganisms in - products intended for human consumption and for the feeding of animals, - environmental samples in the area of food/feed production and food/feed handling, and - samples from the primary production stage. It defines the technical stage (or early stage) of the establishment of a new standardized reference method or of the revision of an existing standardized reference method. It includes, in particular, requirements and guidance on the validation of the selected method. It is intended to be implemented in particular by ISO/TC 34/SC 9 and its corresponding structure at CEN level, CEN/TC 275, Food analysis - Horizontal methods, Working Group 6, Microbiology of the food chain.

ISO 18744:2016 specifies a method that is applicable for the detection and enumeration of Cryptosporidium oocysts and Giardia cysts on or in food products that are described herein as fresh leafy green vegetables and berry fruits. With suitable controls, it may also be applicable for the examination of other fresh produce. The microscopy descriptions are for Cryptosporidium spp. oocysts and Giardia duodenalis cysts of size ranges which include those species (Cryptosporidium) or assemblages (Giardia) known to be pathogenic to humans. This method does not include any molecular analysis and therefore is not suitable for the determination of the species or genotypes/assemblages of Cryptosporidium oocysts and Giardia cysts. The method will detect all species and genotypes/assemblages that are known to be pathogenic for humans and also others that are not. For further identification, molecular typing assays are required. However, these cannot be reliably performed if process positive controls have been spiked into the samples, as the result of molecular typing assays will be obfuscated. This method does not allow the determination of viability or infectivity of any Cryptosporidium oocysts and Giardia cysts which may be present.