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Analyses under the microscope: How are bacteria in food analyzed in the laboratory?

Analyzing bacteria in food is crucial to ensuring food safety. Microbiological analyses help producers, regulators and researchers understand whether food is safe for consumption, and what types of bacteria are present. In this article, we explain what techniques are used, the pros and cons, and how to interpret the results.

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Various methods for microbiological analyses.

Counting bacteria:

This involves measuring how many bacteria are present in a given weight of food (e.g., per gram. Most commonly used technique: Plate Count Method (culture on agar plates):

  • A food sample is diluted and spread on a culture medium (agar plate). After incubation, microbiologists count the number of colonies (Colony Forming Units, CFU).
  • Advantages: Gives an idea of the total bacterial load and can be specific to certain bacteria by using selective media.
  • Disadvantages: Only live bacteria that can grow on the medium used are counted; sluggish bacteria or species that are difficult to culture may be missed.

Presence/absence test:

This looks at whether a specific bacteria is present or not, usually in a standard amount such as 10g or 25g of food. This is often used for pathogens such as Salmonella or Listeria.

  • Selective enrichment media followed by culture on specific agar plates or Molecular techniques such as PCR (Polymerase Chain Reaction) to detect bacterial DNA.
  • Advantages: Fast and highly sensitive, suitable for pathogens.
  • Disadvantages: Does not detect quantity, only presence; PCR also detects dead bacteria that do not pose a risk.

Interpretation of results.

Count (CFU/g or CFU/mL):

  • Results give an indication of microbial load. High counts may indicate poor hygiene, improper storage or spoilage.
  • Guidelines (e.g. by the EU or FDA) often specify maximum allowable CFU values for consumption.

Presence/absence in 10g or 25g:

  • If a bacterium is found in a sample, it may represent a potential risk even if the overall count is low.
  • Usually applied to pathogens; any detectable signal in the test sample is interpreted as "positive."

Accuracy and reliability.

No analytical method is completely perfect; the accuracy and reliability of microbiological tests are influenced by several factors. For example, the representativeness of the sample plays a major role: a small piece of food can never contain all the bacteria present, so proper mixing and representative sampling is essential. In addition, there is the detection limit of the test; in presence/absence tests, bacteria present below this limit may be falsely represented as "not detected." Technical variation also affects, as differences in incubation time, temperature, medium and even human interpretation can alter results. In addition, certain bacteria may be inhibited by the food matrix itself or by other microorganisms, further affecting reliability.

Laboratories overcome these challenges in several ways. They take multiple, representative samples and often perform dilutions to get a better picture of the population of bacteria. Repeated testing and confirmatory testing are used to detect and rule out chance abnormalities or false positives. Standardization of procedures, such as fixed incubation times, controlled temperatures and standardized media, reduces variation between tests and operators. In addition, laboratories use internal controls and reference samples to continuously monitor test performance. By combining these measures, laboratories can minimize the impact of natural variation and technical limitations and provide reliable, reproducible results that are essential for food safety and quality management.

The importance of accreditation in microbiological food analysis

Accreditation is essential for laboratories performing microbiological analyses on food products. The process ensures that laboratories meet international standards, such as ISO/IEC 17025, and that they have the appropriate resources, procedures and expertise to provide reliable and consistent results

Accreditation plays a critical role in ensuring reliability and confidence in laboratory testing. Accreditation ensures that test results are consistent and reproducible, which is essential for consumer, producer and regulator confidence. In addition, accreditation ensures that laboratories comply with laws and regulations; in many countries it is mandatory for laboratories performing official food safety analyses to be accredited, ensuring analyses are in line with both national and international standards. In addition, accreditation requires laboratories to maintain strict quality management systems, leading to continuous process improvement and a reduction in errors. Another key benefit is international acceptance: accreditation to recognized international standards allows test results to be recognized worldwide, which is especially important for exports and international trade.

In practice, accreditation means that laboratories strictly document and standardize their processes and procedures. This includes using validated analytical methods, regular calibration of equipment and conducting internal and external audits to continuously monitor the quality of testing. Personnel must be demonstrably qualified and trained, and all test execution is accurately recorded to ensure reproducibility and traceability. In case of deviations or unexpected results, there are clear protocols for re-analysis and root cause analysis so that errors are quickly identified and corrected. This systematic approach enables accredited laboratories to deliver reliable results that meet rigorous quality standards and are internationally recognized, providing the basis for trust from both customers and government agencies.

Accredited method vs. accredited laboratory

It is important to distinguish between an accredited analytical method and an accredited laboratory.

  • An accredited method means that the analytical method itself is officially recognized and validated to international standards and included in a laboratory's accreditation certificate.
  • An accredited laboratory means that the entire laboratory, including personnel, equipment, procedures and quality management systems, has been officially assessed and meets the ISO/IEC 17025 standard.

However, there are important national differences. In Belgium (through BELAC), an accredited method is often strictly prescribed, with little room for variations in the protocol; a laboratory must follow the method exactly as accredited. In the Netherlands, accreditation offers more flexibility: a laboratory can choose how certain steps are performed within the general method, as long as the method as a whole meets the accreditation and ISO standards. As a result, a method accredited in one country is not automatically performed identically in another, even if the same method is used. Accreditation does guarantee that the method is officially approved and meets international quality standards, but details of implementation may vary from country to country or laboratory to laboratory. By using both accredited methods and accredited laboratories, producers, regulators and consumers can have confidence in the accuracy of results while remaining aware of possible differences in implementation between countries.

Accreditation in the Netherlands, Belgium, Germany and France

The Netherlands

In the Netherlands, the Raad voor Accreditatie (RvA) is the national body that grants accreditation to laboratories. Laboratories performing microbiological analyses on food must meet the NEN-EN-ISO/IEC 17025 standard, which sets requirements for competence, independence and reliability of test results. In addition to this standard, there are additional guidelines for specific food analyses, for example for pathogen detection, residue testing and contaminants. The RvA conducts periodic audits and assesses both the management system and the technical competence of the laboratories. Accreditation is often combined with recognition by regulators such as the Dutch Food and Consumer Product Safety Authority (NVWA).

Germany

In Germany, the Bundesanstalt für Verbraucherschutz und Lebensmittelsicherheit (BVL) is involved in the accreditation of laboratories, particularly for official analyses such as residue testing and food safety monitoring. Laboratories must comply with DIN EN ISO/IEC 17025, which is the international standard for testing and calibration laboratories. There are also national guidelines that specify the performance of analyses, quality assurance and validation of methods. German laboratories are regularly inspected to ensure that results are reliable for official reporting and law enforcement purposes.

Belgium

In Belgium, BELAC is the national accreditation body and grants accreditations based on ISO/IEC 17025 for laboratories analyzing food samples. Laboratories performing official analyses are supervised by the Federal Agency for the Safety of the Food Chain (FASFC). The FAVV maintains a network of approved laboratories that are required to meet strict quality standards, including protocols for microbiological testing, contaminant detection and analytical methods that are officially recognized in Belgium. Accreditation by BELAC ensures that results are reliable and internationally comparable, and it includes regular inspections and in-service training of personnel.

France

In France, COFRAC (Comité Français d'Accréditation) is the national body that grants accreditations to laboratories. Laboratories performing microbiological and chemical analyses on food must comply with ISO/IEC 17025. COFRAC assesses both the technical competence of laboratory staff and the quality of the management system. There are also national guidelines for food safety, contaminant monitoring and pathogen detection. Accreditation by COFRAC is recognized by the French government and is often a requirement for participation in official controls and certification processes.

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