A Question of Confidence – How Food Microbiology Labs Ensure Reliable Results

The global food production industry has witnessed an expansion and complexification of supply chains, necessitating rigorous monitoring at every phase for safety purposes. Central to this monitoring is microbiological testing, a critical tool in combating food contamination.

With the growth in the food sector, laboratories today are furnished with cutting-edge facilities and are staffed by professionals trained to provide accurate results. However, recent studies on lab accuracy indicate the importance of constant vigilance. While these labs are proficient, there’s an ongoing need to ensure the results’ reliability, fostering trust among consumers.

Historically, microbiological testing was a primary means by which food manufacturers ensured the absence of foodborne pathogens in their products. This changed in the 1980s when HACCP-based food safety management systems began to supersede earlier quality control methods. Instead of serving as the main defense against pathogens, microbiological testing evolved into a method for verifying the efficacy of HACCP systems.

Contrary to the expected decline in the number of tests, there has been a surge, with a market report suggesting nearly a billion such tests were conducted in 2013. This marks a 128% increase over 15 years, primarily driven by the growth of the food industry, extended supply chains, and notable safety issues like the 2011 E. coli outbreak in Germany. This necessitates testing at multiple points, from production to retail, ensuring the safety of ingredients and verifying the functionality of HACCP systems. The advent of rapid testing methods further bolsters this approach, offering quicker results than traditional culture-based techniques.

Laboratories Progress but Old Problems Remain

Since the 1980s, the laboratory infrastructure serving the food industry has experienced significant changes. Previously, many food manufacturers and retailers operated in-house microbiology labs. Today, this trend has shifted towards outsourcing with many small independent labs closing down.

Now, the sector is mainly dominated by larger centralized facilities that are frequently parts of multinational chains. These centralized systems are possible due to enhanced sample collection and logistics, enabling testing from remote locations, even in different countries. This centralization and the resultant economies of scale have facilitated investments in advanced instrumentation and automation, decreasing the need for many technicians and emphasizing higher-standard training.

However, despite the extensive modernization and transformation of the infrastructure, many routine lab methods have remained unchanged for the past three decades. Most still rely on traditional culturing methods for identifying target microorganisms, followed by biochemical or immunological tests for confirmation.

Originating from nineteenth-century medical microbiology, these methods can be influenced by various factors like culture medium composition, sterilization processes, temperature fluctuations, and staff expertise, leading to inconsistent results.

Moreover, certain pathogens may enter a ‘viable but non-culturable’ state, making them nearly undetectable by conventional means. Recent research highlights concerning rates of false negatives and positives in US labs, indicating potential discrepancies in lab results globally, which could pose significant health risks.

Managing Quality

Effective quality management is essential for minimizing errors and variation in laboratory test results, particularly in food microbiology laboratories. These systems should encompass every facet of the testing process, from the reception of samples to the reporting of results. Confidence in test results is significantly bolstered by several key factors. Foremost among these is the suitability of the laboratory’s accommodation and facilities.

Historically, some microbiology labs were ill-placed, sharing spaces with chemical analysis, or lacking proper separation from production areas. Modern standards, however, largely driven by health and safety concerns and the rise of third-party testing, mandate improved design and infrastructure of labs. Reliable performance hinges not just on advanced equipment and trained staff but also on the lab’s foundational setup.

Furthermore, the equipment selected for the lab must be apt for its intended use, well-maintained, regularly calibrated, and operated within specified parameters. Notably, as food microbiology progresses and integrates more instrumentation, maintaining equipment within designated operational limits is becoming even more critical.

Human capital is undeniably at the heart of a lab’s operation. Clear role definitions and comprehensive, documented training are prerequisites for all technicians. While hands-on training is invaluable, technicians must also meet certain baseline qualifications and skills. Whenever there’s an introduction of new methodologies or tools, ongoing training becomes essential.

The credibility of a lab’s results is contingent upon traceability; every step, from sample receipt to result reporting, must be accounted for. In instances of unexpected results or non-compliances, this traceability allows for a thorough assessment to ascertain whether the outcome is genuine or a product of an error.

The evolution of record-keeping has seen many labs transition from traditional paperwork to integrated digital systems like LIMS (Laboratory Information Management System). Such systems often connect directly to automated equipment, further reducing manual record-keeping and potential errors.

Choosing the Right Test Methods

The reliability of test results in food microbiology laboratories hinges significantly on the choice of test methods used. It’s imperative that these methods are appropriate for the intended purpose and the food material under examination. A vital aspect of these methods is their validation, which implies they have undergone rigorous scrutiny to ensure their fitness for the designated use.

One way to ensure reliability is by adopting recognized standard methods like those published by the International Standards Organisation (ISO). These ISO methods are exhaustively validated and trusted, covering a broad spectrum of tests conducted in food microbiology, from pathogen detection to spoilage organism enumeration.

Other sources of such validated methods include the FDA’s Bacteriological Analytical Manual (BAM) and methods from reputable scientific entities, professional organizations, and trade associations.

While laboratories have the latitude to employ non-standard or develop bespoke in-house methods, these must undergo rigorous validation, which is often a time-consuming and expensive process. This encompasses testing with reference cultures, contrasting with other approved methods, assessing reproducibility, and more. Hence, many laboratories opt for standard methods when accessible.

Despite concerns that over-reliance on these standards might stifle innovation, especially in rapid methods rooted in molecular biology, this hasn’t stymied the trend of adopting innovative methods. For instance, while many ISO methods are culture-based, they permit faster immunological tests for confirmation. Several rapid tests have received certification from bodies like the AOAC, NordVal, and AFNOR, which confers its NF VALIDATION mark to rigorously evaluated alternative food microbiology methods. Thus, labs can confidently leverage these advanced methods, albeit with some necessary in-lab validation and assessment.

Demonstrating Competence

An excellent way to check the reliability of a lab’s test results is to take part in an external quality assurance scheme, usually referred to as proficiency testing. This involves receiving samples prepared by a third party, which contain known pathogens or levels of microbiological contamination, and testing them according to standard laboratory procedures. The results are then returned to the body that prepared the samples for assessment.

Proficiency testing is valuable as a means of alerting management to potential quality issues in the laboratory and as an objective assessment of the competence of the laboratory. An example of such a scheme is the Food Examination Performance Assessment Scheme (FEPAS) run by the Food and Environment Research Agency in the UK.

The FEPAS scheme sends out samples to its members periodically that are carefully prepared to mimic real food samples – even to the extent of containing background microflora – and have been inoculated with known pathogens, indicators, or spoilage organisms. The laboratory then tests the samples according to its usual procedures and submits the results. These are analyzed statistically and an assessment report is sent back to the lab.

Most food microbiology laboratories now undertake external proficiency testing, often as a requirement of the quality management system.


Over the past two decades, acquiring third-party accreditation has become crucial for food microbiology laboratories to showcase their competence and trustworthiness. To achieve this accreditation, these labs must ensure their operations adhere to recognized standards, after which they undergo an evaluation by a certification body. Once accredited, periodic reassessments are required to maintain their status.

While accreditation typically covers specific tests and not the entire range of services offered, it serves as a significant marker of a laboratory’s credibility. Many major food safety authorities and food businesses mandate that testing is conducted by accredited labs, emphasizing the importance of this certification.

The most prevalent standard adopted by these laboratories is ISO/IEC 17025:2005, which outlines the overarching requirements for effective and ethical laboratory operations. While it’s not exclusively crafted for food labs, guidance for its interpretation in the food context, like the document by the European Co-operation for Accreditation, has been provided.

The evolution of food microbiology labs over the last three decades has been significant. Modern labs are expected to be well-equipped, accredited, and have a robust quality management system, ensuring the authenticity of their test processes and overall operations.

While methods and technicians have become more advanced and competent, expecting absolute accuracy is unrealistic due to the numerous variables, such as the inherent diversity in microbial populations.

The introduction of DNA-based detection techniques might enhance routine test reliability by concentrating on stable genetic markers. However, these molecular methods come with their uncertainties. For instance, certain food components can disrupt the PCR process or microbial DNA extraction.

As these techniques progress, quality assurance approaches must also evolve to address potential uncertainties. Ultimately, the quest for perfect food microbiology tests may remain elusive, emphasizing the continuous need for quality management in a successful laboratory.