Words By Chitra Muthiah, Operations and Resource Manager FMCG, Supply Chain & Product Assurance, DNV 

Imagine the food supply chain as a relay race. Each stage hands over the baton of safety to the next. If just one person fumbles, the entire outcome is at risk. Microbial safety is that baton. It is not just a technical checkbox. It is a strategic responsibility that requires foresight, teamwork, and care at every step. 

After more than twenty years working alongside food businesses developing systems, mentoring teams, and auditing operations, I’ve come to see microbial safety not as a single task, but as a living system. Despite massive progress in science, regulation, and technology, food businesses still face complex and shifting challenges when it comes to microbial risks. 

Let’s take a closer look at how and where this baton can be dropped, and what we can do to keep it firmly in hand. 

It starts at the drawing board: R&D  

Food safety starts long before a product hits the shelf. In the research & development phase, many teams focus on taste, texture, cost, and shelf life. But when microbial risks are not considered early, especially with high-moisture or low-acid products, safety gets compromised before production even begins. 

Think of a plant-based yogurt. It may be a hit with health-conscious consumers, but if its water activity and pH are not carefully controlled, it can become a perfect breeding ground for spoilage organisms. 

The solution lies in integrating microbiological risk assessments right from the start. From selecting ingredients and equipment to designing packaging and distribution conditions, every decision should consider how microorganisms will behave. Predictive microbiology tools and shelf-life models help forecast risks and support better decisions in formulation, preservation, and packaging. 

Scaling up: Commercial production and hidden risks 

As production moves from the lab to large-scale manufacturing, gaps or inconsistencies in microbial control often emerge. One of the most common culprits is a poorly validated Clean-In-Place (CIP) system. If equipment surfaces are not fully cleaned and sanitized, biofilms may form. These biofilms are like microscopic fortresses; once they form, they are incredibly hard to remove and can persistently contaminate future batches. 

To avoid this, CIP systems need to be designed, validated, and regularly re-verified. Simply assuming they are working is not enough. The same goes for packaging and preservation methods. Extended shelf life may sound appealing, but without validation of how the product behaves over time under different conditions, risks can quietly build up. 

Overuse of antimicrobial agents is another concern. It may seem like a shortcut to safety, but it can actually promote resistance in microbes. Rotating cleaning agents, using natural preservatives, and conducting regular challenge studies can help reduce dependence on chemicals while maintaining safety. 

Good infrastructure is essential in the food industry to keep food safe from harmful microbes. Key parts like smart layout (zoning), controlled air circulation, and easy-to-clean equipment help prevent contamination. These features work together to maintain a clean environment, reduce risks, and ensure safe food production. 

Water quality: The hidden ingredient 

Water is everywhere in food processing. It cleans, cools, dilutes, and even becomes part of the product itself. Yet it is often overlooked when assessing microbial risk. Poor-quality water or biofilm buildup in pipelines can introduce contamination even after thorough cleaning. 

Many plants rely on borewell, surface, or recycled water without routine microbial testing of the right indicator organisms. Others assume treatment steps like chlorination or UV are sufficient without validating their effectiveness. The truth is, water can be a major carrier of contamination if biofilms develop in pipes or if microbial loads are not consistently monitored. 

To mitigate this risk, water should be treated like a raw material. A water safety plan aligned with global standards (such as WHO or ISO) should include regular testing for microbial indicators like total viable counts and coliforms, along with maintenance of filtration and disinfection systems. 

Raw materials: Risk starts at the source 

Even the most hygienic process can be compromised by a single contaminated ingredient. Moisture-rich ingredients like dairy, meats, and fresh produce are particularly vulnerable. Inconsistent quality from suppliers, lack of audits, or insufficient incoming material testing can allow contaminants to enter unnoticed. Recycled or repurposed materials that have not been properly sanitized introduce additional risks. 

To manage this, food companies must invest in routine supplier audits, incoming raw material testing protocols, strong supplier relationships, and risk mapping. Relying on Certificates of Analysis alone is not enough. Early intervention at the source is far more effective than attempting to correct issues later in the process. 

Microbial toxins: the unseen threat that outlasts the heat 

Some microbial hazards don’t just spoil food; they make it dangerous to eat, even after cooking. Certain bacteria, such as Clostridium botulinum and Staphylococcus aureus, produce toxins that are heat-stable, meaning they can survive standard cooking temperatures. These toxins are invisible, tasteless, and odourless, but they can cause serious illness if not addressed early in the production process. 

Toxin formation typically results from poor storage practices such as high humidity, elevated temperatures, damaged packaging, temperature abuse, or inadequate hygiene. Products like high-moisture food grains, ready-to-eat meals, canned foods, and cream-based desserts are particularly susceptible. Prevention starts with proper ingredient screening, using methods such as ELISA or HPLC, along with validated heat treatments, strict storage conditions, and robust hygiene protocols. 

Environmental monitoring and biofilm control, especially in high-moisture environments, are essential. These steps, combined with clean handling practices and supplier due diligence, help reduce the risk of heat-stable toxin contamination. 

Storage and transport: Safety on the move 

Products can be well-designed and safely produced, but if storage and transport are not tightly controlled, microbial risks can still emerge. Temperature abuse, humidity, poor ventilation, and long storage times create ideal environments for microbial growth. 

Sealed products are not immune. Even small fluctuations in storage conditions can lead to condensation or spoilage, particularly for perishable items like dairy or beverages. 

To safeguard product safety, storage facilities and transport systems must maintain tight control over environmental conditions. Cold chains need to be monitored, and warehouse staff should be trained to handle products appropriately. Spot checks and audits can help ensure that what was safe at dispatch remains safe on arrival. 

Retail and consumer handling: The final mile 

The final stretch of the race is no less important. At the retail level, issues like broken cold chains, poor stock rotation, and damaged packaging can lead to spoilage or contamination. Overloaded chillers, broken packaging, and staff unfamiliar with FIFO (first-in, first-out) practices can all reduce product integrity just before it reaches the consumer. 

Retailers must be trained in basic food safety, storage, and hygiene practices. Clear labelling, appropriate refrigeration, and equipment maintenance help prevent problems at the final point of sale. Retailers also play a role in customer education, helping consumers understand how to store products safely at home. 

Microbiologists: The untapped resource 

One of the most underutilized assets in food safety is the microbiologist. In many companies, these professionals are confined to lab testing roles, performing enumeration and plating without being involved in broader decision-making. But their knowledge is most powerful when applied to prevention, not just detection. 

Microbiologists should be involved in product development, process validation, root cause analysis, and sanitation planning. Empowering them to contribute across departments helps close safety gaps before they become problems. Their expertise not only strengthens safety systems but also supports innovation.  

The future of food safety: A shared responsibility 

The future of food safety lies in prediction, not just prevention. Technologies such as Whole Genome Sequencing (WGS), environmental microbiome profiling, and in-line biosensors allow for early detection of contamination risks. Blockchain tools and supplier scoring enhance transparency and traceability. AI-powered dashboards and digital CIP validation systems help teams respond before issues escalate.  

But technology alone is not enough. Training people to use these tools effectively is just as important. Leaders must support advanced training in microbiology, data interpretation, and implementation of the latest food safety technologies. From operations to quality assurance, every team member needs to understand their role in upholding safety. 

Microbial safety is not a single department’s job. It is a collective effort that spans the entire food lifecycle. From design and development through to consumer handling, each step carries the baton. Dropping it at any stage can jeopardize not just a product, but public trust and brand reputation. 

By embedding safety into every decision, empowering technical teams, and embracing modern tools, we can build a more resilient food system.  

Because in the end, passing the baton of safety is not just about meeting standards. It’s about delivering on a promise — that every bite is safe, every time. 

About the author 

Chitra Muthiah is the Resource and Operations Manager for DNV’s FMCG Department under the Supply Chain & Product Assurance Business Unit in India. With over 23 years of experience in the food manufacturing, retail, and service sectors, she brings deep expertise in food safety systems, regulatory compliance, and third-party audits. Since joining DNV in 2016, Chitra has grown into a multifaceted role—leading operations, auditing, training, and mentoring teams. She holds a Master’s degree in Food Technology from the Central Food Technological Research Institute (CFTRI), Mysore. Passionate about building food safety culture, Chitra has played a key role in driving quality assurance programs, supporting new product development, and enhancing customer-focused compliance across the supply chain. 

This story first came out in our May/June 2025 issue.