Microbial contamination might not grab headlines like inflation or ultra-processed foods, but for food and beverage manufacturers, it remains one of the most persistent threats to product quality, brand equity, and public health. Eric Stevens, vertical segment manager at Hygiena, explores the challenges around food safety across the world.

Each year, unsafe food is estimated to cause around 600 million illnesses and 420,000 deaths worldwide. Bacteria such as non-typhoidal Salmonella, pathogenic E. coli, and Campylobacter are among the main culprits.

Yet bacteria tell only part of the story. Moulds and spoilage fungi are equally dangerous and costly. Toxigenic species that produce aflatoxins, fumonisins, or ochratoxin A can introduce both acute and chronic health risks, particularly in cereals, nuts, coffee and animal-derived products.

Even non-pathogenic mould growth in a chilled dessert, soft drink or plant-based snack can shorten shelf life, drive quality complaints and trigger social media storms, with consequences that extend well beyond a single batch.

For high-growth segments such as bakery, dairy, beverages, ready-to-eat (RTE) meals and plant-based alternatives, the line between a safe, premium product and a costly withdrawal can be as thin as a missed biofilm under a conveyor. Furthermore, these risks can result in damage to brand reputation, often leading to bankruptcy.

The industry is also fighting this battle in a changing landscape of regulatory requirements and consumer demands. A century of progress in hygiene, preservation and process control has undoubtedly raised the bar, but modern supply chains add new layers of complexity. Globalised ingredient sourcing, climate-driven volatility in raw material quality, fast-moving product innovation and reformulation away from traditional preservatives or being labelled as ‘ultra-processed’ all create fresh opportunities for bacteria and moulds to exploit. At the same time, regulatory regimes such as the Food Safety Modernisation Act (FSMA) and the EU’s microbiological criteria have moved the conversation firmly from end-product testing to preventive controls and verification, including more rigorous environmental monitoring for quality indicators and pathogens like Listeria monocytogenes and Salmonella.

This feature explores why microbial and mould contamination remain so stubbornly persistent, how innovators such as Hygiena are helping manufacturers detect and manage risk in real time, and what changes in regulation, technology, and collaboration could further strengthen control of pathogens and spoilage organisms across the food and beverage value chain.

Why is bacterial and mould contamination so prevalent in F&B?

Ask any microbiologist where bacteria, yeasts and moulds come from, and the honest answer is, “everywhere.”

Microorganisms are part of the fabric of life; they’re on raw materials, in the air, on equipment and on people. The human body alone hosts more microorganism cells than human cells. Put those microbes into contact with food, a matrix rich in nutrients, moisture and often close-to-neutral pH, and you’ve created an almost perfect growth medium. For many products in beverages, dairy and RTE categories, warm, humid processing environments simply tilt the odds further in the microbes’ favour, encouraging the formation of biofilms and the spread of spore-forming moulds.

Contamination can occur at almost any point from the farm to the finished pack. During pre-harvest, fungi such as Aspergillus, Fusarium and Penicillium can infect crops in the field, particularly under climatic or agronomic stress, leading to mycotoxin risks in grains, nuts, coffee and cocoa. Pathogenic bacteria can be introduced via soil, irrigation water, manure, or animal intrusion in produce fields. By the time these materials reach a processor, their microbiological “starting point” may already be challenging to control.

When considering the next stage of post-harvest and processing, once inside the plant, poorly cleaned conveyors, fillers, and gaskets provide bacteria, yeasts, and moulds with a hiding place, potentially allowing them to establish biofilms. These complex microbial communities can tolerate detergents and sanitisers far better than free-floating cells, seeding recurring contamination even when surfaces appear visually clean. Condensate, standing water, and hard-to-reach areas (under equipment, inside hollow rollers, around drains) become persistent reservoirs for both spoilage organisms and pathogens.

Several powerful trends in food and beverage are unintentionally making life easier for microbes. For instance, reformulations that reduce salt, sugar, nitrite and synthetic preservatives are attractive to consumers, but they also remove intrinsic hurdles that once held spoilage microbes and pathogens in check. That places more pressure on hygiene, temperature control and packaging to maintain safety and shelf life. The growth of RTE meals, freshly prepared foods and home-delivered convenience has lengthened cold chains and shelf lives, which organisms such as Listeria monocytogenes and cold-tolerant yeasts and moulds are perfectly adapted to exploit these conditions.

Finally, new plant proteins, alternative fats, fermented components, and functional inclusions often come with more complex sourcing and less well-characterised microbiota. This can result in greater variability in incoming quality and unfamiliar spoilage profiles on the line.

But it isn’t just about the individual processes; modern manufacturing amplifies any weakness. Large, highly automated plants run high-throughput, multi-SKU lines with frequent changeovers, and every changeover is another opportunity for a cleaning miss or cross-contamination event. At the same time, global ingredient sourcing means contaminants can be introduced far upstream. A single contaminated lot of nuts, dried vegetables, botanicals or protein powder can end up in dozens of SKUs across multiple brands and markets before an issue is detected.

Recent high-profile recalls linked to Salmonella in nuts and seeds, dried plant ingredients and prepared meals underscore how quickly a microbiological problem can spread throughout the value chain once it’s established. To further complicate this fact is that yeast and mould pose additional unique challenges, including heat resistance and the ability to survive and grow in diverse environmental conditions, such as high and low pH levels, low water activity and complex organic environments. Even though many moulds perish during high-temperature processing, their spores can survive by remaining dormant, creating havoc later, necessitating strict hygiene measures for control.

One method to address these issues has been the use of preservatives such as benzoates, sorbates and propionates. However, some moulds can develop resistance to these preservatives over time, necessitating the use of both chemical and physical control measures. The introduction of MAP (modified atmospheric packaging) has helped alleviate some issues, as levels of various gases can be controlled to minimise fungal growth (such as elevated CO2), but must be optimised to prevent favourable growth of other pathogens (such as C. botulinum).

The bottom line: yeast and mould prevention absolutely requires strict hygiene protocols, controlled storage conditions, and continuous monitoring of raw materials. Airborne spores and surface contamination pose significant risks, underscoring the importance of comprehensive sanitation measures.

What’s the best way to verify sanitation effectiveness beyond visual inspection?

Ask any QA or sanitation manager and they’ll tell you: you can’t manage what you can’t see.

The problem in modern plants is that most of the risk is precisely where you can’t see it. That’s why verifying sanitation effectiveness has to be viewed as a spectrum, not a single tick-box. Visual inspection still remains the starting point, but it’s only one piece in a layered approach that runs from ATP through indicators to full pathogen and spoilage monitoring.

But visual inspections can’t tell you whether a “clean” surface still harbours a low-level biofilm or whether a piece of equipment is slowly drifting out of control from a microbiological standpoint. For that, you need objective data and comprehensive data that speaks to your entire food safety plan. From ATP to indicator to pathogen and mould testing, all of this leads back to a simple but easy-to-forget principle: Verification is a system, not a single test.

The strongest and most robust food safety programmes combine:

(1) Visual and functional checks to confirm that cleaning was carried out as intended;

(2) ATP testing to verify that surfaces are truly free of organic residues before production;

(3) Indicator and spoilage tests to keep an eye on the general microbiological picture;

(4) Pathogen-focused and yeast/mold monitoring in higher-risk areas, products and situations; and

(5) Digital trending tools (such as SureTrend and similar platforms) to spot creeping deterioration in hygiene before it shows up as a complaint or recall.

Taken together, these layers turn sanitation from a one-time event into a continuous, data-driven process; one where problems are surfaced and addressed early, rather than discovered after the product is already in the market.

If we want to get serious about Listeria and Salmonella in the long term, technology alone won’t be enough. The regulatory and collaboration frameworks around that technology also need to evolve.

Choosing partners that elevate your food safety plan

Food is, by definition, a fantastic growth medium, and modern F&B supply chains are vast, fast and intricately connected. The real challenge in 2026 and beyond isn’t recognising that contamination might occur; it’s maintaining continuous control in real time, across multiple sites, suppliers, and product categories.

The plants that stay ahead are building control strategies on three pillars:

• Prevention: Hygienic design, well-engineered cleaning and sanitation, and robust raw material controls that minimise the opportunities for bacteria, yeasts and moulds to take hold in the first place.

• Rapid verification: ATP, indicator tests and targeted pathogen and spoilage assays used as routine tools, not emergency responses – checking that cleaning worked, that environments remain under control, and that packaged product is as sound as the process design assumes.

• Data-driven decisions: Trending, heatmapping, and risk-based sampling that turn thousands of individual test results into a clearer picture of where risk is increasing, where interventions are working, and where the next investment should go.

In this context, the choice of partners matters. Diagnostic and technology suppliers need to offer more than a catalogue of tests.

The most valuable will bring:

(1) Independently validated methods (AOAC, ISO, AFNOR, MicroVal and similar) for hygiene verification and for pathogen, mycotoxin, and allergen testing, making it easier to defend programs under FSMA, GFSI, and retailer standards;

(2) Integrated platforms that link ATP and indicator testing with PCR-based pathogen detection, in-pack screening, and cloud analytics, so that data are captured once and reused many times, rather than fragmenting across instruments and spreadsheets;

(3) scientific and regulatory expertise, helping QA and food safety teams interpret results, refine sampling plans, and translate numbers into preventive controls that stand up to regulatory and customer scrutiny.

Completely eliminating mould and bacterial contamination may never be realistic. But detecting problems early, understanding where and why they emerge, and reacting quickly and proportionately is absolutely achievable with today’s tools, and is already a reality in many best-in-class plants.

In a world where a single image of a mouldy drink or a contaminated ready meal can travel the globe in hours, choosing partners and platforms that elevate your food safety plan isn’t just prudent: it’s a strategic imperative.