Troubleshooting Microbial Contamination In An Industrial Environment

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Processing industries such as pharmaceutical, personal hygiene and beauty products, food (including dairy) have microbial contamination control procedures in place.

Regular hygiene monitoring of a plant and equipment, and microbiological sampling of products and raw materials are invaluable in detecting potential sources and routes of contamination. Contamination especially in food industry can result to not only business losses but also to human illness and death.

When is troubleshooting microbial contamination necessary?

Picture of mouldy bread

Rye bread contaminated with mould

Microbiological troubleshooting is called for when safety and quality systems fail. This will be evident by contamination of products or equipment with microbial pathogens and/or spoilage organisms at unacceptable levels.

The significance of contamination in a processing industry is determined by a number of factors as well as properties of the microorganism(s) concerned, the product and environmental factors. Environmental factors may include pH and water activity of the product or raw material, available nutrients (e.g., aerosolized product), and the ambient temperature. These factors determine what microorganism(s) would be the dominant contaminant(s) and the level of spoilage of the product or raw material.

Generally, in each manufacturing environment a unique microbial community “natural-microflora” will be present since the local conditions tend to select for a particular assemblage of microorganisms. Similarly, microorganisms of concern are often present in small numbers as part of the natural microflora of raw materials and could not be totally eliminated.

Factors contributing to multiplication of microorganisms to unacceptable levels may include improper storage conditions, improper handling by the workers. Contamination originating from raw materials can contaminate hands of workers and then be transferred to the product and equipment.

Troubleshooting microbial contamination would be necessary if:

  • Routine microbial monitoring indicates contamination levels exceeds acceptable limits.
  • The product or raw materials get contaminated.

Troubleshooting Microbial Contamination

When troubleshooting microbial contamination in an industrial setting, it is important to have an idea of the possible contaminants (i.e., the “natural-flora”), likely sources of contamination and the stages in the processing where contamination of the product or raw material is most likely to occur. The goal of the investigation could be to determine the nature of primary contamination and the causes.

The first thing is to have a walk-through of the plant and analyze in detail the stages of processing or production and using microbiological knowledge identify the stage(s) in the entire production process where possible contamination is likely to occur. The source or the cause of primary contamination requires to be identified for appropriate action to be taken. The primary contamination may be:

  • Intrinsic- i.e., of raw materials or
  • Extrinsic- i.e., during or after processing

The sources of contamination may be:

  • General- i.e., from air, soil and water
  • Packaging materials
  • From carriers- i.e., human/animals. Workers may contaminate a product or raw material from contaminated surfaces, from another product, or from hands contaminated with organisms from their cloths or skin.

Since contamination of raw materials or the product may originate from contaminated air, water used in the processing, equipment or even the workers handling the product/raw materials, microbiological analysis of the product/raw material and the air within the processing area is recommended.

Microbial Sampling

If contamination involves the product or raw material, samples of the contaminated material should be sent to a reputable laboratory for analyses. Once the contaminating organism has been identified, it is then easy to design suitable sampling strategies to trace the source of contamination.

Selection of Sampling Media

The media used in sampling for micro-organisms are many and selection would depend on the target organisms. If the target organisms are moulds, a mycological (instead of bacteriological) medium should be used. Mycological media are also diverse and if there is no strong clue which media would be most suitable, it is best to use two types of media. One of high water activity (e.g., sabouraud, malt extract agar) that allow growth of a wide range of moulds and a medium of low water activity for isolation of moderately osmotolerant to xerophilic moulds (e.g., dichloran 18% glycerol agar).


A well designed microbiological troubleshooting strategy should be easy to implement and the results measurable. To see the guidelines for interpreting non-viable air sample results click Guidelines for Interpreting Non-viable Air Samples. To see guidelines for interpreting viable air sample results, click Guidelines for Interpreting Viable Air Samples.

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Dr Jackson Kung'u
Dr. Jackson Kung’u is a Microbiologist who has specialized in the field of mycology (the study of moulds and yeasts). He is a member of the Mycological Society of America. He graduated from the University of Kent at Canterbury, UK, with a Masters degree in Fungal Technology and a PhD in Microbiology. He has published several research papers in international scientific journals. Jackson has analyzed thousands of mould samples from across Canada. He also regularly teaches a course on how to recognize mould, perform effective sampling and interpret laboratory results. Jackson provides how-to advice on mould and bacteria issues. Get more information about indoor mould and bacteria at
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