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Microbial Identifications: Managing Bioburden Monitoring Results

Bioburden monitoring is required to demonstrate the control of the manufacturing lines of medical devices and to validate a cleaning or sterilization process, among other reasons. The bioburden must be controlled not only quantitatively, but qualitatively as well. To monitor the type of living microorganisms on a medical device, identifications are required. But several techniques can be used to identify the microorganisms.


Medical device manufacturers are commonly challenged by Notified Bodies (NBs) to justify the technique for microbial identifications they are using, and the precision of the results obtained. Several techniques can be used with different levels of identification.

Techniques for Microbial Identification

The first step to classify the living microorganisms is examining the culture conditions used for bioburden testing. Although many laboratories propose to test bioburden using only one culture condition for cost reasons, the main point for an informative bioburden monitoring is to choose the most appropriate conditions regarding the risk analysis of the manufacturer (aerobes, anaerobes, fungi, sporulating germs, etc.). Remember that whatever the technique used to identify a bioburden, germs must be cultivated first!

Macroscopic characterization, microscopy, or Gram staining can roughly classify microorganisms by their phenotypic characteristics. However, they don’t guarantee accurate identification of the genus or species.

Identification using mass spectrometry technology is a fast and cost-effective solution to quickly screen the bioburden present on a medical device. In most circumstances, it allows the microorganisms to be identified at the species level. But, its efficiency can be limited for some microbial types such as fungi or rarely cultivated germs. This limit can present an issue for medical device manufacturers because environmental microbes are often the main source of contamination, in contrast to pharmaceuticals.

The most efficient technique remains the molecular identification by PCR, which allows identification at the species level and compares the phylogenetic position of the studied microbe when unidentified. This technique remains costly and time-consuming and its use needs to be evaluated against the real monitoring need.

 Managing the Identification Results

Some NBs request to identify the microorganisms at the species level. The main reason is to monitor a potential recurrent contamination or to identify specific challenging germs as radioresistant microorganisms.

To identify the species range of a germ is not often as informative as we would like, leading to questions from manufacturers regarding their identification results. “The literature says my germ was isolated from a surface of the International Spatial Station! How was this concluded?” “The literature says my germ was isolated from the human gut. Do that mean it can be considered a human germ?

Be aware that for rarely cultivated microbes, the publication used as the official description gives the phenotypic characteristics of a microorganism (fitness, Gram, atmosphere, etc.) but does not necessarily reveal its ecological niche. The environment from where a germ is primo-isolated is not necessarily representative of its real living environment (environmental, human-associated germ, etc.).

Additionally, care must be taken with global publications using metagenomics analyses. Metagenomics is a power tool, but it is based on residual DNA detection and not culture of living microorganisms. For example, presence of DNA in the human gut could refer to commensal germs or only dead microorganisms issued from feeding.

Thus, the best strategy to choose a relevant identification technique is to consider what information is needed and what level of information can be given by each identification technique.

Choosing the Best Identification Technique

The most efficient strategy to analyze bioburden content is to determine which microorganism types are representative of each contamination source (not exhaustively: Gram positive for environment, Gram negative for water-mediated contamination, fungi for storage and moisture presence, etc.) and to focus only on the most challenging germs (hand-carried, radioresistant, etc.) for the manufacturer risk analysis. This risk analysis could include the necessity to identify specific pathogen germs, microorganisms involved in endotoxin production, and more.

How Can NAMSA Help?

With world-class microbiology testing capabilities, global state-of-the-art facilities and unmatched expertise, NAMSA is well equipped to support your microbial identifications and to analyze the obtained results. Our experienced and dedicated team can help you to navigate regulatory obstacles and recommend testing requirements according to the standards.

Frédéric Cadoret, PhD

Frédéric Cadoret is a microbiology expert who joined NAMSA in 2019. With over nine years of experience in microbiology in vitro testing, he provides support to medical device manufacturers in microbiological evaluations and submissions to Notified Bodies. Frédéric holds a PhD in microbiology, vegetal biology, and biotechnology. He conducts training sessions on microbiology according to ISO standards and AAMI guidelines, and offers consulting services for reprocessing validation projects. He also assists manufacturers in developing appropriate bioburden, sterility, and endotoxin strategies for single-use devices. In addition, Frédéric lectures to Master degree students at the Université de Montpellier and has developed new microbiological testing methods.